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2021

Zhonghua Zheng, Jeffrey H. Curtis, Yu Yao, Jessica T. Gasparik, Valentine G. Anantharaj, Lei Zhao, Matthew West, and Nicole Riemer: "Estimating Submicron Aerosol Mixing State at the Global Scale with Machine Learning and Earth System Modeling", Earth and Space Science, American Geophysical Union, Vol 8, Num 2, pp e2020EA001500, 2021, doi:10.1029/2020EA001500


Paul M. Hime, Alan R. Lemmon, Emily C. Moriarty Lemmon, Elizabeth Prendini, Jeremy M. Brown, Robert C. Thomson, Justin D. Kratovil, Brice P. Noonan, R. Alexander Pyron, Pedro L. V. Peloso, Michelle L. Kortyna, J. Scott Keogh, Stephen C. Donnellan, Rachel Lockridge Mueller, Christopher J. Raxworthy, Krushnamegh Kunte, Santiago R. Ron, Sandeep Das, Nikhil Gaitonde, David M. Green, Jim Labisko, Jing Che, and David W. Weisrock: "Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life", Systematic Biology, Oxford University Press, Vol 70, Num 1, pp 49-66, 2021, doi:10.1093/sysbio/syaa034


D. Li, A. Peyvan, Z. Ghiasi, J. Komperda, and F. Mashayek: "Compressibility Effects on Energy Exchange Mechanisms in a Spatially Developing Plane Shear Layer", Journal of Fluid Mechanics, Cambridge University Press, Vol 910, pp A9, 2021, doi:10.1017/jfm.2020.932


Hiroki Nagakura, Adam Burrows, David Vartanyan, and David Radice: "Core-collapse supernova neutrino emission and detection informed by state-of-the-art three-dimensional numerical models", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 500, Num 1, pp 696–717, 2021, doi:10.1093/mnras/staa2691


O. Ashraf, Andrei Rykhlevskii, G. V. Tikhomirov, and Kathryn D. Huff: "Preliminary design of control rods in the single-fluid double-zone thorium molten salt reactor (SD-TMSR)", Annals of Nuclear Energy, Elsevier Ltd., Vol 152, pp 108035, 2021, doi:10.1016/j.anucene.2020.108035


Jon MacArt, Justin Sirignano, and Jonathan Freund: "Embedded training of neural-network sub-grid-scale turbulence models", Physical Review Fluids (in press), American Physical Society, 2021


Wendy K. Tam Cho and Yan Y. Liu: "A Parallel Evolutionary Multiple-Try Metropolis Markov Chain Monte Carlo Algorithm for Sampling Spatial Partitions", Statistics and Computing, Springer Nature Switzerland AG, Vol 31, Num 1, pp 10, 2021, doi:10.1007/s11222-020-09977-z


Fereshteh A. Sabet, Seid Koric, Ashraf Idkaidek, and Iwona Jasiuk: "High-Performance Computing Comparison of Implicit and Explicit Nonlinear Finite Element Simulations of Trabecular Bone", Computer Methods and Programs in Biomedicine (in press), Elsevier B.V., 2021, doi:10.1016/j.cmpb.2020.105870


Kendra Noneman, Christopher Muhich, Kevin Ausman, Mike Henry, and Eric Jankowski: "Molecular simulations for understanding the stabilization of fullerenes in water", Journal of Computational Science Education, The Shodor Education Foundation, Vol 12, Num 1, pp 39-48, 2021, doi:10.22369/issn.2153-4136/12/1/6


Pikee Priya and N.R. Aluru: "A multiscale framework to predict electrochemical characteristics of yttrium doped Barium Zirconate based solid oxide cells", Journal of Power Sources, Elsevier B.V., Vol 481, pp 228969, 2021, doi:10.1016/j.jpowsour.2020.228969


Melih Sener, Stuart Levy, John E. Stone, A.J. Christensen, Barry Isralewitz, Robert Patterson, Kalina Borkiewicz, Jeffrey Carpenter, C. Neil Hunter, Zaida Luthey-Schulten, and Donna Cox: "Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales", Parallel Computing (in press), Elsevier B.V., pp 102698, 2021, doi:10.1016/j.parco.2020.102698


Guillermo Araya and Ernie Rivera: "Transport Phenomena in High-speed Wall-bounded Flows Subject to Concave Surface Curvature", Journal of Computational Science Education, The Shodor Education Foundation, Vol 12, Num 1, pp 16-23, 2021, doi:10.22369/issn.2153-4136/12/1/3


Carlos A. Barragan and Michael N. Groves: "Training Neural Networks to Accurately Determine Energies of Structures Outside of the Training Set Using Agglomerative Clustering", Journal of Computational Science Education, The Shodor Education Foundation, Vol 12, Num 1, pp 32-38, 2021, doi:10.22369/issn.2153-4136/12/1/5


Tulin Kaman, Alaina Edwards, and John McGarigal: "Performance Analysis of the Parallel CFD Code for Turbulent Mixing Simulations", Journal of Computational Science Education, The Shodor Education Foundation, Vol 12, Num 1, pp 49-58, 2021, doi:10.22369/issn.2153-4136/12/1/7


2020

Dawit Belayneh, Federico Carminati, Amir Farbin, Benjamin Hooberman, Gulrukh Khattak, Miaoyuan Liu, Junze Liu, Dominick Olivito, Vitória Barin Pacela, Maurizio Pierini, Alexander Schwing, Maria Spiropulu, Sofia Vallecorsa, Jean-Roch Vlimant, Wei Wei, and Matt Zhang: "Calorimetry with Deep Learning: Particle Simulation and Reconstruction for Collider Physics", European Physical Journal C, Springer Nature, Vol 80, Num 7, pp 688, 2020, doi:10.1140/epjc/s10052-020-8251-9


Tak Chu Li, Yi-Hsin Liu, Michael Hesse, and Ying Zou: "Three-Dimensional X-line Spreading in Asymmetric Magnetic Reconnection", Journal of Geophysical Research: Space Physics, American Geophysical Union, Vol 125, Num 2, pp e2019JA027094, 2020, doi:10.1029/2019JA027094


J. N. B. Rodrigues and Lucas K. Wagner: "Identifying materials with charge-spin physics using charge-spin susceptibility computed from first principles", Journal of Chemical Physics, AIP Publishing LLC, Vol 153, Num 7, pp 074105, 2020, doi:10.1063/1.5144911


Kuan-Wei Huang, Yueying Ni, Yu Feng, and Tiziana Di Matteo: "The early growth of supermassive black holes in cosmological hydrodynamic simulations with constrained Gaussian realizations", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 496, Num 1, pp 1-12, 2020, doi:10.1093/mnras/staa1515


Stephen M. Wilkins, Christopher C. Lovell, Ciaran Fairhurst, Yu Feng, Tiziana Di Matteo, Rupert Croft, Jussi Kuusisto, Aswin P. Vijayan, and Peter Thomas: "Nebular Line Emission During the Epoch of Reionization", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 493, Num 4, pp 6079-6094, 2020, doi:10.1093/mnras/staa649


Eugen Hruska, Vivekanandan Balasubramanian, Hyungro Lee, Shantenu Jha, and Cecilia Clementi: "Extensible and Scalable Adaptive Sampling on Supercomputers", Journal of Chemical Theory and Computation, American Chemical Society, Vol 16, Num 12, pp 7915-7925, 2020, doi:10.1021/acs.jctc.0c00991


M. Liska, C. Hesp, A. Tchekhovskoy, A. Ingram, M. van der Klis, S.B. Markoff, and M. Van Moer: "Disc Tearing and Bardeen-Petterson Alignment in GRMHD Simulations of Highly Tilted Thin Accretion Discs", Monthly Notices of the Royal Astronomical Society (in press), The Royal Astronomical Society, 2020, doi:10.1093/mnras/staa099


R. B. Baker, K. D. Launey, S. Bacca, N. Nevo Dinur, and T. Dytrych: "Benchmark calculations of electromagnetic sum rules with a symmetry-adapted basis and hyperspherical harmonics", Physical Review C, American Physical Society, Vol 102, Num 1, pp 014320, 2020, doi:10.1103/PhysRevC.102.014320


Yuhang Jing and N. R. Aluru: "The role of A-site ion on proton diffusion in perovskite oxides (ABO3)", Journal of Power Sources, Elsevier B.V., Vol 445, pp 227327, 2020, doi:10.1016/j.jpowsour.2019.227327


Matthew L. S. Zappulla, S. Koric, S.–M. Cho, H.–J. Lee, S.–H. Kim, and B. G. Thomas: "Multiphysics modeling of continuous casting of stainless steel", Journal of Materials Processing Technology, Elsevier B.V., Vol 278, pp 116469, 2020, doi:10.1016/j.jmatprotec.2019.116469


J. Yan, X. Deng, F. Xu, and S. Xu: "High fidelity numerical simulations of two back-to-back horizontal axis tidal stream turbines in free-surface flows", Journal of Applied Mechanics, American Society of Mechanical Engineers, Vol 87, Num 6, 2020, doi:10.1115/1.4046317


Oliver M. Browne, Anthony P. Haas, Hermann F. Fasel, and Christoph Brehm: "An Efficient Nonlinear Wavepacket Tracking Method for Hypersonic Boundary-Layer Flows: Complex Geometries", American Institute of Aeronautics and Astronautics, AIAA Aviation 2020 Forum, Virtual location, 2020, doi:10.2514/6.2020-2985


Di Wen, Athol J. Kemball, and William C. Saslaw: "Halo counts-in-cells for cosmological models with different dark energy", Astrophysical Journal, American Astronomical Society, Vol 890, Num 2, pp 160, 2020, doi:10.3847/1538-4357/ab6d6f


Supraj Prakash, Romain Fiévet, Venkat Raman, Jason Burr, and Kenneth H. Yu: "Analysis of the detonation wave structure in a linearized rotating detonation engine", AIAA Journal, American Institute of Aeronautics and Astronautics, Vol 58, Num 12, pp 5063-5077, 2020, doi:10.2514/1.J058156


Robert L. Cieri and C. G. Farmer: "Computational Fluid Dynamics Reveals a Unique Net Unidirectional Pattern of Pulmonary Airflow in the Savannah Monitor Lizard (Varanus exanthematicus)", Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology, American Association for Anatomy, Vol 303, Num 7, pp 1768-1791, 2020, doi:10.1002/ar.24293


Chongya Jiang, Kaiyu Guan, Ming Pan, Youngryel Ryu, Bin Peng, and Sibo Wang: "BESS-STAIR: a framework to estimate daily, 30-meter, and all-weather crop evapotranspiration using multi-source satellite data for the U. S. Corn Belt", Hydrology and Earth System Sciences, The European Geosciences Union, Vol 24, Num 3, pp 1251-1273, 2020, doi:10.5194/hess-24-1251-2020


Saurabh Jha, Shengkun Cui, Subho Sankar Banerjee, Tianyin Xu, Jeremy Enos, Michael Showerman, Zbigniew T. Kalbarczyk, and Ravishankar K. Iyer: "Live Forensics for HPC Systems: A Case Study on Distributed Storage Systems", Institute of Electrical & Electronics Engineers Press, SC '20: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, pp 65, Atlanta, Georgia, U.S.A., 2020, doi:10.5555/3433701.3433787


Elaad Applebaum, Alyson M. Brooks, Thomas R. Quinn, and Charlotte R. Christensen: "A Stochastically Sampled IMF Alters the Stellar Content of Simulated Dwarf Galaxies", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 492, Num 1, pp 8-21, 2020, doi:10.1093/mnras/stz3331


Vitaly Gorelov, Markus Holzmann, David M. Ceperley, and Carlo Pierleoni: "Energy gap closure of crystalline molecular hydrogen with pressure", Physical Review Letters, American Physical Society, Vol 124, Num 11, pp 116401, 2020, doi:10.1103/PhysRevLett.124.116401


Yubo Yang, Vitaly Gorelov, Carlo Pierleoni, David M. Ceperley, and Markus Holzmann: "Electronic band gaps from Quantum Monte Carlo methods", Physical Review B, American Physical Society, Vol 101, Num 8, pp 085115, 2020, doi:10.1103/PhysRevB.101.085115


N. Hiraoka, Y. Yang, T. Hagiya, A. Niozu, K. Matsuda, S. Huotari, M. Holzmann, and D. M. Ceperley: "Direct observation of the momentum distribution and renormalization factor in lithium", Physical Review B, American Physical Society, Vol 101, Num 16, pp 165124, 2020, doi:10.1103/PhysRevB.101.165124


Alexander A. Kunitsa and So Hirata: "Grid-based diffusion Monte Carlo for fermions without the fixed-node approximation", Physical Review E, American Physical Society, Vol 101, Num 1, pp 013311, 2020, doi:10.1103/PhysRevE.101.013311


Lauren Corlies, Molly S. Peeples, Jason Tumlinson, Brian W. O'Shea, Nicolas Lehner, J. Christopher Howk, John M. O'Meara, and Britton D. Smith: "Figuring Out Gas & Galaxies in Enzo (FOGGIE). II. Emission from the z=3 Circumgalactic Medium", Astrophysical Journal, American Astronomical Society, Vol 896, Num 2, pp 125, 2020, doi:10.3847/1538-4357/ab9310


Justin Sirignano, Jonathan F. MacArt, and Jonathan B. Freund: "DPM: A deep learning PDE augmentation method with application to large-eddy simulation", Journal of Computational Physics, Elsevier Inc., Vol 423, pp 109811, 2020, doi:10.1016/j.jcp.2020.109811


Lake A. Singh, William R. Whittecar, Marc D. DiPrinzio, Jonathan D. Herman, Matthew P. Ferringer, and Patrick M. Reed: "Low cost satellite constellations for nearly continuous global coverage", Nature Communications, Springer Nature Limited, Vol 11, Num 1, 2020, doi:10.1038/s41467-019-13865-0


C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Zhao, John S. Parkinson, Phillip J. Stansfeld, Zaida Luthey-Schulten, and Peijun Zhang: "Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations", Communications Biology, Springer Nature Limited, Vol 3, Num 1, 2020, doi:10.1038/s42003-019-0748-0


J. T. Gasparik, Q. Ye, J. H. Curtis, A. A. Presto, N. M. Donahue, R. C. Sullivan, M. West. and N. Riemer: "Quantifying errors in the aerosol mixing-state index based on limited particle sample size", Aerosol Science and Technology, Taylor & Francis, Vol 54, Num 12, pp 1527-1541, 2020, doi:10.1080/02786826.2020.1804523


Sergei Kotelnikov, Andrey Alekseenko, Cong Liu, Mikhail Ignatov, Dzmitry Padhorny, Emiliano Brini, Mark Lukin, Evangelos Coutsias, Ken A. Dill, and Dima Kozakov: "Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4", Journal of Computer-Aided Molecular Design, Springer Nature Switzerland AG, Vol 34, Num 2, pp 179-189, 2020, doi:10.1007/s10822-019-00257-1


Luke Cuculis, Chuankai Zhao, Zhanar Abil, Huimin Zhao, Diwakar Shukla, and Charles M. Schroeder: "Divalent cations promote TALE DNA-binding specificity", Nucleic Acids Research, Oxford University Press, Vol 48, Num 3, pp 1406-1422, 2020, doi:10.1093/nar/gkz1174


Guillermo Araya, Christian Lagares, and Kenneth E. Jansen: "Reynolds number dependency in supersonic spatially-developing turbulent boundary layers", American Institute of Aeronautics and Astronautics, AIAA Scitech 2020 Forum, Orlando, Florida, U.S.A., 2020, doi:10.2514/6.2020-0574


Mohammad Heiranian and Narayana R. Aluru: "Nanofluidic Transport Theory with Enhancement Factors Approaching One", ACS Nano, American Chemical Society, Vol 14, Num 1, pp 272-281, 2020, doi:10.1021/acsnano.9b04328


Zahra Shamsi and Diwakar Shukla: "How does evolution design functional free energy landscapes of proteins? A case study on the emergence of regulation in the Cyclin Dependent Kinase family", Molecular Systems Design & Engineering, Royal Society of Chemistry, Vol 5, Num 1, pp 392-400, 2020, doi:10.1039/C9ME00097F


Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, Ananya Yammanuru, and Tandy Warnow: "Non-parametric correction of estimated gene trees using TRACTION", Algorithms for Molecular Biology, Springer Nature Switzerland AG, Vol 15, Num 1, pp 1, 2020, doi:10.1186/s13015-019-0161-8


Ankita Bhutani, Xiao Zhang, Piush Behera, Rangarajan Thiruvengadam. Shannon E. Murray, André Schleife, and Daniel P. Shoemaker: "New Family of Anisotropic Zinc-Based Semiconductors in a Shallow Energy Landscape", Chemistry of Materials, American Chemical Society, Vol 32, Num 1, pp 326-332, 2020, doi:10.1021/acs.chemmater.9b03829


Faisal Aldukhi, Aniket Deb, Chuankai Zhao, Alexander S. Moffett, and Diwakar Shukla: "Molecular Mechanism of Brassinosteroid Perception by the Plant Growth Receptor BRI1", Journal of Physical Chemistry B, American Chemical Society, Vol 124, Num 2, pp 355-365, 2020, doi:10.1021/acs.jpcb.9b09377


John A. Regan, John H. Wise, Brian W. O’Shea, and Michael L. Norman: "The emergence of the first star-free atomic cooling haloes in the Universe", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 492, Num 2, pp 3021-3031, 2020, doi:10.1093/mnras/staa035


Hadjer Ouldali, Kumar Sarthak, Tobias Ensslen, Fabien Piguet, Philippe Manivet, Juan Pelta, Jan C. Behrends, Aleksei Aksimentiev, and Abdelghani Oukhaled: "Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore", Nature Biotechnology, Springer Nature Limited, Vol 38, pp 176-181, 2020, doi:10.1038/s41587-019-0345-2


Hongyang Zhou and Gábor Tóth: "Efficient OpenMP parallelization to a complex MPI parallel magnetohydrodynamics code", Journal of Parallel and Distributed Computing, Elsevier, Vol 139, pp 65-74, 2020, doi:10.1016/j.jpdc.2020.02.004


Seong-Mook Cho, Mingyi Liang, Hamed Olia, Lipsa Das, and Brian G. Thomas: "Multiphase Flow-Related Defects in Continuous Casting of Steel Slabs", Springer, TMS 2020 149th Annual Meeting and Exhibition Supplemental Proceedings, pp 1161-1173, San Diego, California, U.S.A., 2020, doi:10.1007/978-3-030-36296-6_108


Varvara E. Zemskova, Brian L. White, and Alberto Scotti: "Energetics of a Rotating Wind-forced Horizontal Convection Model of a Reentrant Channel", Journal of Physical Oceanography (in press), American Meteorological Society, 2020, doi:10.1175/JPO-D-19-0169.1


C. T. H. Davies, C. DeTar, A. X. El-Khadra, E. Gámiz, Steven Gottlieb, D. Hatton, A. S. Kronfeld, J. Laiho, G. P. Lepage, Yuzhi Liu, P. B. Mackenzie, C. McNeile, E. T. Neil, T. Primer, J. N. Simone, D. Toussaint, R. S. Van de Water, and A. Vaquero (Fermilab Lattice, HPQCD, and MILC Collaborations): "Hadronic-vacuum-polarization contribution to the muon’s anomalous magnetic moment from four-flavor lattice QCD", Physical Review D, American Physical Society, Vol 101, Num 3, pp 034512, 2020, doi:10.1103/PhysRevD.101.034512


Alister Burt, C. Keith Cassidy, Peter Ames, Maria Bacia-Verloop, Megghane Baulard, Karine Huard, Zaida Luthey-Schulten, Ambroise Desfosses, Phillip J. Stansfeld, William Margolin, John S. Parkinson, and Irina Gutsche: "Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain", Nature Communications, Springer Nature Limited, Vol 11, Num 1, pp 743, 2020, doi:10.1038/s41467-020-14350-9


Jacob D. Durrant, Sarah E. Kochanek, Lorenzo Casalino, Pek U. Ieong, Abigail C. Dommer, and Rommie E. Amaro: "Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism", ACS Central Science, American Chemical Society, Vol 6, Num 2, pp 189-196, 2020, doi:10.1021/acscentsci.9b01071


Jamila Taaki, Farzad Kamalabadi, and Athol J. Kemball: "Bayesian Methods for Joint Exoplanet Transit Detection and Systematic Noise Characterization", Astronomical Journal, The American Astronomical Society, Vol 159, Num 6, pp 283, 2020, doi:10.3847/1538-3881/ab8e38


Revathi Jambunathan and Deborah A. Levin: "A Self-Consistent Open Boundary Condition for Fully Kinetic Plasma Thruster Plume Simulations", IEEE Transactions on Plasma Science, Institute of Electrical & Electronics Engineers, Vol 48, Num 3, pp 610-630, 2020, doi:10.1109/TPS.2020.2968887


Revathi Jambunathan and Deborah A. Levin: "Kinetic, 3-D, PIC-DSMC Simulations of Ion Thruster Plumes and the Backflow Region", IEEE Transactions on Plasma Science, Institute of Electrical & Electronics Engineers, Vol 48, Num 6, pp 2017-2034, 2020, doi:10.1109/TPS.2020.2988010


Guangyu Zhao, Muqun Yang, Yizhao Gao, Yizhe Zhan, H. Joe Lee, and Larry Di Girolamo: "PYTAF: A Python Tool for Spatially Resampling Earth Observation Data", Earth Science Informatics (in press), Springer Nature Switzerland AG, 2020, doi:10.1007/s12145-020-00461-w


Alvin Yu, Katarzyna A. Skorupka, Alexander J. Pak, Barbie K. Ganser-Pornillos, Owen Pornillos, and Gregory A. Voth: "TRIM5 alpha self-assembly and compartmentalization of the HIV-1 viral capsid", Nature Communications, Springer Nature Limited, Vol 11, Num 1, 2020, doi:10.1038/s41467-020-15106-1


Justin A. Drake and B. Montgomery Pettitt: "Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder", Journal of Physical Chemistry B, American Chemical Society, Vol 124, Num 22, pp 4379-4390, 2020, doi:10.1021/acs.jpcb.0c02489


E. J. Zirnstein, T. K. Kim, P. Mostafavi, J. Heerikhuisen, D. J. McComas, and N. V. Pogorelov: "Response of Pickup Ions in the Very Local Interstellar Medium to Solar Variations: Implications for the Evolution of the IBEX Ribbon and Interstellar Helium", Astrophysical Journal, American Astronomical Society, Vol 891, Num 1, pp 56, 2020, doi:10.3847/1538-4357/ab744b


Ming Zhang, N. V. Pogorelov, Y. Zhang, H. B. Hu, and R. Schlickeiser: "The Original Anisotropy of TeV Cosmic Rays in the Local Interstellar Medium", Astrophysical Journal, American Astronomical Society, Vol 889, Num 2, pp 97, 2020, doi:10.3847/1538-4357/ab643c


Michael A. Lively, Brandon Holybee, Michael Toriyama, Stefan Facsko, and Jean Paul Allain: "Nonlinear compositional and morphological evolution of ion irradiated GaSb prior to nanostructure formation", Scientific Reports, Springer Nature Limited, Vol 10, Num 1, pp 8253, 2020, doi:10.1038/s41598-020-64971-9


T. K. Kim, N. V. Pogorelov, C. N. Arge, C. J. Henney, S. I. Jones-Mecholsky, W. P. Smith, S. D. Bale, J. W. Bonnell, T. Dudok de Wit, K. Goetz, P. R. Harvey, R. J. MacDowall, D. M. Malaspina, M. Pulupa, J. C. Kasper, K. E. Korreck, M. Stevens, A. W. Case, P. Whittlesey, R. Livi, D. E. Larson, K. G. Klein, and G. P. Zank: "Predicting the Solar Wind at the Parker Solar Probe Using an Empirically Driven MHD Model", Astrophysical Journal Supplement Series, The Astrophysical Society, Vol 246, Num 2, pp 40, 2020, doi:10.3847/1538-4365/ab58c9


Joshua L. Lansford and Dionisios G. Vlachos: "Infrared spectroscopy data- and physics-driven machine learning for characterizing surface microstructure of complex materials", Nature Communications, Springer Nature Limited, Vol 11, Num 1, pp 1513, 2020, doi:10.1038/s41467-020-15340-7


Vincenzo Cirigliano, William Detmold, Amy Nicholson, and Phiala Shanahan: "Lattice QCD Inputs for nuclear double beta decay", Progress in Particle and Nuclear Physics, Elsevier B.V., Vol 112, pp 103771, 2020, doi:10.1016/j.ppnp.2020.103771


Milton Ruiz, Antonios Tsokaros, and Stuart L. Shapiro: "Magnetohydrodynamic simulations of binary neutron star mergers in general relativity: Effects of magnetic field orientation on jet launching", Physical Review D, American Physical Society, Vol 101, Num 6, pp 064042, 2020, doi:10.1103/PhysRevD.101.064042


Scott A. Lathrop, Katharine Cahill, Steven I. Gordon, Jennifer Houchins; Robert M. Panoff, and Aaron Weeden: "Preparing a Computationally Literate Workforce", Computing in Science & Engineering, Institute of Electrical & Electronics Engineers, Vol 22, Num 4, pp 7-16, 2020, doi:10.1109/MCSE.2020.2994763


Jennifer Houchins, Scott Lathrop, Robert Panoff, and Aaron Weeden: "Blue Waters Workforce Development: Delivering National Scale HPC Workforce Development", Journal of Computational Science Education, Shodor Education Foundation, Vol 11, Num 1, pp 26-28, 2020, doi:10.22369/issn.2153-4136/11/1/5


Jaime D. Guevara, Matthew L. Jones, Peter Müllner, and Eric Jankowski: "Development of a Molecular Model for Understanding the Polymer-metal Interface in Solid State Pumps", Journal of Computational Science Education, The Shodor Education Foundation, Vol 11, Num 2, pp 12-22, 2020, doi:10.22369/issn.2153-4136/11/2/3


Caroline MacDonald and Andrew Mercer: "Using Blue Waters to Assess Tornadic Outbreak Forecast Capability by Lead Time", Journal of Computational Science Education, The Shodor Education Foundation, Vol 11, Num 2, pp 23-28, 2020, doi:10.22369/issn.2153-4136/11/2/4


Nicholas Kellas and Michael N. Groves: "Improvement of the Evolutionary Algorithm on the Atomic Simulation Environment Though Intuitive Starting Population Creation and Clustering", Journal of Computational Science Education, The Shodor Education Foundation, Vol 11, Num 2, pp 29-35, 2020, doi:10.22369/issn.2153-4136/11/2/5


S. Kasra Tabatabaei, Boya Wang, Nagendra Bala Murali Athreya, Behnam Enghiad, Alvaro Gonzalo Hernandez, Christopher J. Fields, Jean-Pierre Leburton, David Soloveichik, Huimin Zhao, and Olgica Milenkovic.: "DNA punch cards for storing data on native DNA sequences via enzymatic nicking", Nature Communications, Springer Nature, Vol 11, Num 1, pp 1742, 2020, doi:10.1038/s41467-020-15588-z


Nagendra Athreya, Olgica Milenkovic, and Jean-Pierre Leburton: "Interaction Dynamics and Site-Specific Electronic Recognition of DNA-Nicks with 2D Solid State Nanopores", npj 2D Materials and Applications, Springer Nature Limited, Vol 4, Num 1, pp 32, 2020, doi:10.1038/s41699-020-00166-0


Nagendra Athreya, Aditya Sarathy, Mingye Xiong, and Jean-Pierre Leburton: "2D Solid-state Nanopore Field-effect Transistors: Comprehensive Computational Methodology for Biosensing Applications", IEEE Nanotechnology Magazine, Institute of Electrical & Electronics Engineers, Vol 14, Num 6, pp 42-51, 2020, doi:10.1109/MNANO.2020.3024388


Zhongchao Zhao, Joseph Che-Yen Wang, Carolina Perez-Segura, Jodi A. Hadden-Perilla, and Adam Zlotnick: "The integrity of the intradimer interface of the Hepatitis B Virus capsid protein dimer regulates capsid self-assembly", ACS Chemical Biology, American Chemical Society, Vol 15, Num 12, pp 3124-3132, 2020, doi:10.1021/acschembio.0c00277


Lauren M. Foster, Kenneth H. Williams, and Reed M. Maxwell: "Resolution matters when modeling climate change in headwaters of the Colorado River", Environmental Research Letters, IOP Publishing Ltd, Vol 15, Num 10, pp 104031, 2020, doi:10.1088/1748-9326/aba77f


Felipe González-Cataldo, François Soubiran, Henry Peterson, and Burkhard Militzer: "Path integral Monte Carlo and density functional molecular dynamics simulations of warm dense MgSiO3", Physical Review B, American Physical Society, Vol 101, Num 2, pp 024107, 2020, doi:10.1103/PhysRevB.101.024107


Felipe González-Cataldo and Burkhard Militzer: "Thermal and pressure ionization in warm, dense MgSiO3 studied with first-principles computer simulations", AIP Publishing, AIP Conference Proceedings (Conference of the American Physical Society Topical Group on Shock Compression of Condensed Matter 2019), Vol 2272, Num 1, pp 090001, Portland, Oregon, U.S.A., 2020, doi:10.1063/12.0000793


George M. Slota, Cameron Root, Karen Devine, Kamesh Madduri, and Sivasankaran Rajamanickam: "Scalable, Multi-Constraint, Complex-Objective Graph Partitioning", IEEE Transactions on Parallel and Distributed Systems, Institute of Electrical & Electronics Engineers, Vol 31, Num 12, pp 2789-2801, 2020, doi:10.1109/TPDS.2020.3002150


David Radice: "Binary Neutron Star Merger Simulations with a Calibrated Turbulence Model", Symmetry, MDPI AG, Vol 12, Num 8, pp 1249, 2020, doi:10.3390/sym12081249


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Michalis Agathos, Francesco Zappa, Sebastiano Bernuzzi, Albino Perego, Matteo Breschi, and David Radice: "Inferring prompt black-hole formation in neutron star mergers from gravitational-wave data", Physical Review D, American Physical Society, Vol 101, Num 4, pp 044006, 2020, doi:10.1103/PhysRevD.101.044006


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Graham R. Huesmann, Hillary Schwarb, Daniel R. Smith, Ryan T. Pohlig, Aaron T. Anderson, Matthew D. J. McGarry, Keith D. Paulsen, Tracey Mencio Wszalek, Bradley P. Sutton, and Curtis L. Johnson: "Hippocampal stiffness in mesial temporal lobe epilepsy measured with MR elastography: Preliminary comparison with healthy participants", NeuroImage-Clinical, Elsevier Inc., Vol 27, pp 102313, 2020, doi:10.1016/j.nicl.2020.102313


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Matthew S. Clement, Alessandro Morbidelli, Sean N. Raymond, Nathan A. Kaib: "A record of the final phase of giant planet migration fossilized in the asteroid belt's orbital structure", Monthly Notices of the Royal Astronomical Society: Letters, Royal Astronomical Society, Vol 492, Num 1, pp L56-L60, 2020, doi:10.1093/mnrasl/slz184


Daniel Dumett Torres, Sudhakar Pamidighantam, and Prashant K. Jain: "Crystal Symmetry, Strain, and Facet-Dependent Nature of Topological Surface States in Mercury Selenide", Journal of Physical Chemistry C, American Chemical Society, Vol 124, Num 19, pp 10344-10352, 2020, doi:10.1021/acs.jpcc.0c01663


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Hiroki Nagakura, Adam Burrows, David Radice, and David Vartanyan: "A systematic study of proto-neutron star convection in three-dimensional core-collapse supernova simulations", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 492, Num 4, pp 5764-5779, 2020, doi:10.1093/mnras/staa261


David Vartanyan and Adam Burrows: "Gravitational Waves from Neutrino Asymmetries in Core-Collapse Supernovae", Astrophysical Journal, The American Astronomical Society, Vol 901, Num 2, pp 108, 2020, doi:10.3847/1538-4357/abafac


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Erin K. Molloy and Tandy Warnow: "FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models", Bioinformatics, Oxford University Press, Vol 36, Num Supplement 1, pp i57-i65, 2020, doi:10.1093/bioinformatics/btaa444


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Ray S. Sharma, Alyson M. Brooks, Rachel S. Somerville, Michael Tremmel, Jillian Bellovary, Anna C. Wright, and Thomas R. Quinn: "Black Hole Growth and Feedback in Isolated ROMULUS25 Dwarf Galaxies", Astrophysical Journal, The American Astronomical Society, Vol 897, Num 1, pp 103, 2020, doi:10.3847/1538-4357/ab960e


Michael Tremmel, Anna C. Wright, Alyson M. Brooks, Ferah Munshi, Daisuke Nagai, and Thomas R. Quinn: "The Formation of Ultradiffuse Galaxies in the RomulusC Galaxy Cluster Simulation", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 497, Num 3, pp 2786-2810, 2020, doi:10.1093/mnras/staa2015


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Akash Singh, Xin Chen, Yumeng Li, Seid Koric, and Erman Guleryuz: "Development of Artificial Neural Network Potential for Graphene", American Institute of Aeronautics and Astronautics, AIAA Scitech 2020 Forum, Orlando, Florida, U.S.A., 2020, doi:10.2514/6.2020-1861


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DIana Sobota, Himanshu Joshi, Alexander Ohmann, Aleksei Aksimentiev, and Ulrich F. Keyser: "Tailoring Interleaflet Lipid Transfer with a DNA-based Synthetic Enzyme", Nano Letters, American Chemical Society, Vol 20, Num 6, pp 4306-4311, 2020, doi:10.1021/acs.nanolett.0c00990


David Winogradoff, Shalini Johnb, and Aleksei Aksimentiev: "Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly", Nanoscale, The Royal Society of Chemistry, Vol 12, Num 9, pp 5422-5434, 2020, doi:10.1039/C9NR09135A


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Christopher Maffeo and Aleksei Aksimentiev: "MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems", Nucleic Acids Research, Oxford University Press, Vol 48, Num 9, pp 5135-5146, 2020, doi:10.1093/nar/gkaa200


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Lina Necib, Bryan Ostdiek, Mariangela Lisanti, Timothy Cohen, Marat Freytsis, Shea Garrison-Kimmel, Philip F. Hopkins, Andrew Wetzel, and Robyn Sanderson: "Evidence for a vast prograde stellar stream in the solar vicinity", Nature Astronomy, Springer Nature Limited, Vol 4, Num 11, pp 1078-1083, 2020, doi:10.1038/s41550-020-1131-2


Steffen M. Sedlak, Leonard C. Schendel, Hermann E. Gaub, and Rafael C. Bernardi: "Streptavidin/biotin: Tethering geometry defines unbinding mechanics", Science Advances, American Association for the Advancement of Science, Vol 6, Num 13, pp eaay5999, 2020, doi:10.1126/sciadv.aay5999


Anuj K. Yadav, Christopher J. Reinhardt, Andres S. Arango, Hannah C. Huff, Liang Dong, Michael G. Malkowski, Aditi Das, Emad Tajkhorshid, and Jefferson Chan: "An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells", Angewandte Chemie International Edition, John Wiley & Sons, Inc., Vol 59, Num 8, pp 3307-3314, 2020, doi:10.1002/anie.201914845


Chia-Hao Lee, Abid Khan, Di Luo, Tatiane P. Santos, Chuqiao Shi, Blanka E. Janicek, Sangmin Kang, Wenjuan Zhu, Nahil A. Sobh, André Schleife, Bryan K. Clark, and Pinshane Y. Huang: "Deep Learning Enabled Strain Mapping of Single-Atom Defects in Two-Dimensional Transition Metal Dichalcogenides with Sub-Picometer Precision", Nano Letters, American Chemical Society, Vol 20, Num 5, pp 3369-3377, 2020, doi:10.1021/acs.nanolett.0c00269


Steffen Richter, Oliver Herrfurth, Shirly Espinoza, Mateusz Rebarz, Miroslav Kloz, Joshua Leveillee, André Schleife, Stefan Zollner, Marius Grundmann, Jakob Andreasson and Rüdiger Schmidt-Grund: "Ultrafast dynamics of hot charge carriers in an oxide semiconductor probed by femtosecond spectroscopic ellipsometry", New Journal of Physics, IOP Publishing Ltd on behalf of Deutsche Physikalische Gesellschaft and the Institute of Physics, Vol 22, Num 8, pp 083066, 2020, doi:10.1088/1367-2630/aba7f3


Kexin Yang, Kisung Kang, Zhu Diao, Manohar H. Karigerasi, Daniel P. Shoemaker, André Schleife, and David G. Cahill: "Magnetocrystalline anisotropy of the easy-plane metallic antiferromagnet Fe2As", Physical Review B, American Physical Society, Vol 102, Num 6, pp 064415, 2020, doi:10.1103/PhysRevB.102.064415


Chuanxu Ma, Zhongcan Xiao, Alexander A. Puretzky, Hao Wang, Ali Mohsin, Jingsong Huang, Liangbo Liang, Yingdong Luo, Benjamin J. Lawrie, Gong Gu, Wenchang Lu, Kunlun Hong, Jerzy Bernholc, and An-Ping Li: "Engineering Edge States of Graphene Nanoribbons for Narrow-Band Photoluminescence", ACS Nano, American Chemical Society, Vol 14, Num 4, pp 5090-5098, 2020, doi:10.1021/acsnano.0c01737


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Shardul Natu, Ketan Date, and Rakesh Nagi: "GPU-accelerated Lagrangian heuristic for multidimensional assignment problems with decomposable costs", Parallel Computing, Elsevier B.V., Vol 97, pp 102666, 2020, doi:10.1016/j.parco.2020.102666


Shivesh Pathaka and Lucas K. Wagner: "A light weight regularization for wave function parameter gradients in quantum Monte Carlo", AIP Advances, AIP Publishing LLC, Vol 10, Num 8, pp 085213, 2020, doi:10.1063/5.0004008


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Kartik P. Iyer, Katepalli R. Sreenivasan, and P. K. Yeung: "Scaling exponents saturate in three-dimensional isotropic turbulence", Physical Review Fluids, American Physical Society, Vol 5, Num 5, pp 054605, 2020, doi:10.1103/PhysRevFluids.5.054605


Yong Zheng, Molly S. Peeples, Brian W. O'Shea, Raymond C. Simons, Cassandra Lochhaas, Lauren Corlies, Jason Tumlinson, Britton D. Smith, and Ramona Augustin: "Figuring Out Gas & Galaxies in Enzo (FOGGIE). III. The Mocky Way: Investigating Biases in Observing the Milky Way's Circumgalactic Medium", Astrophysical Journal, The American Astronomical Society, Vol 896, Num 2, pp 143, 2020, doi:10.3847/1538-4357/ab960a


Raymond C. Simons, Molly S. Peeples, Jason Tumlinson, Brian W. O'Shea, Britton D. Smith, Lauren Corlies, Cassandra Lochhaas, Yong Zheng, Ramona Augustin, Deovrat Prasad, Gregory F. Snyder, and Erik Tollerud: "Figuring Out Gas & Galaxies In Enzo (FOGGIE). IV. The Stochasticity of Ram Pressure Stripping in Galactic Halos", Astrophysical Journal, American Astronomical Society, Vol 905, Num 2, pp 167, 2020, doi:10.3847/1538-4357/abc5b8


Tanmay S. Chavan, Ricky C. Cheng, Tao Jiang, Irimpan I. Mathews, Richard A. Stein, Antoine Koehl, Hassane S. Mchaourab, Emad Tajkhorshid, and Merritt Maduke: "A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl–/H+ transport cycle", eLife, eLife Sciences Publications, Ltd., Vol 9, pp e53479, 2020, doi:10.7554/eLife.53479


Tao Jiang, Po-Chao Wen, Noah Trebesch, Zhiyu Zhao, Shashank Pant, Karan Kapoor, Mrinal Shekhar, and Emad Tajkhorshid: "Computational Dissection of Membrane Transport at a Microscopic Level", Trends in Biochemical Sciences, Elsevier Ltd., Vol 45, Num 3, pp 202-216, 2020, doi:10.1016/j.tibs.2019.09.001


Felipe González-Cataldo, François Soubiran, and Burkhard Militzer: "Equation of state of hot, dense magnesium derived with first-principles computer simulations", Physics of Plasmas, AIP Publishing LLC, Vol 27, Num 9, pp 092706, 2020, doi:10.1063/5.0017555


Takuma Sato, Fabian Chacon, Logan White, Venkat Raman, and Mirko Gamba: "Mixing and detonation structure in a rotating detonation engine with an axial air inlet", Proceedings of the Combustion Institute (in press), The Combustion Institute, 2020, doi:10.1016/j.proci.2020.06.283


Z. Gelzer, C. DeTar, A. X. El-Khadra, E. Gámiz, S. Gottlieb, A. Kronfeld, Y. Liu, Y. Meurice, J.N. Simone, D. Toussaint, R. S. Van de Water: "B-meson semileptonic form factors on (2+1+1)-flavor HISQ ensembles", Sissa Medialab srl, Proceedings of 37th International Symposium on Lattice Field Theory - Proceedings of Science (Lattice 2019), Vol 363, pp 236, Wuhan, China, 2020, doi:10.22323/1.363.0236


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Jiaren Zhang, Eung Chang Kim, Congcong Chen, Erik Procko, Shashank Pant, Kin Lam, Jaimin Patel, Rebecca Choi, Mary Hong, Dhruv Joshi, Eric Bolton, Emad Tajkhorshid, and Hee Jung Chung: "Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy", Scientific Reports, Springer Nature Limited, Vol 10, Num 1, pp 4756, 2020, doi:10.1038/s41598-020-61697-6


Zohreh Davoudi, William Detmold, Phiala Shanahan, Kostas Orginos, Assumpta Parreño, Martin J. Savage, and Michael L. Wagman: "Nuclear matrix elements from lattice QCD for electroweak and beyond-Standard-Model processes", Physics Reports-Review Section of Physics Letters (in press), Elsevier B.V., 2020, doi:10.1016/j.physrep.2020.10.004


James Healy, Carlos O. Lousto, and Nicole Rosato: "Adapted gauge to a quasilocal measure of the black holes recoil", Physical Review D, American Physical Society, Vol 102, Num 2, pp 024040, 2020, doi:10.1103/PhysRevD.102.024040


Uriel N. Morzan, Pablo E. Videla, Micheline B. Soley, Erik T. J. Nibbering, and Victor S. Batista: "Vibronic Dynamics of Photodissociating ICN from Simulations of Ultrafast X-Ray Absorption Spectroscopy", Angewandte Chemie International Edition, John Wiley & Sons, Inc., Vol 59, Num 45, pp 20044-20048, 2020, doi:10.1002/anie.202007192


Andrew Emerick, Greg L. Bryan, and Mordecai-Mark Mac Low: "Simulating Metal Mixing of Both Common and Rare Enrichment Sources in a Low-mass Dwarf Galaxy", Astrophysical Journal, American Astronomical Society, Vol 890, Num 2, pp 155, 2020, doi:10.3847/1538-4357/ab6efc


Philipp Mösta, David Radice, Roland Haas, Erik Schnetter, and Sebastiano Bernuzzi: "A Magnetar Engine for Short GRBs and Kilonovae", Astrophysical Journal Letters, The American Astronomical Society, Vol 901, Num 2, pp L37, 2020, doi:10.3847/2041-8213/abb6ef


Martin Brandt, Compton J. Tucker, Ankit Kariryaa, Kjeld Rasmussen, Christin Abel, Jennifer Small, Jerome Chave, Laura Vang Rasmussen, Pierre Hiernaux, Abdoul Aziz Diouf, Laurent Kergoat, Ole Mertz, Christian Igel, Fabian Gieseke, Johannes Schöning, Sizhuo Li, Katherine Melocik, Jesse Meyer, Scott Sinno, Eric Romero, Erin Glennie, Amandine Montagu, Morgane Dendoncker, and Rasmus Fensholt: "An unexpectedly large count of trees in the West African Sahara and Sahel", Nature, Springer Nature Limited, Vol 587, Num 7832, pp 78-82, 2020, doi:10.1038/s41586-020-2824-5


Alexander E. Doran and So Hirata: "Convergence acceleration of Monte Carlo many-body perturbation methods by direct sampling", Journal of Chemical Physics, AIP Publishing, Vol 153, Num 10, pp 104112, 2020, doi:10.1063/5.0020583


Alexander E. Doran and So Hirata: "Convergence acceleration of Monte Carlo many-body perturbation methods by using many control variates", Journal of Chemical Physics, AIP Publishing, Vol 153, Num 9, pp 094108, 2020, doi:10.1063/5.0020584


Amir Taqieddin, Mohammad Heiranian, and Narayana R. Aluru: "Interfacial Properties of Water on Hydrogenated and Fluorinated Graphene Surfaces: Parametrization of Nonbonded Interactions", Journal of Physical Chemistry C, American Chemical Society, Vol 124, Num 39, pp 21467-21475, 2020, doi:10.1021/acs.jpcc.0c05951


Yechan Noh and Narayana R. Aluru: "Ion Transport in Electrically Imperfect Nanopores", ACS Nano, American Chemical Society, Vol 14, Num 8, pp 10518-10526, 2020, doi:10.1021/acsnano.0c04453


James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, João V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoît Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid: "Scalable molecular dynamics on CPU and GPU architectures with NAMD", Journal of Chemical Physics, AIP Publishing, Vol 153, Num 4, pp 044130, 2020, doi:10.1063/5.0014475


Eric Jankowski, Neale Ellyson, Jenny W. Fothergill, Michael M. Henry, Mitchell H. Leibowitz, Evan D. Miller, Mone’t Alberts, Samantha Chesser, Jaime D. Guevara, Chris D. Jones, Mia Klopfenstein, Kendra K. Noneman, Rachel Singleton, Ramon A. Uriarte-Mendoza, Stephen Thomas, Carla E. Estridge, and Matthew L. Jones: "Perspective on coarse-graining, cognitive load, and materials simulation", Computational Materials Science, Elsevier B.V., Vol 171, pp 109129, 2020, doi:10.1016/j.commatsci.2019.109129


Marc E. Canby, Aidana Karipbayeva, Bryan J. Lunt, Sahand Mozaffari, Charlotte R. Yoder, and Julia Hockenmaier: "University of Illinois Submission to the SIGMORPHON 2020 Shared Task 0: Typologically Diverse Morphological Inflection", Association for Computational Linguistics, Proceedings of the 17th SIGMORPHON Workshop on Computational Research in Phonetics, Phonology, and Morphology, pp 137-145, virtual workshop, 2020, doi:10.18653/v1/2020.sigmorphon-1.15


Saurabh S. Sawant, Ozgur Tumuklu, Vassilis Theofilis, and Deborah A. Levin: "Analysis of Spanwise Homogeneous Perturbations in Laminar Hypersonic Shock-Boundary Layer Interactions", American Institute of Aeronautics and Astronautics, AIAA Scitech 2020 Forum, Orlando, Florida, U.S.A., 2020, doi:10.2514/6.2020-0108


Jordi Casanova, Eirik Endeve, Eric J. Lentz, O. E. Bronson Messer, W. Raphael Hix, J. Austin Harris, and Stephen W. Bruenn: "On the character of turbulent-like flows in self-consistent models of core-collapse supernovae", Physica Scripta, IOP Publishing Ltd., Vol 95, Num 6, pp 064005, 2020, doi:10.1088/1402-4896/ab7dd1


Pramod Kumar, Yuhang Wang, Zhening Zhang, Zhiyu Zhao, Gisela D. Cymes, Emad Tajkhorshid, and Claudio Grosman: "Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 117, Num 3, pp 1788-1798, 2020, doi:10.1073/pnas.1906823117


Ankita Sarkar and Adrian E. Roitberg: "pH-Dependent Conformational Changes Lead to a Highly Shifted pKa for a Buried Glutamic Acid Mutant of SNase", Journal of Physical Chemistry B, American Chemical Society, Vol 124, Num 49, pp 11072-11080, 2020, doi:10.1021/acs.jpcb.0c07136


Mohammad H. Motevaselian and Narayana R. Aluru: "Confinement-Induced Enhancement of Parallel Dielectric Permittivity: Super Permittivity Under Extreme Confinement", Journal of Physical Chemistry Letters, American Chemical Society, Vol 11, Num 24, pp 10532-10537, 2020, doi:10.1021/acs.jpclett.0c03219


Abir Ganguly, Benjamin P. Weissman, Timothy J. Giese, Nan-Sheng Li, Shuichi Hoshika, Saieesh Rao, Steven A. Benner, Joseph A. Piccirilli, and Darrin M. York: "Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme", Nature Chemistry, Springer Nature Limited, Vol 12, Num 2, pp 193–201, 2020, doi:10.1038/s41557-019-0391-x


S. E. Hough and R. W. Graves: "The 1933 Long Beach Earthquake (California, USA): Ground Motions and Rupture Scenario", Scientific Reports, Springer Nature Limited, Vol 10, Num 1, pp 10017, 2020, doi:10.1038/s41598-020-66299-w


Changsoon Choi, Juyoung Leem, Min Sung Kim, Amir Taqieddin, Chullhee Cho, Kyoung Won Cho, Gil Ju Lee, Hyojin Seung, Hyung Jong Bae, Young Min Song, Taeghwan Hyeon, Narayana R. Aluru, SungWoo Nam, and Dae-Hyeong Kim: "Curved neuromorphic image sensor array using a MoS2-organic heterostructure inspired by the human visual recognition system", Nature Communications, Springer Nature Limited, Vol 11, Num 1, pp 5934, 2020, doi:10.1038/s41467-020-19806-6


Nakul Nuwal, Revathi Jambunathan, and Deborah A. Levin: "Kinetic Modeling of Spacecraft Surfaces in a Plume Backflow Region", IEEE Transactions on Plasma Science, Institute of Electrical & Electronics Engineers, Vol 48, Num 12, pp 4305-4325, 2020, doi:10.1109/TPS.2020.3039110


Mohammad Heiranian, Amir Taqieddin, and Narayana R. Aluru: "Revisiting Sampson's theory for hydrodynamic transport in ultrathin nanopores", Physical Review Research, American Physical Society, Vol 2, Num 4, pp 043153, 2020, doi:10.1103/PhysRevResearch.2.043153


Shan Zhou, Kaustubh S. Panse, Mohammad Hossein Motevaselian, Narayana R. Aluru, and Yingjie Zhang: "Three-Dimensional Molecular Mapping of Ionic Liquids at Electrified Interfaces", ACS Nano, American Chemical Society, Vol 14, Num 12, pp 17515-17523, 2020, doi:10.1021/acsnano.0c07957


Ryan Levy, Edgar Solomonik, and Bryan K. Clark: "Distributed-Memory DMRG via Sparse and Dense Parallel Tensor Contractions", Institute of Electrical & Electronics Engineers Press, SC '20: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, Num 24, Atlanta, Georgia, U.S.A., 2020, doi:10.5555/3433701.3433732


R. Abbott, T. Blum, P.  A. Boyle, M. Bruno, N. H. Christ, D. Hoying, C. Jung, C. Kelly, C. Lehner, R. D. Mawhinney, D. J. Murphy, C. T. Sachrajda, A. Soni, M. Tomii, and T. Wang (RBC and UKQCD Collaborations): "Direct CP violation and the Delta I=1/2 rule in K -> pi pi decay from the standard model", Physical Review D, American Physical Society, Vol 102, Num 5, pp 054509, 2020, doi:10.1103/PhysRevD.102.054509


2019

Amanda Bienz, William D. Gropp, and Luke N. Olson: "Node Aware Sparse Matrix-Vector Multiplication", Journal of Parallel and Distributed Computing, Academic Press, Vol 130, pp 166-178, 2019, doi:10.1016/j.jpdc.2019.03.016


Robert J. Trapp, Kimberly A. Hoogewind, and Sonia Lasher-Trapp: "Future Changes in Hail Occurrence in the United States Determined through Convection-Permitting Dynamical Downscaling", Journal of Climate, The American Meteorological Society, Vol 32, Num 17, pp 5493-5509, 2019, doi:10.1175/JCLI-D-18-0740.1


G. R. Hart and A. L. Ferguson: "Computational design of hepatitis C virus immunogens from host-pathogen dynamics over empirical viral fitness landscapes", Physical Biology, IOP Publishing Ltd., Vol 16, Num 1, pp 016004, 2019, doi:10.1088/1478-3975/aaeec0


Hui Li and Ryan L. Sriver: "Impact of air-sea coupling on the simulated global tropical cyclone activity in the high-resolution Community Earth System Model (CESM)", Climate Dynamics, Springer Nature Switzerland AG, Vol 53, Num 7-8, pp 3731-3750, 2019, doi:10.1007/s00382-019-04739-8


Brian D. Busemeyer, Greg MacDougall, and Lucas K. Wagner: "Prediction for the singlet-triplet excitation energy for the spinel MgTi2O4 using first-principles diffusion Monte Carlo", Physical Review B, American Physical Society, Vol 99, Num 8, pp 081118, 2019, doi:10.1103/PhysRevB.99.081118


Azza Ahmed, Jacob Heldenbrand, Yan Asmann, Faisal Fadlelmola, Daniel S. Katz, Katherine Kendig, Matthew Kendzior, Tiffany Li, Yingxue Ren, Elliott Rodriguez, Matthew Weber, Justin M. Wozniak, Jennie Zermeno, and Liudmila S. Mainzer: "Managing genomic variant calling workflows with Swift/T", PLoS ONE, Vol 14, Num 7, pp e0211608, 2019, doi:10.1371/journal.pone.0211608


Daniel Langr, Tomáš Dytrych, Kristina D. Launey, and Jerry P. Draayer: "Accelerating Many-Nucleon Basis Generation for High Performance Computing Enabled Ab Initio Nuclear Structure Studies", International Journal of High Performance Computing Applications, SAGE Publications, Vol 33, Num 3, pp 522-533, 2019, doi:10.1177/1094342019838314


Balaji Selvam, Ya-Chi Yu, Li-Qing Chen, and Diwakar Shukla: "Molecular Basis of Glucose Transport Mechanism in Plants", ACS Central Science, American Chemical Society, Vol 5, Num 6, pp 1085-1096, 2019, doi:10.1021/acscentsci.9b00252


Erin G. Teich, Greg van Anders, and Sharon C. Glotzer: "Identity Crisis in Alchemical Space Drives the Entropic Colloidal Glass Transition", Nature Communications, Springer Nature, Vol 10, Num 1, pp 64, 2019, doi:10.1038/s41467-018-07977-2


Ananth Tenneti, Stephen M. Wilkins, Tiziana Di Matteo, Rupert A.C. Croft, and Yu Feng: "A tiny host galaxy for the first giant black hole: z= 7.5 quasar in BlueTides", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 483, Num 1, pp 1388-1399, 2019, doi:10.1093/mnras/sty3161


Philip F. Hopkins and Michael Y. Grudić: "Numerical Problems in Coupling Photon Momentum (Radiation Pressure) to Gas", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 483, Num 3, pp 4187-4196, 2019, doi:10.1093/mnras/sty3089/5184498


Siyao Xu, Sudip K. Garain, Dinshaw S. Balsara, and A. Lazarian: "Turbulent dynamo in a weakly ionized medium", Astrophysical Journal, The American Astronomical Society, Vol 872, Num 1, pp 62, 2019, doi:10.3847/1538-4357/aafbe8


John H. Wise, John A. Regan, Brian W. O’Shea, Michael L. Norman, Turlough P. Downes, and Hao Xu: "Formation of massive black holes in rapidly growing pre-galactic gas clouds", Nature, Springer Nature, Vol 566, Num 7742, pp 85-88, 2019, doi:10.1038/s41586-019-0873-4


Vadim Roytershteyn, Stanislav Boldyrev, Gian Luca Delzanno, Christopher H. K. Chen, Daniel Grošelj, and Nuno F. Loureiro: "Numerical Study of Inertial Kinetic-Alfvén Turbulence", Astrophysical Journal, American Astronomical Society, Vol 870, Num 2, pp 103, 2019, doi:10.3847/1538-4357/aaf288


Dhawal Buaria, Alain Pumir, Eberhard Bodenschatz, and P. K. Yeung: "Extreme velocity gradients in turbulent flows", New Journal of Physics, IOP Publishing Ltd., Vol 21, Num 4, pp 043004, 2019, doi:10.1088/1367-2630/ab0756


Dereka L. Carroll-Smith, Logan C. Dawson, and Robert J. Trapp: "High Resolution Real-data WRF Modeling and Verification of Tropical Cyclone Tornadoes Associated with Hurricane Ivan 2004", Electronic Journal of Severe Storms Meteorology, Vol 14, Num 2, 2019


Caroline Bernier, Mattia Gazzola, Renaud Ronsse, and Philippe Chatelain: "Simulations of propelling and energy harvesting articulated bodies via vortex particle-mesh methods", Journal of Computational Physics, Elsevier B.V., Vol 392, pp 34-55, 2019, doi:10.1016/j.jcp.2019.04.036


Tejaswin Parthasarathy, Fan Kiat Chan, and Mattia Gazzola: "Streaming enhanced flow mediated transport", Journal of Fluid Mechanics, Cambridge University Press, Vol 878, pp 647–662, 2019, doi:10.1017/jfm.2019.643


Xiaotian Zhang, Fan Kiat Chan, Tejaswin Parthasarathy, and Mattia Gazzola: "Modeling and simulation of complex dynamic musculoskeletal architectures", Nature Communications, Springer Nature, Vol 10, Num 1, 2019, doi:10.1038/s41467-019-12759-5


M. Liska, A. Tchekhovskoy, A. Ingram, and M. van der Klis: "Bardeen–Petterson alignment, jets, and magnetic truncation in GRMHD simulations of tilted thin accretion discs", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 487, Num 1, pp 550-561, 2019, doi:10.1093/mnras/stz834


Jacob Heerikhuisen, Eric J. Zirnstein, Nikolai V. Pogorelov, Gary P. Zank, and Mihir Desai: "The Effect of Suprathermal Protons in the Heliosheath on the Global Structure of the Heliosphere and Heliotail", Astrophysical Journal, American Astronomical Society, Vol 874, Num 1, pp 76, 2019, doi:10.3847/1538-4357/ab05e3


Scott Lathrop, Celso Mendes, Jeremy Enos, Brett Bode, Gregory H. Bauer, Roberto Sisneros, and William Kramer: "Best Practices for Management and Operation of Large HPC Installations", Concurrency and Computation: Practice and Experience, John Wiley & Sons, Inc, Vol 31, Num 16 (Special Issue of the Cray User Group, CUG 2018), pp e5069, Stockholm, Sweden, 2019, doi:10.1002/cpe.5069


Tatu J.K. Haataja, Rafael C. Bernardi, Simon Lecointe, Romain Capoulade, Jean Merot, and Ulla Pentikäinen: "Non-Syndromic Mitral Valve Dysplasia Mutation Changes the Force Resilience and Interaction of Human Filamin A", Structure, Elsevier BV, Vol 27, Num 1, pp 102-112.e4, 2019, doi:10.1016/j.str.2018.09.007


Federico Fraternale, Nikolai V. Pogorelov, John D. Richardson, and Daniela Tordella: "Magnetic turbulence spectra and intermittency in the heliosheath and in the local interstellar medium", Astrophysical Journal, American Astronomical Society, Vol 872, Num 1, pp 40, 2019, doi:10.3847/1538-4357/aafd30


Rafael C. Bernardi, Ellis Durner, Constantin Schoeler, Klara H. Malinowska, Bruna G. Carvalho, Edward A. Bayer, Zaida Luthey-Schulten, Hermann E. Gaub, and Michael A. Nash: "Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy", Journal of the American Chemical Society, The American Chemical Society, Vol 141, Num 37, pp 14752-14763, 2019, doi:10.1021/jacs.9b06776


Salme Cook, Thomas C. Lippmann, and James D. Irish: "Modeling Nonlinear Tidal Evolution in an Energetic Estuary", Ocean Modelling, Elsevier BV, Vol 136, pp 13-27, 2019, doi:10.1016/j.ocemod.2019.02.009


Talwinder Singh, Mehmet Sarp Yalim, Nikolai Pogorelov, and Nat Gopalswamy: "Simulating Solar Coronal Mass Ejections constrained by Observations of their Speed and Poloidal flux", Astrophysical Journal Letters, American Astronomical Society, Vol 875, Num 2, pp L17, 2019, doi:10.3847/2041-8213/ab14e9


Saurabh Shukla, Chuankai Zhao, and Diwakar Shukla: "Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling", Structure, Elsevier BV, Vol 27, pp 1-11, 2019, doi:10.1016/j.str.2018.12.005


Michael Tremmel, Thomas R. Quinn, Angelo Ricarte, Arif Babul, Urmila Chadayammuri, Priyamvada Natarajan, Daisuke Nagai, Andrew Pontzen, and Marta Volonteri: "Introducing RomulusC: A Cosmological Simulation of a Galaxy Cluster with Unprecedented Resolution", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 483, Num 3, pp 3336-3362, 2019, doi:10.1093/mnras/sty3336


Andrei Rykhlevskii, Jin Whan Bae, and Kathryn D. Huff: "Modeling and Simulation of Online Reprocessing in the Thorium-Fueled Molten Salt Breeder Reactor", Annals of Nuclear Energy, Elsevier BV, Vol 128, pp 366--379, 2019, doi:10.1016/j.anucene.2019.01.030


Jin Whan Bae, Joshua L. Peterson-Droogh, and Kathryn D. Huff: "Standardized Verification of the Cyclus Fuel Cycle Simulator", Annals of Nuclear Energy, Elsevier BV, Vol 128, pp 288--291, 2019, doi:10.1016/j.anucene.2019.01.014


Robert Nißler, Florian A. Mann, Parth Chaturvedi, Jan Horlebein, Daniel Meyer, Lela Vuković, and Sebastian Kruss: "Quantification of the Number of Adsorbed DNA Molecules on Single-Walled Carbon Nanotubes", Journal of Physical Chemistry C, American Chemical Society, Vol 123, Num 8, pp 4837-4847, 2019, doi:10.1021/acs.jpcc.8b11058


Matthew S. Clement, Nathan A. Kaib, Sean N. Raymond, John E. Chambers, and Kevin J. Walsh: "The Early Instability Scenario: Terrestrial Planet Formation During the Giant Planet Instability, and the Effect of Collisional Fragmentation", Icarus, Elsevier BV, Vol 321, pp 778--790, 2019, doi:10.1016/j.icarus.2018.12.033


Kisung Kang, Alina Kononov, Cheng-Wei Lee, Joshua A. Leveillee, Ethan P. Shapera, Xiao Zhang, and Andre Schleife: "Pushing the Frontiers of Modeling Excited Electronic States and Dynamics to Accelerate Materials Engineering and Design", Computational Materials Science, Elsevier BV, Vol 160, pp 207-216, 2019, doi:10.1016/j.commatsci.2019.01.004


Tarek A. Ameen, Hesameddin Ilatikhameneh, Patrick Fay, Alan Seabaugh, Rajib Rahman, and Gerhard Klimeck: "Alloy Engineered Nitride Tunneling Field-Effect Transistor: A Solution for the Challenge of Heterojunction TFETs", IEEE Transactions on Electron Devices, Institute of Electrical and Electronics Engineers, Vol 66, Num 1, pp 736-742, 2019, doi:10.1109/ted.2018.2877753


Maureen T. Brooks, Victoria J. Coles, and William C. Coles: "Inertia Influences Pelagic Sargassum Advection and Distribution", Geophysical Research Letters, American Geophysical Union, Vol 46, 2019, doi:10.1029/2018gl081489


Chenchao Shou: "Learning-accelerated algorithms for simulation and optimization", University of Illinois at Urbana-Champaign, Illinois Digital Environment for Access to Learning and Scholarship, Vol Doctoral dissertation, 2019


Ethan Kruse, Eric Agol, Rodrigo Luger, and Daniel Foreman-Mackey: "Detection of Hundreds of New Planet Candidates and Eclipsing Binaries in K2 Campaigns 0–8", Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 244, Num 1, 2019, doi:10.3847/1538-4365/ab346b


Michael Y. Grudić, Philip F. Hopkins, Eve J. Lee, Norman Murray, Claude-André Faucher-Giguère, and L. Clifton Johnson: "On The Nature of Variations in the Measured Star Formation Efficiency of Molecular Clouds", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 488, Num 2, pp 1501-1518, 2019, doi:10.1093/mnras/stz1758


Albino Perego, Sebastiano Bernuzzi, and David Radice: "Thermodynamics conditions of matter in neutron star mergers", European Physical Journal A, Springer Nature Switzerland AG, Vol 55, Num 8, pp 124, 2019, doi:10.1140/epja/i2019-12810-7


Wendy K Tam Cho: "Technology-Enabled Coin Flips for Judging Partisan Gerrymandering", Southern California Law Review, Southern California Law Review Postscript, Vol 93, pp 11-27, 2019


Colin S. Gaines, Timothy J. Giese, and Darrin M. York: "Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology", ACS Catalysis, Vol 9, Num 7, pp 5803-5815, 2019, doi:10.1021/acscatal.9b01155


Alexander J. Pak, John M. A. Grime, Alvin Yu, and Gregory A. Voth: "Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation", Journal of the American Chemical Society, Vol 141, Num 26, pp 10214-10224, 2019, doi:10.1021/jacs.9b01413


Erin K. Molloy and Tandy Warnow: "TreeMerge: a new method for improving the scalability of species tree estimation methods", Bioinformatics, Oxford University Press, Vol 35, Num 14, pp i417–i426, 2019, doi:10.1093/bioinformatics/btz344


Yueying Ni, Mei-Yu Wang, Yu Feng, and Tiziana Di Matteo: "Predictions for the Abundance of High-Redshift Galaxies in a Fuzzy Dark Matter Universe", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 488, Num 4, pp 5551-5565, 2019, doi:10.1093/mnras/stz2085


Jennifer M. Hays, David S. Cafiso, and Peter M. Kasson: "Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data", Journal of Physical Chemistry Letters, American Chemical Society, Vol 10, Num 12, pp 3410-3414, 2019, doi:10.1021/acs.jpclett.9b01407


Yue Cui and Huck Beng Chew: "A simple numerical approach for reconstructing the atomic stresses at grain boundaries from quantum-mechanical calculations", Journal of Chemical Physics, AIP Publishing, Vol 150, Num 14, pp 144702, 2019, doi:10.1063/1.5085061


Wenyang Qu, Soumendu Bagchi, Xiaoming Chen, Huck Beng Chew, and Changhong Ke: "Bending and interlayer shear moduli of ultrathin boron nitride nanosheet", Journal of Physics D: Applied Physics, IOP Publishing, Vol 52, Num 46, pp 465301, 2019, doi:10.1088/1361-6463/ab3953


Saurabh S. Sawant, Pooja Rao, Abhilash Harpale, Huck Beng Chew, and Deborah A. Levin: "Multi-scale thermal response modeling of an AVCOAT-like thermal protection material", International Journal of Heat and Mass Transfer, Elsevier, Vol 133, pp 1176-1195, 2019, doi:10.1016/j.ijheatmasstransfer.2018.12.182


Gino Cingolani, Michael McCauley, Anna Lobley, Alexander J. Bryer, Jordan Wesolowski, Deanna L. Greco, Ravi Kumar Lokareddy, Erik Ronzone, Juan R. Perilla, and Fabienne Paumet: "Structural basis for the homotypic fusion of chlamydial inclusions by the SNARE-like protein IncA", Nature Communications, Springer Nature Publishing AG, Vol 10, Num 1, pp 2747, 2019, doi:10.1038/s41467-019-10806-9


Moshe Matalon: "The ramifications of the Darrieus-Landau instability in turbulent premixed flames", American Institute of Aeronautics and Astronautics, AIAA Scitech 2019 Forum, San Diego, Calif., 2019, doi:10.2514/6.2019-0182


Dennis B. Bowen, Vassilios Mewes, Scott C. Noble, Mark Avara, Manuela Campanelli, and Julian H. Krolik: "Quasi-periodicity of Supermassive Binary Black Hole Accretion Approaching Merger", Astrophysical Journal, The American Astronomical Society, Vol 879, Num 2, pp 76, 2019, doi:10.3847/1538-4357/ab2453


Alireza Moradzadeh and Narayana R. Aluru: "Transfer-Learning-Based Coarse-Graining Method for Simple Fluids: Toward Deep Inverse Liquid-State Theory", Journal of Physical Chemistry Letters, Vol 10, Num 6, pp 1242-1250, 2019, doi:10.1021/acs.jpclett.8b03872


Oliver M. Browne, Sayed M. Hasnine, and Christoph Brehm: "Towards Modeling and Simulation of Particulate Interactions with High-Speed Transitional Boundary-Layer Flows", American Institute of Aeronautics and Astronautics, AIAA Aviation 2019 Forum, Dallas, Texas, U.S.A., 2019, doi:10.2514/6.2019-2971


Gaurav Shukla, Kanchan Sarkar, and Renata M. Wentzcovitch: "Thermoelasticity of Iron- and Aluminum-Bearing MgSiO3 Postperovskite", Journal of Geophysical Research: Solid Earth, American Geophysical Union, Vol 124, Num 3, pp 2417-2427, 2019, doi:10.1029/2018JB016379


Z. Zhang, D.-B. Zhang, T. Sun, and R. M. Wentzcovitch: "phq: A Fortran code to compute phonon quasiparticle properties and dispersions", Computer Physics Communications, Elsevier, Vol 243, pp 110-120, 2019, doi:10.1016/j.cpc.2019.05.003


E. A. Huerta, Roland Haas, Shantenu Jha, Mark Neubauer, and Daniel S. Katz: "Supporting High-Performance and High-Throughput Computing for Experimental Science", Computing and Software for Big Science, Springer International Publishing, Vol 3, Num 1, pp 5, 2019, doi:10.1007/s41781-019-0022-7


Daniel Langr, Tomáš Dytrych, Jerry P. Draayer, Kristina D. Launey, and Pavel Tvrdík: "Efficient algorithm for representations of U(3) in U(N)", Computer Physics Communications, Elsevier B. V., Vol 244, pp 442-447, 2019, doi:10.1016/j.cpc.2019.05.018


František Knapp, Tomas Dytrych, Daniel Langr, and Tomáš Oberhuber: "Importance Basis Truncation in the Symmetry-adapted No-core Shell Model", Acta Physica Polonica B, Jagiellonian University (Cracow, Poland), Vol 50, Num 3, pp 541, 2019, doi:10.5506/APhysPolB.50.541


Ruotsalainen, P. and Henderson, J. and Hackman, G. and Sargsyan, G. H. and Launey, K. D. and Saxena, A. and Srivastava, P. C. and Stroberg, S. R. and Grahn, T. and Pakarinen, J. and Ball, G. C. and Julin, R. and Greenlees, P. T. and Smallcombe, J. and Andreoiu, C. and Bernier, N. and Bowry, M. and Buckner, M. and Caballero-Folch, R. and Chester, A. and Cruz, S. and Evitts, L. J. and Frederick, R. and Garnsworthy, A. B. and Holl, M. and Kurkjian, A. and Kisliuk, D. and Leach, K. G. and McGee, E. and Measures, J. and Mücher, D. and Park, J. and Sarazin, F. and Smith, J. K. and Southall, D. and Starosta, K. and Svensson, C. E. and Whitmore, K. and Williams, M. and Wu, C. Y.: "Isospin symmetry in B (E2) values: Coulomb excitation study of 21 Mg", Physical Review C, American Physical Society, Vol 99, Num 5, pp 051301, 2019, doi:10.1103/PhysRevC.99.051301


M. Burrows, Ch. Elster, S. P. Weppner, K. D. Launey, P. Maris, A. Nogga, and Popa, G.: "Ab initio folding potentials for nucleon-nucleus scattering based on no-core shell-model one-body densities", Physical Review C, American Physical Society, Vol 99, Num 4, pp 044603, 2019, doi:10.1103/PhysRevC.99.044603


Zhongcanm Xiao, Chuanxu Ma, Jingsong Huang, Liangbo Liang, Wenchang Lu, Kunlun Hong, Bobby G. Sumpter, An-Ping Li, and Jerzy Bernholc: "Design of Atomically Precise Nanoscale Negative Differential Resistance Devices", Advanced Theory and Simulations, Wiley‐VCH Verlag GmbH & Co., Vol 2, Num 2, pp 1800172, 2019, doi:10.1002/adts.201800172


Chuanxu Ma, Zhongcan Xiao, Jingsong Huang, Liangbo Liang, Wenchang Lu, Kunlun Hong, Bobby G. Sumpter, J. Bernholc, and An-Ping Li: "Direct writing of heterostructures in single atomically precise graphene nanoribbons", Physical Review Materials, American Physical Society, Vol 3, Num 1, pp 016001, 2019, doi:10.1103/PhysRevMaterials.3.016001


Seong-Mook Cho, Brian G. Thomas, and Seon-Hyo Kim: "Effect of Nozzle Port Angle on Transient Flow and Surface Slag Behavior During Continuous Steel-Slab Casting", Metallurgical and Materials Transactions B, Springer Nature Switzerland AG, Vol 50, Num 1, pp 52-76, 2019, doi:10.1007/s11663-018-1439-9


Matthew L. S. Zappulla, Seong‐Mook Cho, and Brian G. Thomas: "Visualization of Steel Continuous Casting Including a New Integral Method for Post‐Processing Temperature Data", Steel Research International, Wiley-VCH Verlag GmbH, Vol 90, Num 4, pp 1800540, 2019, doi:10.1002/srin.201800540


Matthew L.S. Zappulla and Brian G. Thomas: "Surface Defect Formation in Steel Continuous Casting", Trans Tech Publications Ltd., Materials Science Forum: THERMEC 2018 (10th International Conference on Processing and Manufacturing of Advanced Materials), Vol 941, pp 112-117, Paris, France, 2019, doi:10.4028/www.scientific.net/MSF.941.112


D. Liu, S. Koric, and A. Kontsos: "Parallelized Finite Element Analysis of Knitted Textile Mechanical Behavior", Journal of Engineering Materials and Technology, The American Society of Mechanical Engineers, Vol 141, Num 2, pp 021008, 2019, doi:10.1115/1.4041869


Dongru Li, Jonathan Komperda, Zia Ghiasi, Ahmad Peyvan, and Farzad Mashayek: "Compressibility effects on the transition to turbulence in a spatially developing plane free shear layer", Theoretical and Computational Fluid Dynamics, Springer Berlin Heidelberg, Vol 33, Num 6, pp 577-602, 2019, doi:10.1007/s00162-019-00507-w


Changsong Xu, Bin Xu, Bertrand Dupé, and L. Bellaiche: "Magnetic interactions in BiFeO 3 : A first-principles study", Physical Review B, The American Physical Society, Vol 99, Num 10, pp 104420, 2019, doi:10.1103/PhysRevB.99.104420


Lian Duan, Meelan M. Choudhari, Amanda Chou, Federico Munoz, Rolf Radespiel, Thomas Schilden, Wolfgang Schröder, Eric C. Marineau, Katya M. Casper, Ross S. Chaudhry, Graham V. Candler, Kathryn A. Gray, and Steven P. Schneider: "Characterization of Freestream Disturbances in Conventional Hypersonic Wind Tunnels", Journal of Spacecraft and Rockets, American Institute of Aeronautics and Astronautics, Vol 56, Num 5, pp 357-368, 2019, doi:10.2514/1.A34290


John F. Hawley and Julian H. Krolik: "Tilt Dependence of Alignment in Accretion Disks Subjected to Lense-Thirring Torques", Astrophysical Journal, The American Astronomical Society, Vol 878, Num 2, pp 149, 2019, doi:10.3847/1538-4357/ab1f6e


German Saltar and Guillermo Araya: "Turbulence modeling of boundary layers subject to very strong favorable pressure gradient (FPG) with passive scalar transport", The American Society of Thermal and Fluids Engineers, Proceedings of the 4th Thermal and Fluids Engineering Conference, pp 1819-1833, Las Vegas, Nevada, U.S.A., 2019, doi:10.1615/TFEC2019.tfl.028426


Hitesh J. Changlani, Sumiran Pujari, Chia-Min Chung, and Bryan K. Clark: "Resonating quantum three-coloring wave functions for the kagome quantum antiferromagnet", Physical Review B, The American Physical Society, Vol 99, Num 10, pp 104433, 2019, doi:10.1103/PhysRevB.99.104433


Di Luo and Bryan K. Clark: "Backflow Transformations via Neural Networks for Quantum Many-Body Wave Functions", Physical Review Letters, The American Physical Society, Vol 122, Num 22, pp 226401, 2019, doi:10.1103/PhysRevLett.122.226401


D. Reig-i-Plessis, S. V. Geldern, A. A. Aczel, D. Kochkov, B. K. Clark, and G. J. MacDougall: "Deviation from the dipole-ice model in the spinel spin-ice candidate MgEr2Se4", Physical Review B, The American Physical Society, Vol 99, Num 13, pp 134438, 2019, doi:10.1103/PhysRevB.99.134438


Giovanni Rillo, Miguel A. Morales, David M. Ceperley, and Carlo Pierleoni: "Optical properties of high-pressure fluid hydrogen across molecular dissociation", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 116, Num 20, pp 9770-9774, 2019, doi:10.1073/pnas.1818897116


Vitaly Gorelov, Carlo Pierleoni, and David M. Ceperley: "Benchmarking vdW‐DF first‐principles predictions against Coupled Electron–Ion Monte Carlo for high‐pressure liquid hydrogen", Contributions to Plasma Physics, Wiley-VCH Verlag GmbH & Co, Vol 59, Num 4-5, pp e201800185, 2019, doi:10.1002/ctpp.201800185


Wendy K. Tam Cho and Simon Rubinstein-Salzedo: "Understanding Significance Tests From a Non-Mixing Markov Chain for Partisan Gerrymandering Claims", Statistics and Public Policy, Taylor and Francis, Vol 6, Num 1, pp 44-49, 2019, doi:10.1080/2330443X.2019.1574687


Wendy K. Tam Cho and Simon Rubinstein-Salzedo: "Rejoinder to "Understanding our Markov Chain Significance Test"", Statistics and Public Policy, Taylor and Francis, Vol 6, Num 1, pp 54, 2019, doi:10.1080/2330443X.2019.1619427


Jefferson Davis, Sparsh Ganju, Neil Ashton, Sean Bailey, and Christoph Brehm: "A DNS Study to Investigate Turbulence Suppression in Rotating Pipe Flows", American Institute of Aeronautics and Astronautics, AIAA Aviation 2019 Forum, Dallas, Texas, U.S.A., 2019, doi:10.2514/6.2019-3639


Neil Ashton, Jefferson Davis, and Christoph Brehm: "Assessment of the Elliptic Blending Reynolds Stress Model for a Rotating Turbulent Pipe Flow Using New DNS Data", American Institute of Aeronautics and Astronautics, AIAA Aviation 2019 Forum, Dallas, Texas, U.S.A., 2019, doi:10.2514/6.2019-2966


Dinshaw S. Balsara, Vladimir Florinski, Sudip Garain, Sethupathy Subramanian, and Katharine F. Gurski: "Efficient, Divergence-Free, High Order MHD on 3D Spherical Meshes with Optimal Geodesic Meshing", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 487, Num 1, pp 1283-1314, 2019, doi:10.1093/mnras/stz1263


Kartik P. Iyer, Jörg Schumacher, Katepalli R. Sreenivasan, and P. K. Yeung: "Scaling of locally averaged energy dissipation and enstrophy density in isotropic turbulence", New Journal of Physics, IOP Publishing Ltd., Vol 21, Num 3, pp 03316, 2019, doi:10.1088/1367-2630/ab05e8


Taishan Zhu and Elif Ertekin: "Mixed phononic and non-phononic transport in hybrid lead halide perovskites: glass-crystal duality, dynamical disorder, and anharmonicity", Energy and Environmental Science, The Royal Society of Chemistry, Vol 12, Num 1, pp 216-229, 2019, doi:10.1039/C8EE02820F


Matthew S. Clement, Sean N. Raymond, and Nathan A. Kaib: "Excitation and Depletion of the Asteroid Belt in the Early Instability Scenario", Astronomical Journal, The American Astronomical Society, Vol 157, Num 1, pp 38, 2019, doi:10.3847/1538-3881/aaf21e


Matthew S. Clement, Nathan A. Kaib, and John E. Chambers: "Dynamical Constraints on Mercury's Collisional Origin", Astronomical Journal, The American Astronomical Society, Vol 157, Num 5, pp 208, 2019, doi:10.3847/1538-3881/ab164f


Saurabh S. Sawant, Ozgur Tumuklu, Vassilis Theofilis, and Deborah A. Levin: "Study of Spanwise Perturbations in Hypersonic Shock-Wave/Boundary Layer Interactions on a Double Wedge", American Institute of Aeronautics and Astronautics, AIAA Aviation 2019 Forum, Dallas, Texas, U.S.A., 2019, doi:10.2514/6.2019-3442


Adam Burrows, David Radice, and David Vartanyan: "Three-Dimensional Supernova Explosion Simulations of 9-, 10-, 11-, 12-, and 13-M-circle dot stars", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 485, Num 3, pp 3153-3168, 2019, doi:10.1093/mnras/stz543


M. Aaron Skinner, Joshua C. Dolence, Adam Burrows, David Radice, and David Vartanyan: "Fornax: A Flexible Code for Multiphysics Astrophysical Simulations", Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 241, Num 1, pp 7, 2019, doi:10.3847/1538-4365/ab007f


Hiroki Nagakura, Adam Burrows, David Radice, and David Vartanyan: "Towards an Understanding of the Resolution Dependence of Core-Collapse Supernova Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press on behalf of the Royal Astronomical Society, Vol 490, Num 4, pp 4622-4637, 2019, doi:10.1093/mnras/stz2730


David Radice, Viktoriya Morozova, Adam Burrows, David Vartanyan, and Hiroki Nagakura: "Characterizing the Gravitational Wave Signal from Core-collapse Supernovae", Astrophysical Journal, The American Astronomical Society, Vol 876, Num 1, pp L9, 2019, doi:10.3847/2041-8213/ab191a


Alexander E. Doran and So Hirata: "Monte Carlo Second- and Third-Order Many-Body Green’s Function Methods with Frequency-Dependent, Nondiagonal Self-Energy", Journal of Chemical Theory and Computation, The American Chemical Society, Vol 15, Num 11, pp 6097-6110, 2019, doi:10.1021/acs.jctc.9b00693


Ketan Date and Rakesh Nagi: "Level 2 Reformulation Linearization Technique-Based Parallel Algorithms for Solving Large Quadratic Assignment Problems on Graphics Processing Unit Clusters", INFORMS Journal on Computing, The Institute for Operations Research and the Management Sciences (INFORMS), Vol 31, Num 4, pp 771-789, 2019, doi:10.1287/ijoc.2018.0866


Ran Sun, Zilong Li, and Thomas C. Bishop: "TMB Library of Nucleosome Simulations", Journal of Chemical Information and Modeling, The American Chemical Society, 2019, doi:10.1021/acs.jcim.9b00252


Aaron Weeden, Colleen Heinemann, Skylar Thompson, Cameron Foss, Mobeen Ludin, and Jennifer Houchins: "The Blue Waters Petascale Institute: Longitudinal Impact and Assessment-Driven Development of an Intensive, Hands-on Curriculum for Teaching Applications in HPC", Association for Computing Machinery, PEARC '19: Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (Learning), pp 85:1-85:8, Chicago, Illinois, U.S.A., 2019, doi:10.1145/3332186.3337771


Wen Yang, C. Keith Cassidy, Peter Ames, Christoph A. Diebolder, Klaus Schulten, Zaida Luthey-Schulten, John S. Parkinson, and Ariane Briegel: "In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States", mBio, American Society for Microbiology, Vol 10, Num 4, 2019, doi:10.1128/mBio.00973-19


Jonathan A. Coleman, Dongxue Yang, Zhiyu Zhao, Po-Chao Wen, Craig Yoshioka, Emad Tajkhorshid, and Eric Gouaux: "Serotonin transporter–ibogaine complexes illuminate mechanisms of inhibition and transport", Nature, Springer Nature, Vol 569, Num 7754, pp 141-145, 2019, doi:10.1038/s41586-019-1135-1


Yongyang Cai and Thomas S. Lontzek: "The Social Cost of Carbon with Economic and Climate Risks", Journal of Political Economy, The University of Chicago, Vol 127, Num 6, pp 2684-2734, 2019, doi:10.1086/701890


George M. Fuller, Alexander Kusenko, David Radice, and Volodymyr Takhistov: "Positrons and 511 keV radiation as tracers of recent binary neutron star mergers", Physical Review Letters, The American Physical Society, Vol 122, Num 12, pp 121101, 2019, doi:10.1103/PhysRevLett.122.121101


David Radice and Liang Dai: "Multimessenger Parameter Estimation of GW170817", European Physical Journal A, Springer Nature Switzerland AG, Vol 55, Num 4, pp 50, 2019, doi:10.1140/epja/i2019-12716-4


David Vartanyan, Adam Burrows, David Radice, Aaron Skinner, and Joshua Dolence: "A Successful 3D Core-Collapse Supernova Explosion Model", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 482, Num 1, pp 351-369, 2019, doi:10.1093/mnras/sty2585


Ian M. Howat, Claire Porter, Benjamin E. Smith, Myoung-Jong Noh, and Paul Morin: "The Reference Elevation Model of Antarctica", Cryosphere, European Geosciences Union, Vol 13, Num 2, pp 665-674, 2019, doi:10.5194/tc-13-665-2019


Ferah Munshi, Alyson M. Brooks, Charlotte Christensen, Elaad Applebaum, Kelly Holley-Bockelmann, Thomas R. Quinn, and James Wadsley: "Dancing in the Dark: Uncertainty in ultra-faint dwarf galaxy predictions from cosmological simulations", Astrophysical Journal, The American Astronomical Society, Vol 874, Num 1, pp 40, 2019, doi:10.3847/1538-4357/ab0085


Michael Boyle, Daniel Hemberger, Dante A.B. Iozzo, Geoffrey Lovelace, Serguei Ossokine, Harald P. Pfeiffer, Mark A. Scheel, Leo C. Stein, Charles J. Woodford, Aaron B. Zimmerman, Nousha Afshari, Kevin Barkett, Jonathan Blackman, Katerina Chatziioannou, Tony Chu, Nicholas Demos, Nils Deppe, Scott E. Field, Nils L. Fischer, Evan Foley, Heather Fong, Alyssa Garcia, Matthew Giesler, Francois Hebert, Ian Hinder, Reza Katebi, Haroon Khan, Lawrence E. Kidder, Prayush Kumar, Kevin Kuper, Halston Lim, Maria Okounkova, Teresita Ramirez, Samuel Rodriguez, Hannes R. Rüter, Patricia Schmidt, Bela Szilagyi, Saul A. Teukolsky, Vijay Varma, and Marissa Walker: "The SXS collaboration catalog of binary black hole simulations", Classical and Quantum Gravity, IOP Publishing, Vol 36, Num 19, pp 195006, 2019, doi:10.1088/1361-6382/ab34e2


Holly M. Mallinson and Sonia G. Lasher-Trapp: "An Investigation of Hydrometeor Latent Cooling upon Convective Cold Pool Formation, Sustainment, and Properties", Monthly Weather Review, The American Meteorological Society, Vol 147, Num 9, pp 3205-3222, 2019, doi:10.1175/MWR-D-18-0382.1


Zhao Yang and Francina Dominguez: "Investigating Land Surface Effects on the Moisture Transport over South America with a Moisture Tagging Model", Journal of Climate, The American Meteorological Society, Vol 32, Num 19, pp 6627-6644, 2019, doi:10.1175/JCLI-D-18-0700.1


Y. Zhan, P. M. Gregg, H. Le Mével, C. A. Miller, and C. Cardona: "Integrating reservoir dynamics, crustal stress, and geophysical observations of the Laguna del Maule magmatic system by FEM models and data assimilation", Journal of Geophysical Research: Solid Earth, American Geophysical Union, Vol 124, Num 12, pp 13547-13562, 2019, doi:10.1029/2019JB018681


Chunyuan Diao: "Complex network-based time series remote sensing model in monitoring the fall foliage transition date for peak coloration", Remote Sensing of Environment, Elsevier B.V., Vol 229, pp 179-192, 2019, doi:10.1016/j.rse.2019.05.003


Chunyuan Diao: "Innovative pheno-network model in estimating crop phenological stages with satellite time series", ISPRS Journal of Photogrammetry and Remote Sensing, Elsevier B.V., Vol 153, pp 96-109, 2019, doi:10.1016/j.isprsjprs.2019.04.012


Yan Li, Kaiyu Guan, Albert Yu, Bin Peng, Lei Zhao, Bo Li, and Jian Peng: "Toward building a transparent statistical model for improving crop yield prediction: Modeling rainfed corn in the U.S.", Field Crops Research, Elsevier B.V., Vol 234, pp 55-65, 2019, doi:10.1016/j.fcr.2019.02.005


Erin K. Molloy and Tandy Warnow: "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge", Algorithms for Molecular Biology, Springer Nature, Vol 14, Num 1, pp 14, 2019, doi:10.1186/s13015-019-0151-x


William D. Gropp: "Using node and socket information to implement MPI Cartesian topologies", Parallel Computing, Elsevier B.V., Vol 85, pp 98-108, 2019, doi:10.1016/j.parco.2019.01.001


Edward Hutter and Edgar Solomonik: "Communication-avoiding Cholesky-QR2 for rectangular matrices", Institute of Electrical & Electronics Engineers, 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS 2019), pp 89-100, Rio de Janeiro, Brazil, 2019, doi:10.1109/IPDPS.2019.00020


Iryna S. Butsky, Joseph N. Burchett, Daisuke Nagai, Michael Tremmel, Thomas R. Quinn, and Jessica K. Werk: "Ultraviolet Signatures of the Multiphase Intracluster and Circumgalactic Media in the Romulus C Simulation", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 490, Num 3, pp 4292-4306, 2019, doi:10.1093/mnras/stz2859


Milton Ruiz, Antonios Tsokaros, Vasileios Paschalidis, and Stuart L. Shapiro: "Effects of spin on magnetized binary neutron star mergers and jet launching", Physical Review D, The American Physical Society, Vol 99, Num 8, pp 084032, 2019, doi:10.1103/PhysRevD.99.084032


Lunan Sun, Milton Ruiz, and Stuart L. Shapiro: "Magnetic Braking and Damping of Differential Rotation in Massive Stars", Physical Review D, The American Physical Society, Vol 99, Num 6, pp 064057, 2019, doi:10.1103/PhysRevD.99.064057


Gustavo Caetano-Anollés, M. Fayez Aziz, Fizza Mughal, Frauke Gräter, Ibrahim Koç, Kelsey Caetano-Anollés, and Derek Caetano-Anollés: "Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis", Evolutionary Bioinformatics, Sage Publications, Vol 15, pp 1176934319872980, 2019, doi:10.1177/1176934319872980


Matthias Diener, Daniel J. Bodony, and Laxmikant Kale: "Accelerating Scientific Applications on Heterogeneous Systems with HybridOMP", Springer International Publishing, Lecture Notes in Computer Science: High Performance Computing for Computational Science (VECPAR 2018), 13th International Conference, pp 174-187, São Pedro, Brazil, 2019, doi:10.1007/978-3-030-15996-2_13


Drishti Guin, Shriyaa Mittal, Brian Bozymski, Diwakar Shukla, and Martin Gruebele: "Dodine as a Kosmo-Chaotropic Agent", Journal of Physical Chemistry Letters, American Chemical Society, Vol 10, Num 10, pp 2600-2605, 2019, doi:10.1021/acs.jpclett.9b00379


Shaomeng Li, Stanislaw Jaroszynski, Scott Pearse, Leigh Orf, and John Clyne: "VAPOR: A Visualization Package Tailored to Analyze Simulation Data in Earth System Science", Atmosphere, MDPI AG, Vol 10, Num 9, pp 488, 2019, doi:10.3390/atmos10090488


Leigh Orf: "A Violently Tornadic Supercell Thunderstorm Simulation Spanning a Quarter-Trillion Grid Volumes: Computational Challenges, I/O Framework, and Visualizations of Tornadogenesis", Atmosphere, MDPI AG, Vol 10, Num 10, pp 578, 2019, doi:10.3390/atmos10100578


Ameen Eetemadi and Ilias Tagkopoulos: "Genetic Neural Networks: an artificial neural network architecture for capturing gene expression relationships", Bioinformatics, Oxford University Press, Vol 35, Num 13, pp 2226-2234, 2019, doi:10.1093/bioinformatics/bty945


Navneet Rai, Linh Huynh, Minseung Kim, and Ilias Tagkopoulos: "Population collapse and adaptive rescue during long-term chemostat fermentation", Biotechnology and Bioengineering, John Wiley & Sons, Vol 116, Num 3, pp 693-703, 2019, doi:10.1002/bit.26898


Matthew D. Duez and Yosef Zlochower: "Numerical relativity of compact binaries in the 21st century", Reports on Progress in Physics, IOP Publishing, Vol 82, Num 1, pp 016902, 2019, doi:10.1088/1361-6633/aadb16


B. P. Abbott et al. (The LIGO Scientific Collaboration and the Virgo Collaboration): "Binary Black Hole Population Properties Inferred from the First and Second Observing Runs of Advanced LIGO and Advanced Virgo", Astrophysical Journal Letters, American Astronomical Society, Vol 882, Num 2, pp L24, 2019, doi:10.3847/2041-8213/ab3800


B. P. Abbott et al. (LIGO Scientific Collaboration and Virgo Collaboration): "GWTC-1: A Gravitational-Wave Transient Catalog of Compact Binary Mergers Observed by LIGO and Virgo during the First and Second Observing Runs", Physical Review X, American Physical Society, Vol 9, Num 3, pp 031040, 2019, doi:10.1103/PhysRevX.9.031040


James Healy, Carlos O. Lousto, Jacob Lange, Richard O’Shaughnessy, Yosef Zlochower, and Manuela Campanelli: "Second RIT binary black hole simulations catalog and its application to gravitational waves parameter estimation", Physical Review D, American Physical Society, Vol 100, Num 2, pp 024021, 2019, doi:10.1103/PhysRevD.100.024021


Cameron B. Hummels, Britton D. Smith, Philip F. Hopkins, Brian W. O'Shea, Devin W. Silvia, Jessica K. Werk, Nicolas Lehner, John H. Wise, David C. Collins, and Iryna S. Butsky: "The Impact of Enhanced Halo Resolution on the Simulated Circumgalactic Medium", Astrophysical Journal, American Astronomical Society, Vol 882, Num 2, pp 156, 2019, doi:10.3847/1538-4357/ab378f


Molly S. Peeples, Lauren Corlies, Jason Tumlinson, Brian W. O'Shea, Nicolas Lehner, John M. O'Meara, J. Christopher Howk, Britton D. Smith, John H. Wise, and Cameron B. Hummels: "Figuring Out Gas & Galaxies in Enzo (FOGGIE). I. Resolving Simulated Circumgalactic Absorption at 2 <= z <= 2.5", Astrophysical Journal, American Astronomical Society, Vol 873, Num 2, pp 129, 2019, doi:10.3847/1538-4357/ab0654


J. Williams, G. C. Ball, A. Chester, T. Domingo, A. B. Garnsworthy, G. Hackman, J. Henderson, R. Henderson, R. Krücken, Anil Kumar, K. D. Launey, J. Measures, O. Paetkau, J. Park, G. H. Sargsyan, J. Smallcombe, P. C. Srivastava, K. Starosta, C. E. Svensson, K. Whitmore, and M. Williams: "Structure of Mg-28 and influence of the neutron pf shell", Physical Review C, American Physical Society, Vol 100, Num 1, pp 014322, 2019, doi:10.1103/PhysRevC.100.014322


James C. Robertson, Roy Nassar, Cong Liu, Emiliano Brini, Ken A. Dill, and Alberto Perez: "NMR-assisted protein structure prediction with MELD x MD", Proteins: Structure, Function, and Bioinformatics, John Wiley and Sons, Inc., Vol 87, Num 12, pp 1333-1340, 2019, doi:10.1002/prot.25788


Emiliano Brini, Dima Kozakov, and Ken A. Dill: "Predicting Protein Dimer Structures Using MELD x MD", Journal of Chemical Theory and Computation, American Chemical Society, Vol 15, Num 5, pp 3381-3389, 2019, doi:10.1021/acs.jctc.8b01208


Paul R. Woodward, Pei-Hung Lin, Huaqing Mao, Robert Andrassy, and Falk Herwig: "Simulating 3-D Stellar Hydrodynamics using PPM and PPB Multifluid Gas Dynamics on CPU and CPU+GPU Nodes", IOP Publishing, Journal of Physics: Conference Series (13th International Conference on Numerical Modeling of Space Plasma Flows, ASTRONUM 2018), Vol 1225, pp 012020, Panama City Beach, Florida, U.S.A., 2019, doi:10.1088/1742-6596/1225/1/012020


K. Kitamura and D. S. Balsara: "Hybridized SLAU2-HLLI and hybridized AUSMPW plus-HLLI Riemann solvers for accurate, robust, and efficient magnetohydrodynamics (MHD) simulations, part I: one-dimensional MHD", Shock Waves, Springer Nature Switzerland AG, Vol 29, Num 5, pp 611-627, 2019, doi:10.1007/s00193-018-0842-0


Peter Garnavich, Colin Littlefield, Stella Kafka, Mark Kennedy, Paul Callanan, Dinshaw S. Balsara, and Maxim Lyutikov: "Driving the Beat: Time-resolved Spectra of the White Dwarf Pulsar AR Scorpii", Astrophysical Journal, American Astronomical Society, Vol 872, Num 1, pp 67, 2019, doi:10.3847/1538-4357/aafb2c


F. Foucart, M. D. Duez, T. Hinderer, J. Caro, Andrew R. Williamson, M. Boyle, A. Buonanno, R. Haas, D. A. Hemberger, L. E. Kidder, H. P. Pfeiffer, and M. A. Scheel: "Gravitational waveforms from spectral Einstein code simulations: Neutron star-neutron star and low-mass black hole-neutron star binaries", Physical Review D, American Physical Society, Vol 99, Num 4, pp 044008, 2019, doi:10.1103/PhysRevD.99.044008


Vijay Varma, Scott E. Field, Mark A. Scheel, Jonathan Blackman, Lawrence E. Kidder, and Harald P. Pfeiffer: "Surrogate model of hybridized numerical relativity binary black hole waveforms", Physical Review D, American Physical Society, Vol 99, Num 6, pp 064045, 2019, doi:10.1103/PhysRevD.99.064045


Aaron Smith, Xiangcheng Ma, Volker Bromm, Steven L. Finkelstein, Philip F. Hopkins, Claude-André Faucher-Giguère, and Dušan Kereš: "The physics of Lyman alpha escape from high-redshift galaxies", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 484, Num 1, pp 39-59, 2019, doi:10.1093/mnras/sty3483


Dávid Guszejnov,, Philip F. Hopkins, and Andrew S. Graus: "Is it possible to reconcile extragalactic IMF variations with a universal Milky Way IMF", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 485, Num 4, pp 4852-4862, 2019, doi:10.1093/mnras/stz736


Kung-Yi Su, Philip F. Hopkins, Christopher C. Hayward, Xiangcheng Ma, Claude-André Faucher-Giguère, Dušan Kereš, Matthew E. Orr, T. K. Chan, and Victor H. Robles: "The failure of stellar feedback, magnetic fields, conduction, and morphological quenching in maintaining red galaxies", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 487, Num 3, pp 4393-4408, 2019, doi:10.1093/mnras/stz1494


Eric R. Moseley, Jonathan Squire, and Philip F. Hopkins: "Non-linear evolution of instabilities between dust and sound waves", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 489, Num 1, pp 325-338, 2019, doi:10.1093/mnras/stz2128


Darryl Seligman, Philip F. Hopkins, and Jonathan Squire: "Non-linear evolution of the resonant drag instability in magnetized gas", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 485, Num 3, pp 3991-3998, 2019, doi:10.1093/mnras/stz666


Michael Y. Grudić and Philip F. Hopkins: "The elephant in the room: the importance of the details of massive star formation in molecular clouds", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 488, Num 2, pp 2970-2975, 2019, doi:10.1093/mnras/stz1820


Shea Garrison-Kimmel, Philip F. Hopkins, Andrew Wetzel, James S. Bullock, Michael Boylan-Kolchin, Dušan Kereš, Claude-André Faucher-Giguère, Kareem El-Badry, Astrid Lamberts, Eliot Quataert, and Robyn Sanderson: "The Local Group on FIRE: dwarf galaxy populations across a suite of hydrodynamic simulations", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 487, Num 1, pp 1380-1399, 2019, doi:10.1093/mnras/stz1317


Victor P. Debattista, Oscar A. Gonzalez, Robyn E. Sanderson, Kareem El-Badry, Shea Garrison-Kimmel, Andrew Wetzel, Claude-André Faucher-Giguère, and Philip F. Hopkins: "Formation, vertex deviation, and age of the Milky Way’s bulge: input from a cosmological simulation with a late-forming bar", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 485, Num 4, pp 5073-5085, 2019, doi:10.1093/mnras/stz746


Oliver Porth, Koushik Chatterjee, Ramesh Narayan, Charles F. Gammie, Yosuke Mizuno, Peter Anninos, John G. Baker, Matteo Bugli, Chi-kwan Chan, Jordy Davelaar, Luca Del Zanna, Zachariah B. Etienne, P. Chris Fragile, Bernard J. Kelly, Matthew Liska, Sera Markoff, Jonathan C. McKinney, Bhupendra Mishra, Scott C. Noble, Héctor Olivares, Ben Prather, Luciano Rezzolla, Benjamin R. Ryan, James M. Stone, Niccolò Tomei, Christopher J. White, Ziri Younsi, and The Event Horizon Telescope Collaboration: "The Event Horizon General Relativistic Magnetohydrodynamic Code Comparison Project", Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 243, Num 2, 2019, doi:10.3847/1538-4365/ab29fd


Vinicius Wilian D. Cruzeiro and Adrian E. Roitberg: "Multidimensional Replica Exchange Simulations for Efficient Constant pH and Redox Potential Molecular Dynamics", Journal of Chemical Theory and Computation, American Chemical Society, Vol 15, Num 2, pp 871-881, 2019, doi:10.1021/acs.jctc.8b00935


Yi Wang, Ping Yang, Souichiro Hioki, Michael D. King, Bryan A. Baum, Larry Di Girolamo, and Dongwei Fu: "Ice Cloud Optical Thickness, Effective Radius, And Ice Water Path Inferred From Fused MISR and MODIS Measurements Based on a Pixel-Level Optimal Ice Particle Roughness Model", Journal of Geophysical Research: Atmospheres, John Wiley and Sons, Inc, Vol 124, Num 22, pp 12126-12140, 2019, doi:10.1029/2019JD030457


Ivan Raikov and Ivan Soltesz: "Data-Driven Modeling of Normal and Pathological Oscillations in the Hippocampus", Springer International Publishing, Multiscale Models of Brain Disorders, pp 185-192, 2019, doi:10.1007/978-3-030-18830-6_17


Alexander Ohmann, Kerstin Göpfrich, Himanshu Joshi, Rebecca F. Thompson, Diana Sobota, Neil A. Ranson, Aleksei Aksimentiev, and Ulrich F. Keyser: "Controlling aggregation of cholesterol-modified DNA nanostructures", Nucleic Acids Research, Oxford University Press, Vol 47, Num 21, pp 11441-11451, 2019, doi:10.1093/nar/gkz914


Artem Petrosyan: "COMPASS Production System Overview", EDP Sciences, EPJ Web of Conferences (23rd International Conference on Computing in High Energy and Nuclear Physics, CHEP 2018), Vol 214, pp 03039, Sofia, Bulgaria, 2019, doi:10.1051/epjconf/201921403039


Gerald A. Meehl, Dongxia Yang, Julie M. Arblaster, Susan C. Bates, Nan Rosenbloom, Richard Neale, Julio Bacmeister, Peter H. Lauritzen, Frank Bryan, Justin Small, John Truesdale, Cecile Hannay, Christine Shields, Warren G. Strand, John Dennis, and Gokhan Danabasoglu: "Effects of Model Resolution, Physics, and Coupling on Southern Hemisphere Storm Tracks in CESM1.3", Geophysical Research Letters, John Wiley and Sons, Inc., Vol 46, Num 21, pp 12408-12416, 2019, doi:10.1029/2019GL084057


Mert Hidayetoğlu, Tekin Biçer, Simon Garcia de Gonzalo, Bin Ren, Doğa Gürsoy, Rajkumar Kettimuthu, Ian T. Foster, and Wen-mei W. Hwu: "MemXCT: Memory-Centric X-ray CT Reconstruction with Massive Parallelization", Association for Computing Machinery, SC '19: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, pp 85:1-85:56, Denver, Colorado, U.S.A., 2019, doi:10.1145/3295500.3356220


Sarah Habib and E. A. Huerta: "Characterization of numerical relativity waveforms of eccentric binary black hole mergers", Physical Review D, American Physical Society, Vol 100, Num 4, pp 044016, 2019, doi:10.1103/PhysRevD.100.044016


Adam Rebei, E. A. Huerta, Sibo Wang, Sarah Habib, Roland Haas, Daniel Johnson, and Daniel George: "Fusing numerical relativity and deep learning to detect higher-order multipole waveforms from eccentric binary black hole mergers", Physical Review D, American Physical Society, Vol 100, Num 4, pp 044025, 2019, doi:10.1103/PhysRevD.100.044025


Feng Pan, Dan Zhou, Siyu Yang, Grigor Sargsyan, Yingwen He, Kristina D. Launey, and Jerry P. Draayer: "A close look at the competition of isovector and isoscalar pairing in A=18 and 20 even-even N approximate to Z nuclei", Chinese Physics C, Chinese Physical Society and the Institute of High Energy Physics of the Chinese Academy of Sciences and the Institute of Modern Physics of the Chinese Academy of Sciences and IOP Publishing Ltd, Vol 43, Num 7, pp 074106, 2019, doi:10.1088/1674-1137/43/7/074106


Tiziana Di Matteo: "Black Holes Across Cosmic History: A Journey Through 13.8 Billion Years", Springer Berlin Heidelberg, Black Hole Formation and Growth: Saas-Fee Advanced Course 48 (Swiss Society for Astrophysics and Astronomy), pp 159-212, 2019, doi:10.1007/978-3-662-59799-6_3


Daniel Langr and Martin Kočička: "Reducing the Impact of Intensive Dynamic Memory Allocations in Parallel Multi-Threaded Programs", IEEE Transactions on Parallel and Distributed Systems, Institute of Electrical & Electronics Engineers, Vol 31, Num 5, pp 1152-1164, 2019, doi:10.1109/TPDS.2019.2960514


Yun-Chiao Yao, Amir Taqieddin, Mohammad A. Alibakhshi, Meni Wanunu, Narayana R. Aluru, and Aleksandr Noy: "Strong Electroosmotic Coupling Dominates Ion Conductance of 1.5 nm Diameter Carbon Nanotube Porins", ACS Nano, American Chemical Society, Vol 13, Num 11, pp 12851-12859, 2019, doi:10.1021/acsnano.9b05118


Joshua Leveillee, Claudine Katan, Jacky Even, Dibyajyoti Ghosh, Wanyi Nie, Aditya D. Mohite, Sergei Tretiak, André Schleife, and Amanda J. Neukirch: "Tuning Electronic Structure in Layered Hybrid Perovskites with Organic Spacer Substitution", Nano Letters, American Chemical Society, Vol 19, Num 12, pp 8732-8740, 2019, doi:10.1021/acs.nanolett.9b03427


Olufemi Emmanuel Kadri, Vishnu Deep Chandran, Migle Surblyte, and Roman S. Voronov: "In vivo measurement of blood clot mechanics from computational fluid dynamics based on intravital microscopy images", Computers in Biology and Medicine, Elsevier B.V., Vol 106, pp 1-11, 2019, doi:10.1016/j.compbiomed.2019.01.001


Wenhui Xi, Elliott K. Vanderford, Qinxin Liao, and Ulrich H. E. Hansmann: "Stability of A beta-fibril fragments in the presence of fatty acids", Protein Science, The Protein Society, Vol 28, Num 11, pp 1973-1981, 2019, doi:10.1002/pro.3719


Hanjue Zhu, Camille Avestruz, and Nickolay Y. Gnedin: "Cosmic Reionization On Computers: Reionization Histories of Present-day Galaxies", Astrophysical Journal, American Astronomical Society, Vol 882, Num 2, pp 152, 2019, doi:10.3847/1538-4357/ab3794


G. L. Delzanno and V. Roytershteyn: "High-Frequency Plasma Waves and Pitch Angle Scattering Induced by Pulsed Electron Beams", Journal of Geophysical Research: Space Physics, American Geophysical Union, Vol 124, Num 9, pp 7543-7552, 2019, doi:10.1029/2019JA027046


V. Roytershteyn, N. V. Pogorelov, and J. Heerikhuisen: "Pickup Ions beyond the Heliopause", Astrophysical Journal, American Astronomical Society, Vol 881, Num 1, pp 65, 2019, doi:10.3847/1538-4357/ab2ad4


Jian-Xun Wang, Junji Huang, Lian Duan, and Heng Xiao: "Prediction of Reynolds stresses in high-Mach-number turbulent boundary layers using physics-informed machine learning", Theoretical and Computational Fluid Dynamics, Springer Nature Switzerland AG, Vol 33, Num 1, pp 1-19, 2019, doi:10.1007/s00162-018-0480-2


Lian Duan, Gary L. Nicholson, Junji Huang, Katya M. Casper, Ross Wagnild, and Neal Bitter: "Direct Numerical Simulation of Nozzle-Wall Pressure Fluctuations in a Mach 8 Wind Tunnel", American Institute of Aeronautics and Astronautics, AIAA Scitech 2019 Forum, San Diego, California, U.S.A., 2019, doi:10.2514/6.2019-0874


Quang Long Pham, Anh Tong, Lydia N. Rodrigues, Yang Zhao, Migle Surblyte, Diomar Ramos, John Brito, Adwik Rahematpura, and Roman S. Voronov: "Ranking migration cue contributions to guiding individual fibroblasts faced with a directional decision in simple microfluidic bifurcations", Integrative Biology, Oxford University Press, Vol 11, Num 5, pp 208-220, 2019, doi:10.1093/intbio/zyz018


Federico Fraternale, Nikolai V. Pogorelov, John D. Richagrdson, and Daniela Tordella: "The structure of magnetic turbulence in the heliosheath region observed by Voyager 2 at 106 AU", IOP Publishing, Journal of Physics: Conference Series (13th International Conference on Numerical Modeling of Space Plasma Flows, ASTRONUM 2018), Vol 1225, pp 012006, Panama City Beach, Florida, U.S.A., 2019, doi:10.1088/1742-6596/1225/1/012006


Yuxi Chen and Gábor Tóth: "Gauss's Law satisfying Energy-Conserving Semi-Implicit Particle-in-Cell method", Journal of Computational Physics, Elsevier, Vol 386, pp 632-652, 2019, doi:10.1016/j.jcp.2019.02.032


Zhenguang Huang, Gábor Tóth, Bart van der Holst, Yuxi Chen, and Tamas Gombosi: "A six-moment multi-fluid plasma model", Journal of Computational Physics, Elsevier, Vol 387, pp 134-153, 2019, doi:10.1016/j.jcp.2019.02.023


Dinshaw S. Balsara and Roger Käppeli: "von Neumann stability analysis of globally constraint-preserving DGTD and PNPM schemes for the Maxwell equations using multidimensional Riemann solvers", Journal of Computational Physics, Elsevier, Vol 376, pp 1108-1137, 2019, doi:10.1016/j.jcp.2018.09.051


Angelo Ricarte, Michael Tremmel, Priyamvada Natarajan, and Thomas Quinn: "Tracing black hole and galaxy co-evolution in the Romulus simulations", Monthly Notices of the Royal Astronomical Society, Royal Astronomical Society, Vol 489, Num 1, pp 802-819, 2019, doi:10.1093/mnras/stz2161


Katerina Chatziioannou, Roberto Cotesta, Sudarshan Ghonge, Jacob Lange, Ken K.-Y. Ng, Juan Calderon Bustillo, James Clark, Carl-Johan Haster, Sebastian Khan, Michael Puerrer, Vivien Raymond, Salvatore Vitale, Nousha Afshari, Stanislav Babak, Kevin Barkett, Jonathan Blackman, Alejandro Bohe, Michael Boyle, Alessandra Buonanno, Manuela Campanelli, Gregorio Carullo, Tony Chu, Eric Flynn, Heather Fong, Alyssa Garcia, Matthew Giesler, Maria Haney, Mark Hannam, Ian Harry, James Healy, Daniel Hemberger, Ian Hinder, Karan Jani, Bhavesh Khamersa, Lawrence E. Kidder, Prayush Kumar, Pablo Laguna, Carlos O. Lousto, Geoffrey Lovelace, Tyson B. Littenberg, Lionel London, Margaret Millhouse, Laura K. Nuttall, Frank Ohme, Richard O'Shaughnessy, Serguei Ossokine, Francesco Pannarale, Patricia Schmidt, Harald P. Pfeiffer, Mark A. Scheel, Lijing Shao, Deirdre Shoemaker, Bela Szilagyi, Andrea Taracchini, Saul A. Teukolsky, and Yosef Zlochower: "On the properties of the massive binary black hole merger GW170729", Physical Review D, American Physical Society, Vol 100, Num 10, pp 104015, 2019, doi:10.1103/PhysRevD.100.104015


B. P. Abbott et al. (LIGO Scientific Collaboration and Virgo Collaboration): "Properties of the Binary Neutron Star Merger GW170817", Physical Review X, American Physical Society, Vol 9, Num 1, pp 011001, 2019, doi:10.1103/PhysRevX.9.011001


B. P. Abbott et al. (The LIGO Scientific Collaboration and the Virgo Collaboration): "Searches for Continuous Gravitational Waves from 15 Supernova Remnants and Fomalhaut b with Advanced LIGO", Astrophysical Journal, American Astronomical Society, Vol 875, Num 2, pp 122, 2019, doi:10.3847/1538-4357/ab113b


B. P. Abbott et al. (The LIGO Scientific Collaboration and the Virgo Collaboration): "Search for Gravitational Waves from a Long-lived Remnant of the Binary Neutron Star Merger GW 170817", Astrophysical Journal, American Astronomical Society, Vol 875, Num 2, pp 160, 2019, doi:10.3847/1538-4357/ab0f3d


B. P. Abbott et al. (The LIGO Scientific Collaboration and the Virgo Collaboration): "Searches for Gravitational Waves from Known Pulsars at Two Harmonics in 2015–2017 LIGO Data", Astrophysical Journal, American Astronomical Society, Vol 879, Num 1, pp 10, 2019, doi:10.3847/1538-4357/ab20cb


Elizabeth Agee: "Below-Ground Root Structure and Ecophysiological Controls of Plant Water Flux During Drought: From Individual to Ecosystem", Michigan Publishing and the University of Michigan Library, Deep Blue, Vol Dissertations and theses, 2019


Matthew Clement: "The Early Instability Scenario for Planet Formation in the Solar System", The University of Oklahoma Libraries, Oklahoma State University Libraries, and the University of Central Oklahoma Max Chambers Library, SHAREOK Repository, Vol Oklahoma University dissertations, 2019


Katelyn Audrey Barber: "Characteristics Of Convectively Induced Turbulence Determined From Tropical And Midlatitude Simulations", University of North Dakota libraries, UND Scholarly Commons, Vol Theses and dissertations, Num 2545, 2019


Salme E. Cook: "Effects of waves, tides, and vegetation on the distribution of bed shear stress in the Great Bay Estuary, NH", University of New Hampshire Library, University of New Hampshire Scholars’ Repository, Vol Doctoral Dissertations, Num 2485, 2019


Abhishek Singharoy, Christopher Maffeo, Karelia H. Delgado-Magnero, David J.K. Swainsbury, Melih Sener, Ulrich Kleinekathöfer, John W. Vant, Jonathan Nguyen, Andrew Hitchcock, Barry Isralewitz, Ivan Teo, Danielle E. Chandler, John E. Stone, James C. Phillips, Taras V. Pogorelov, M. Ilaria Mallus, Christophe Chipot, Zaida Luthey-Schulten, D. Peter Tieleman, C. Neil Hunter, Emad Tajkhorshid, Aleksei Aksimentiev, and Klaus Schulten: "Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism", Cell, Elsevier B.V., Vol 179, Num 5, pp 1098-1111.e23, 2019, doi:10.1016/j.cell.2019.10.021


Alexander J. Bryer, Jodi A. Hadden-Perilla, John E. Stone, and Juan R. Perilla: "High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities", Journal of Chemical Information and Modeling, American Chemical Society, Vol 59, Num 10, pp 4328-4338, 2019, doi:10.1021/acs.jcim.9b00324


Yuanyuan Qi, Dikshant Pradhan, and Mohammed El-Kebir: "Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors", Algorithms for Molecular Biology, Springer Nature, Vol 14, Num 1, 2019, doi:10.1186/s13015-019-0155-6


Michael P. Howard, Thomas M. Truskett, and Arash Nikoubashman: "Cross-stream migration of a Brownian droplet in a polymer solution under Poiseuille flow", Soft Matter, The Royal Society of Chemistry, Vol 15, Num 15, pp 3168-3178, 2019, doi:10.1039/C8SM02552E


Andrew J. Emerick: "Stellar Feedback and Chemical Evolution In Dwarf Galaxies", ProQuest Dissertations Publishing, ProQuest Dissertations and Theses, Vol Doctoral dissertation, 2019


Varvara E. Zemskova: "Global Ocean Energy Budget Analysis: From Large Scale Circulation to Submesoscale Instabilities", ProQuest Dissertations Publishing, ProQuest Dissertations and Theses, Vol Doctoral dissertation, 2019


Kara Marsac: "Investigations of subsurface mineral precipitation reactions associated with brine injection", Colorado School of Mines, Mountain Scholar, Vol Doctoral dissertation, 2019


Rachel Chava Kurchin: "Computational frameworks to enable accelerated development of defect-tolerant photovoltaic materials", MIT Libraries, DSpace@MIT, Vol Doctoral dissertation, 2019


François Soubiran, Felipe González-Cataldo, Kevin P. Driver, Shuai Zhang, and Burkhard Militzer: "Magnesium oxide at extreme temperatures and pressures studied with first-principles simulations", Journal of Chemical Physics, AIP Publishing, Vol 151, Num 21, pp 214104, 2019, doi:10.1063/1.5126624


Shuai Zhang, Amy Lazicki, Burkhard Militzer, Lin H. Yang, Kyle Caspersen, Jim A. Gaffney, Markus W. Däne, John E. Pask, Walter R. Johnson, Abhiraj Sharma, Phanish Suryanarayana, Duane D. Johnson, Andrey V. Smirnov, Philip A. Sterne, David Erskine, Richard A. London, Federica Coppari, Damian Swift, Joseph Nilsen, Art J. Nelson, and Heather D. Whitley: "Equation of state of boron nitride combining computation, modeling, and experiment", Physical Review B, American Physical Society, Vol 99, Num 16, pp 165103, 2019, doi:10.1103/PhysRevB.99.165103


Dongwei Fu, Larry Di Girolamo, Lusheng Liang, and Guangyu Zhao: "Regional Biases in MODIS Marine Liquid Water Cloud Drop Effective Radius Deduced Through Fusion With MISR", Journal of Geophysical Research: Atmospheres, American Geophysical Union, Vol 124, Num 23, pp 13182-13196, 2019, doi:10.1029/2019JD031063


Vsevolod Nedora, Sebastiano Bernuzzi, David Radice, Albino Perego, Andrea Endrizzi, and Néstor Ortiz: "Spiral-wave Wind for the Blue Kilonova", Astrophysical Journal Letters, The American Astronomical Society, Vol 886, Num 2, pp L30, 2019, doi:10.3847/2041-8213/ab5794


Matteo Breschi, Sebastiano Bernuzzi, Francesco Zappa, Michalis Agathos, Albino Perego, David Radice, and Alessandro Nagar: "Kilohertz gravitational waves from binary neutron star remnants: Time-domain model and constraints on extreme matter", Physical Review D, American Physical Society, Vol 100, Num 10, pp 104029, 2019, doi:10.1103/PhysRevD.100.104029


Hillary Schwarb, Curtis L. Johnson, Michael R. Dulas, Matthew D. J. McGarry, Joseph L. Holtrop, Patrick D. Watson, Jane X. Wang, Joel L. Voss, Bradley P. Sutton, and Neal J. Cohen: "Structural and Functional MRI Evidence for Distinct Medial Temporal and Prefrontal Roles in Context-dependent Relational Memory", Journal of Cognitive Neuroscience, The MIT Press, Vol 31, Num 12, pp 1857-1872, 2019, doi:10.1162/jocn_a_01454


Celso L. Mendes, Gregory H. Bauer, Brett Bode, and William T. Kramer: "Evaluating Compiler Vectorization Capabilities on Blue Waters", presented at CUG 2019, Montreal, Quebec, Canada, 2019


Kalina Borkiewicz, J. P. Naiman, Haoming Lai: "Cinematic Visualization of Multiresolution Data: Ytini for Adaptive Mesh Refinement in Houdini", Astronomical Journal, American Astronomical Society, Vol 158, Num 1, pp 10, 2019, doi:10.3847/1538-3881/ab1f6f


Kalina Borkiewicz, A. J. Christensen, Drew Berry, Christopher Fluke, Gregory W. Shirah, and Kel Elkins: "Cinematic Scientific Visualization: The Art of Communicating Science", Association for Computing Machinery, SIGGRAPH Asia 2019 Courses, pp 107, Brisbane, Queensland, Australia, 2019, doi:10.1145/3355047.3359398


Kalina Borkiewicz, A. J. Christensen, Helen Nicole Kostis, Gregory W. Shirah, and Ryan Wyatt: "Cinematic Scientific Visualization: The Art of Communicating Science", Association for Computing Machinery, ACM SIGGRAPH 2019 Courses, pp 5, Los Angeles, California, U.S.A., 2019, doi:10.1145/3305366.3328056


Zhi-Yong Yuan, Bao-Lin Zhang, Christopher J. Raxworthy, David W. Weisrock, Paul M. Hime, Jie-Qiong Jin, Emily M. Lemmon, Alan R. Lemmon, Sean D. Holland, Michelle L. Kortyna, Wei-Wei Zhou, Min-Sheng Peng, Jing Che, and Elizabeth Prendini: "Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean", National Science Review, Oxford University Press, Vol 6, Num 1, pp 10–14, 2019, doi:10.1093/nsr/nwy092


Fizza Mughal and Gustavo Caetano-Anollés: "MANET 3.0: Hierarchy and modularity in evolving metabolic networks", PLoS ONE, Public Library of Science, Vol 14, Num 10, pp 0224201, 2019, doi:10.1371/journal.pone.0224201


Chen Kang, Fengjie Sun, Lei Yan, Rui Li, Jianrong Bai, and Gustavo Caetano-Anollés: "Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants", International Journal of Molecular Sciences, MDPI AG, Vol 20, Num 20, pp 5125, 2019, doi:10.3390/ijms20205125


Seong-Mook Cho and Brian G. Thomas: "Modeling of Transient Behavior of Top-Surface Slag/Molten Steel Interface in Continuous Slab Casting", Association for Iron and Steel Technology, 8th International Conference on Modeling and Simulation of Metallurgical Processes in Steelmaking (STEELSIM 2019), pp 650-663, Toronto, Ontario, Canada, 2019, doi:10.33313/503/068


Onur Aydin, Xiaotian Zhang, Sittinon Nuethong, Gelson J. Pagan-Diaz, Rashid Bashir, Mattia Gazzola, and M. Taher A. Saif: "Neuromuscular actuation of biohybrid motile bots", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 116, Num 40, pp 19841-19847, 2019, doi:10.1073/pnas.1907051116


Nicholas Charles, Mattia Gazzola, and L. Mahadevan: "Topology, Geometry, and Mechanics of Strongly Stretched and Twisted Filaments: Solenoids, Plectonemes, and Artificial Muscle Fibers", Physical Review Letters, American Physical Society, Vol 123, Num 20, pp 208003, 2019, doi:10.1103/PhysRevLett.123.208003


Guillermo Araya, Christian Lagares, and Kenneth E. Jansen: "Direct simulation of a Mach-5 turbulent spatially-developing boundary layer", American Institute of Aeronautics and Astronautics, AIAA Aviation 2019 Forum, Dallas, Texas, U.S.A., 2019, doi:10.2514/6.2019-3340


Guillermo Araya, Guillermo Marin, Fernando Cucchietti, Irene Meta, and Rogeli Grima: "Visualization of a Jet in Turbulent Crossflow", Springer Nature, High Performance Computing: 5th Latin American Conference (CARLA 2018), pp 174-178, Bucaramanga, Colombia, 2019, doi:10.1007/978-3-030-16205-4_13


Ryan L. Marson, Erin G. Teich, Julia Dshemuchadse, Sharon C. Glotzer, and Ronald G. Larson: "Computational self-assembly of colloidal crystals from Platonic polyhedral sphere clusters", Soft Matter, The Royal Society of Chemistry, Vol 15, Num 31, pp 6288-6299, 2019, doi:10.1039/C9SM00664H


Sangmin Lee, Erin G. Teich, Michael Engel, and Sharon C. Glotzer: "Entropic colloidal crystallization pathways via fluid-fluid transitions and multidimensional prenucleation motifs", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 116, Num 30, pp 14843-14851, 2019, doi:10.1073/pnas.1905929116


William Zygmunt, Erin G. Teich, Greg van Anders, and Sharon C. Glotzer: "Topological order in densely packed anisotropic colloids", Physical Review E, American Physical Society, Vol 100, Num 3, pp 032608, 2019, doi:10.1103/PhysRevE.100.032608


Ange Therese Akono, Seid Koric, and Waltraud M. Kriven: "Influence of pore structure on the strength behavior of particle- and fiber-reinforced metakaolin-based geopolymer composites", Cement and Concrete Composites, Elsevier Ltd., Vol 103, pp 103361, 2019, doi:10.1016/j.cemconcomp.2019.103361


D. Liu, S. Koric, and A. Kontsos: "A Multiscale Homogenization Approach for Architectured Knitted Textiles", Journal of Applied Mechanics, The American Society of Mechanical Engineers, Vol 86, Num 11, pp 4044014, 2019, doi:10.1115/1.4044014


David Winogradoff and Aleksei Aksimentiev: "Molecular Mechanism of Spontaneous Nucleosome Unraveling", Journal of Molecular Biology, Elsevier Ltd., Vol 431, Num 2, pp 323-335, 2019, doi:10.1016/j.jmb.2018.11.013


Manish Shankla and Aleksei Aksimentiev: "Step-defect guided delivery of DNA to a graphene nanopore", Nature Nanotechnology, Springer Nature Limited, Vol 14, Num 9, pp 858-865, 2019, doi:10.1038/s41565-019-0514-y


Yiming Yang, Aaron Alford, Veronika Kozlovskaya, Shidi Zhao, Himanshu Joshi, Eunjung Kim, Shuo Qian, Volker Urban, Donald Cropek, Aleksei Aksimentiev, and Eugenia Kharlampieva: "Effect of Temperature and Hydrophilic Ratio on the Structure of Poly(N-vinylcaprolactam)-block-poly(dimethylsiloxane)-block-poly(N-vinylcaprolactam) Polymersomes", ACS Applied Polymer Materials, American Chemical Society, Vol 1, Num 4, pp 722-736, 2019, doi:10.1021/acsapm.8b00259


Megan Farell, Maxwell Wetherington, Manish Shankla, Inseok Chae, Shruti Subramanian, Seong H. Kim, Aleksei Aksimentiev, Joshua Robinson, and Manish Kumar: "Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features", Langmuir, American Chemical Society, Vol 35, Num 13, pp 4726-4735, 2019, doi:10.1021/acs.langmuir.9b00164


James Wilson, Kumar Sarthak, Wei Si, Luyu Gao, and Aleksei Aksimentiev: "Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model", ACS Sensors, American Chemical Society, Vol 4, Num 3, pp 634–644, 2019, doi:10.1021/acssensors.8b01375


Shidi Zhao, Laura Restrepo-Pérez, Misha Soskine, Giovanni Maglia, Chirlmin Joo, Cees Dekker, and Aleksei Aksimentiev: "Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate", ACS Nano, American Chemical Society, Vol 13, Num 2, pp 2398-2409, 2019, doi:10.1021/acsnano.8b09266


Andrew J. Martinolich, Cheng-Wei Lee, I-Te Lu, Sarah C. Bevilacqua, Molleigh B. Preefer, Marco Bernardi, André Schleife, and Kimberly A. See: "Solid-State Divalent Ion Conduction in ZnPS3", Chemistry of Materials, American Chemical Society, Vol 32, Num 10, pp 3652-3661, 2019, doi:10.1021/acs.chemmater.9b00207


Bryce A. Thurston, Ethan P. Shapera, John D. Tovar, André Schleife, and Andrew L. Ferguson: "Revealing the Sequence-Structure-Electronic Property Relation of Self-Assembling pi-Conjugated Oligopeptides by Molecular and Quantum Mechanical Modeling", Langmuir, American Chemical Society, Vol 35, Num 47, pp 15221-15231, 2019, doi:10.1021/acs.langmuir.9b02593


Kexin Yang, Kisung Kang, Zhu Diao, Arun Ramanathan, Manohar H. Karigerasi, Daniel P. Shoemaker, André Schleife, and David G. Cahill: "Magneto-optic response of the metallic antiferromagnet Fe2As to ultrafast temperature excursions", Physical Review Materials, American Physical Society, Vol 3, Num 12, pp 124408, 2019, doi:10.1103/PhysRevMaterials.3.124408


Joshua Leveillee and André Schleife: "Free-electron effects on the optical absorption of the hybrid perovskite CH3NH3PbI3 from first principles", Physical Review B, American Physical Society, Vol 100, Num 3, pp 035205, 2019, doi:10.1103/PhysRevB.100.035205


Zhongcan Xiao, Chuanxu Ma, Wenchang Lu, Jingsong Huang, Liangbo Liang, Kunlun Hong, An-Ping Li, Bobby G. Sumpter, and Jerzy Bernholc: "Ab initio investigation of the cyclodehydrogenation process for polyanthrylene transformation to graphene nanoribbons", npj Computational Materials, Springer Nature Limited, Vol 5, Num 1, pp 91, 2019, doi:10.1038/s41524-019-0228-6


Elizabeth Agee: "The Contributions of Root Systems to Drought Response in the Amazon Rainforest", 2019 Blue Waters Annual Report, pp 332-333, 2019


Rommie Amaro, Lorenzo Casalino: "Influence Virulence and Transmissibility through the Computational Microscope", 2019 Blue Waters Annual Report, pp 244-245, 2019


Aleksei Aksimentiev, Kumar Sarthak, Hadjer Ouldali, Fabien Piguet, Abdelghani Oukhaled, Tobias Ensslen, Jan C. Behrends: "A Nanopore System for Single-Molecule Protein Sequencing", 2019 Blue Waters Annual Report, pp 240-241, 2019


Victor Anisimov, Valery Poltev, Thomas E. Cheatham III, Jerry Bernholc, Rodrigo Galindo–Nurillo: "Improving the Agreement of AMBER Simulation of Crystals of Nucleic Acid Bases with Experimental Data", 2019 Blue Waters Annual Report, pp 314-315, 2019


Narayana R. Aluru: "The Mechanism of Proton Diffusion in ABO3 Perovskite Oxides", 2019 Blue Waters Annual Report, pp 120-121, 2019


Narayana R. Aluru: "Transfer-Learning-Based Coarse-Graining Method for Simple Fluids: Toward Deep Inverse Liquid-State Theory", 2019 Blue Waters Annual Report, pp 124-125, 2019


Aleksei Aksimentiev, Patrick M. Arnott, Himanshu Joshi, Stefan Howorka: "Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes", 2019 Blue Waters Annual Report, pp 242-243, 2019


Aleksei Aksimentiev, Kush Coshic, Christopher M. Maffeo, David Winogradoff: "Resolving the Structure of Bacteriophage HK97 with Atomistic Resolution", 2019 Blue Waters Annual Report, pp 238-239, 2019


Narayana R. Aluru: "Identification of Amino Acids with Sensitive Nanoporous MoS2: Toward Machine Learning-Based Prediction", 2019 Blue Waters Annual Report, pp 122-123, 2019


Oliver M. F. Browne, Christoph Brehm: "An Efficient Method for Hypersonic Laminar–Turbulent Transition Prediction", 2019 Blue Waters Annual Report, pp 134-135, 2019


Elaad Applebaum: "Star Formation in Dwarf Galaxies: Using Simulations to Identify Key Observables to Test Models", 2019 Blue Waters Annual Report, pp 334-335, 2019


Jerzy Bernholc, Emil L. Briggs, Miroslav Hodak, Carl T. Kelley, Wenchang Lu, Zhongcan Xiao: "Design of Atomically Precise Nanoscale Negative Differential Resistance Devices", 2019 Blue Waters Annual Report, pp 128-129, 2019


Rafael C. Bernardi, Hermann E. Gaub: "How Blue Waters Is Aiding the Fight Against Sepsis", 2019 Blue Waters Annual Report, pp 246-247, 2019


Katelyn Barber: "Improving Convectively Induced Turbulence Forecast Parameters through Bulk Numerical Simulations for Aviation Safety", 2019 Blue Waters Annual Report, pp 336-337, 2019


Dinshaw S. Balsara, Alexandre Lazarian, Blakesley Burkhart: "Simulating Two-Fluid MHD Turbulence and Dynamos in Star-Forming Molecular Clouds and a New Paradigm for Computational Astrophysics for Spherical Systems", 2019 Blue Waters Annual Report, pp 14-15, 2019


Guillermo Araya, Guillermo Marin, Fernando Cucchietti: "High-End Visualization of Coherent Structures and Turbulent Events in Wall-Bounded Flows with a Passive Scalar", 2019 Blue Waters Annual Report, pp 126-127, 2019


Maureen T. Brooks: "Modeling Nonlinear Physical–Biological Interactions: Inertia and Sargassum in the North Atlantic", 2019 Blue Waters Annual Report, pp 338-339, 2019


Christoph Brehm, Sean Bailey, Neil Ashton: "Numerical Investigation of Turbulence Suppression in Rotating Flows", 2019 Blue Waters Annual Report, pp 132-133, 2019


Daniel Bodony, Matthias Diener, Sandeep Murthy: "Using OpenMP Offloading to Run Code on Blue Waters’ GPU Nodes", 2019 Blue Waters Annual Report, pp 130-131, 2019


Iryna Butsky: "Predictions About the Invisible Gas in Galaxy Clusters", 2019 Blue Waters Annual Report, pp 340-341, 2019


Adam Burrows, David Radice, Hiroki Nagakura, David Vartanyan, Aaron Skinner, Joshua Dolence: "The Computational Keys to the Supernova Puzzle: How Multiple 3-D Radiation/Hydrodynamic Models Can Unlock the Supernova Mystery", 2019 Blue Waters Annual Report, pp 16-17, 2019


Huck Beng Chew, Soumendu Bagchi: "Role of Interfaces on the Shear Strength and Bending Properties of van der Waals Two-Dimensional Materials", 2019 Blue Waters Annual Report, pp 138-139, 2019


Manuela Campanelli, Scott Noble, Julian Krolik, Mark Avara, Dennis Bowen, Vassilios Mewes: "Accretion Dynamics of Supermassive Black Hole Binaries", 2019 Blue Waters Annual Report, pp 20-21, 2019


Manuela Campanelli, Scott Noble, Julian Krolik, Stephane d’Ascoli, Mark Avara, Dennis Bowen, Vassilios Mewes: "Shedding Light on Supermassive Binary Black Hole Mergers", 2019 Blue Waters Annual Report, pp 18-19, 2019


Yongyang Cai, Kenneth Judd, William Brock, Thomas Hertel: "Climate Policy in a Dynamic Stochastic Economy", 2019 Blue Waters Annual Report, pp 320-321, 2019


Gustavo Caetano–Anollés, Frauke Gräter, Fizza Mughal: "A Phylogenomic History of Protein Function and Dynamics", 2019 Blue Waters Annual Report, pp 248-249, 2019


Matias Carrasco Kind, Brandon Buncher: "Achieving Probabilistic Classification of Cosmic Web Particles using Rapidly Generated Training Data: A Method for Classifying Galaxies into Their Cosmic Web Structural Groups using Supervised Machine Learning", 2019 Blue Waters Annual Report, pp 22-23, 2019


David Ceperley, Carlo Pierleoni: "Quantum Simulations: Properties of Dense Hydrogen", 2019 Blue Waters Annual Report, pp 136-137, 2019


Matthew Clement: "The Early Instability Scenario for Planet Formation in the Solar System", 2019 Blue Waters Annual Report, pp 344-345, 2019


Wendy K. Tam Cho, Yan Liu, Simon Rubinstein–Salzedo: "A Massively Parallel Evolutionary Markov Chain Monte Carlo Algorithm for Sampling Spatial State Spaces", 2019 Blue Waters Annual Report, pp 328-329, 2019


Robert Cieri: "Computational Fluid Dynamics Investigation into Pulmonary Airflow Patterns in Monitor Lizards (Varanidae)", 2019 Blue Waters Annual Report, pp 342-343, 2019


Shanna Chu: "Understanding the Physical Processes Causing Intermediate-Depth Earthquakes", 2019 Blue Waters Annual Report, pp 361, 2019


Bryan Clark, Dmitrii Kochkov, Eli Chertkov, Xiongjie Yu, Di Luo, Greg MacDougall, Hitesh Changlani, Rebecca Flint, Jyotisman Sahoo: "Atypically Entangled Phases and New Methods for the Quantum Many-Body Problem", 2019 Blue Waters Annual Report, pp 140-141, 2019


Colleen E. Clancy, Igor Vorobyov, Kevin R. DeMarco, Sergei Y. Noskov, Van A. Ngo: "Predicting Drug-Induced Cardiac Arrhythmias using Atomistic Simulations", 2019 Blue Waters Annual Report, pp 250-251, 2019


Chunyuan Diao: "Large-Scale Remote Monitoring of Invasive Species Dynamics through a Petascale High-Performance Computing System", 2019 Blue Waters Annual Report, pp 82-83, 2019


Donna Cox, Robert Patterson, Kalina Borkiewicz, A. J. Christensen, Stuart Levy, Jeffrey Carpenter, Thomas Lucas, Melih Sener, John Stone, Barry Isralewitz, Sarah T. Stewart: "Cinematic Scientific Data Visualization for CADENS", 2019 Blue Waters Annual Report, pp 212-213, 2019


Larry Di Girolamo, Matias Carrasco Kind, Gregory Daues, Yulan Hong, Ralph Kahn, Lusheng Liang, Donald Petravick, John Towns, Kent Yang, Ping Yang, Yizhe Zhan, Guangyu Zhao: "Petascale Processing of Satellite Earth Observations", 2019 Blue Waters Annual Report, pp 80-81, 2019


Francina Dominguez, Zhao Yang, and Jorge Eiras-Barca: "Deforestation of the Amazon Forest: Understanding Hydroclimate Impacts by Tracing the Water that Evaporates from the Forest", 2019 Blue Waters Annual Report, pp 84-85, 2019


Julie Dickerson, Gaurav Kandoi: "mRNA Isoform Prediction", 2019 Blue Waters Annual Report, pp 252-253, 2019


Jennifer Corcoran, Brian Huberty, James Klassen, Keith Pelletier, Paul Morin, Joe Knight, Laura Bourgeau–Chavez: "Image Processing to Build a Multitemporal Vegetation Elevation Ecosystem Model of the Great Lakes Basin", 2019 Blue Waters Annual Report, pp 78-79, 2019


Salme Cook: "The Distribution of Shear Stress and Nutrients in a Tidally Energetic Estuary: The Role of Numerical Resolution and Vegetation", 2019 Blue Waters Annual Report, pp 346-347, 2019


Tiziana Di Matteo, Yu Feng, Rupert Croft, Aklant Bhowmick, Yueying Ni, Ananth Tenneti, Steve Wilkins, Madeleine Marshall, Stuart Wyithe: "The Epoch of the First Luminous Black Holes: Evolving the BlueTides Simulation into the First Billion Years of Cosmic History", 2019 Blue Waters Annual Report, pp 24-25, 2019


Ken Dill, Alberto Perez: "Petascale Integrative Approaches to Protein Structure Prediction", 2019 Blue Waters Annual Report, pp 254-255, 2019


Aida X. El–Khadra, Zech Gelzer, Ruth Van de Water, Shaun Lahert, Carleton DeTar, Steve Gottlieb, Andreas Kronfeld, Doug Toussaint: "The Anomalous Magnetic Moment of the Muon: An Improved Ab Initio Calculation of the Hadronic Vacuum Polarization Contribution", 2019 Blue Waters Annual Report, pp 144-145, 2019


Mohammed El–Kebir: "Algorithms for Cancer Phylogenetics", 2019 Blue Waters Annual Report, pp 315, 2019


Iwan Duursma, Hsin–Po Wang: "The Structure and Statistics of Reed–Muller Codes", 2019 Blue Waters Annual Report, pp 214-215, 2019


Lian Duan, Meelan Choudhari: "Direct Numerical Simulation of Pressure Fluctuations Induced by Supersonic Turbulent Boundary Layers", 2019 Blue Waters Annual Report, pp 142-143, 2019


Jerry Draayer, K. D. Launey, T. Dytrych, R. Baker, G. Sargsyan, A. Mercenne, D. Langr, M. Kocourek: "Advancing First-Principle Symmetry-Guided Nuclear Modeling for Studies of Nucleosynthesis and Fundamental Symmetries in Nature", 2019 Blue Waters Annual Report, pp 26-27, 2019


J. Stephen Downie, Sayan Bhattacharyya, José Eduardo González, Boris Capitanu, Craig Willis, Peter Organisciak: "Characterizing Descriptivity in Writing through Text Analysis of Books from the Hathi Trust Digital Library", 2019 Blue Waters Annual Report, pp 322-323, 2019


Patricia M. Gregg, Seid Koric, Yan Zhan, Jack Albright, Haley Cabaniss: "Forecasting Volcanic Unrest and Eruption Potential using Statistical Data Assimilation", 2019 Blue Waters Annual Report, pp 86-87, 2019


Andrew Emerick: "Exascale Astrophysics with Enzo–E: Development of Physics Modules for Galaxy-Scale and Cosmological Simulations", 2019 Blue Waters Annual Report, pp 348-349, 2019


Charles F. Gammie, Patrick Mullen: "Magnetized Models of Giant Impacts", 2019 Blue Waters Annual Report, pp 28-29, 2019


Marcelo García, Paul Fischer, Dimitrios K. Fytanidis, Jose M. Mier: "Turbulence-Resolving Modeling of Oscillatory Boundary Layer Flows", 2019 Blue Waters Annual Report, pp 150-151, 2019


Jonathan Freund, Justin Sirignano, Jonathan MacArt: "Machine-Learning Turbulence Models for Simulations of Turbulent Combustion", 2019 Blue Waters Annual Report, pp 148-149, 2019


Andrew Ferguson: "Discovery of Slow Kinetic Modes from Molecular Simulation Trajectories", 2019 Blue Waters Annual Report, pp 256-257, 2019


Elif Ertekin, Vladan Stevanovic, Eric Toberer, G. Jeffrey Snyder, Michael Toney: "Accelerating Thermoelectrics Materials Discovery via Dopability Predictions", 2019 Blue Waters Annual Report, pp 146-147, 2019


Forrest Glines: "Magnetohydrodynamic Simulation: Galaxies", 2019 Blue Waters Annual Report, pp 350-351, 2019


Nickolay Gnedin: "Cosmic Reionization on Computers", 2019 Blue Waters Annual Report, pp 30-31, 2019


Mattia Gazzola: "Harnessing Viscous Streaming in Complex Active Systems: Minibots in Fluids", 2019 Blue Waters Annual Report, pp 258-259, 2019


Alexander Gurvich: "GPU-Accelerated Interstellar Chemistry with WIND: A General Ordinary Differential Equation Solver", 2019 Blue Waters Annual Report, pp 352-353, 2019


Kaiyu Guan, Jian Peng, Chongya Jiang, Bin Peng, Sibo Wang: "Building an Objective Seasonal Forecasting System for U.S. Corn and Soybean Yields", 2019 Blue Waters Annual Report, pp 90-91, 2019


Kaiyu Guan, Jian Peng, Chongya Jiang, Bin Peng, Sibo Wang: "Monitoring Field-Scale Crop Water Use using a Satellite Data-Driven Mechanistic Modeling Approach", 2019 Blue Waters Annual Report, pp 88-89, 2019


William Gropp, Erin Molloy, Tandy Warnow: "A Parallel Framework for Scaling Phylogeny Estimation Methods to Large Genomic Data Sets", 2019 Blue Waters Annual Report, pp 216-217, 2019


William Gropp, Paul Eller, Ed Karrels: "Algorithms for Extreme-Scale Sytems", 2019 Blue Waters Annual Report, pp 218-219, 2019


Eliu Huerta, Roland Haas, Gabrielle Allen, Ed Seidel, Sarah Habib: "Characterization of Numerical Relativity Waveforms of Eccentric Binary Black Hole Mergers", 2019 Blue Waters Annual Report, pp 38-39, 2019


Jodi A. Hadden–Perilla, Adam Zlotnick, Juan R. Perilla, Michael F. Hagan, Brian Bothner: "Molecular Dynamics Simulations of the HBV Capsid", 2019 Blue Waters Annual Report, pp 260-261, 2019


So Hirata, Alexander E. Doran: "Toward Predictive Computational Design of Precision Molecular Optoelectronics", 2019 Blue Waters Annual Report, pp 264-265, 2019


Benjamin Hooberman, Amir Farbin, Matt Zhang: "Machine Learning for Particle Physics: Employing Deep Learning for Particle Identification and Measurement at Colliders", 2019 Blue Waters Annual Report, pp 152-153, 2019


Jennifer M. Hays: "Using Spectroscopic Data and Molecular Simulations to Estimate Heterogeneous Ensembles: How to Study Complicated, Flexible Proteins When Experimental Data Are Limited", 2019 Blue Waters Annual Report, pp 354-355, 2019


John Hawley, Julian H. Krolik: "Elucidating the Alignment Mechanism for Black Hole Accretion Disks Subjected to Lense–Thirring Torques", 2019 Blue Waters Annual Report, pp 32-33, 2019


Jodi A. Hadden–Perilla, Adam Zlotnick, Juan R. Perilla, Michael F. Hagan, Brian Bothner: "Molecular Dynamics Simulations of the HBV Capsid as a Drug Target", 2019 Blue Waters Annual Report, pp 262-263, 2019


Matthew E. Hudson, Yan W. Asmann, Liudmila Sergeevna Mainzer: "Impact of Batch Effect and Study Design Biases on Identification of Genetic Risk Factors in Sequencing Data", 2019 Blue Waters Annual Report, pp 266-267, 2019


Philip F. Hopkins, Claude–André Faucher–Giguère, Dušan Kereš, Eliot Quataert, Norman Murray, Mike Boylan–Kolchin, James Bullock, Andrew Wetzel, Robyn Sanderson, Chris Hayward, Robert Feldman, Christine Corbett–Moran: "Understanding the Origins of the Stars and Galaxies in our Universe", 2019 Blue Waters Annual Report, pp 34-35, 2019


Shantenu Jha, Cecilia Clementi, Eugen Hruska: "Extensible and Scalable Adaptive Sampling to Fold Proteins on Supercomputers", 2019 Blue Waters Annual Report, pp 222-223, 2019


Eliu Huerta, Gabrielle Allen, Roland Haas, Ed Seidel, Zhizhen Zhao, Asad Khan, Sibo Wang, Robert Gruendl, Elise Jennings, Huihuo Zheng: "Deep Learning at Scale for the Construction of Galaxy Catalogs with the Dark Energy Survey", 2019 Blue Waters Annual Report, pp 36-37, 2019


Prashant K. Jain, Sudhakar Pamidighantam, Daniel Dumett Torres: "A Novel Crystal Structure with Spin-Protected Surface Electronic Conduction", 2019 Blue Waters Annual Report, pp 156-157, 2019


Ravishankar Iyer, Saurabh Jha, Shengkun Cui, Tianyin Xu, Jeremy Enos, Mike Showerman, Greg Bauer, Mark Dalton, Zbigniew Kalbarczyk, Bill Kramer: "Kaleidoscope: Live Forensics for Large-Scale Data Center Storage Systems", 2019 Blue Waters Annual Report, pp 220-221, 2019


Kathryn Huff, Alexander Lindsay, Andrei Rykhlevskii: "Molten-Salt Reactors and Their Fuel Cycles", 2019 Blue Waters Annual Report, pp 154-155, 2019


Eliu Huerta, Adam Rebei, Sibo Wang, Daniel Johnson, Sarah M. Habib, Roland Haas, Daniel George: "Fusing Numerical Relativity and Deep Learning to Detect Eccentric Binary Black Hole Mergers using Higher-Order Waveform Multipoles", 2019 Blue Waters Annual Report, pp 40-41, 2019


Bin Ouyang, Tanmoy Chakraborty, Namhoon Kim, Nicola H. Perry, Tim Mueller, Narayana R. Aluru, and Elif Ertekin: "Cluster Expansion Framework for the Sr(Ti1-xFex)O3-x/2 (0 < x < 1) Mixed Ionic Electronic Conductor: Properties Based on Realistic Configurations", Chemistry of Materials, American Chemical Society, Vol 31, Num 9, pp 3144-3153, 2019, doi:10.1021/acs.chemmater.8b04285


Tao Jiang, Po–Chao Wen, Kin Lam, Zhiyu Zhao, Archit Kumar Vasan, H. Criss Hartzell, Kuai Yu, YuanYuan Cui: "Microscopic Identification of PIP2 Binding Sites on a Ca2+-activated Cl- Channel", 2019 Blue Waters Annual Report, pp 268-269, 2019


David LeBauer, Todd Mockler, Robert Pless, Roman Garnett, Vasit Sagan, Rob Kooper, Duke Pauli, Geoff Morris: "The TERRA Phenotyping Reference Platform: Open Data and Software for Precision Field Crop Measurement and Analysis", 2019 Blue Waters Annual Report, pp 272-273, 2019


Seid Koric, Robert F. Lucas, Erman Guleryuz: "Accelerating Virtual Prototyping and Certification in the Aerospace Industry with Scalable Finite-Element Analysis", 2019 Blue Waters Annual Report, pp 162-163, 2019


Jean–Pierre Leburton, Olgica Milenkovic, Nagendra Athreya: "Graphene Nanopore Transistor for DNA-Nick Detection", 2019 Blue Waters Annual Report, pp 164-165, 2019


Fatemeh Khalili–Araghi, Christopher Weber: "Paracellular Ion Transport", 2019 Blue Waters Annual Report, pp 270-271, 2019


Harley T. Johnson, Purnima Ghale: "Electronic Structure of Microscale Dielectric Barrier Discharges", 2019 Blue Waters Annual Report, pp 160-161, 2019


Athol J. Kemball, Di Wen, Michael Katolik, Samantha Thrush, Jamila Serena Taaki: "Data- and Compute-Intensive Challenges for Observational Astronomy in the Great Survey Era", 2019 Blue Waters Annual Report, pp 42-43, 2019


Eric Johnsen, Shahaboddin Alahyari Beig, Mauro Rodriguez, Minki Kim: "Inertial Collapse of Individual Bubbles near Solid/Free Boundaries", 2019 Blue Waters Annual Report, pp 158-159, 2019


Sonia Lasher–Trapp: "Inflow and Outflow from Thunderstorms: Tracking Their Influence on Precipitation and Further Growth", 2019 Blue Waters Annual Report, pp 92-93, 2019


Joshua Lansford: "Electron Density-Based Machine Learning for Accelerating Quantum Calculations", 2019 Blue Waters Annual Report, pp 356-357, 2019


Nancy Makri: "Quantum–Classical Path Integral Simulation of Proton Translocation in Biological Channels", 2019 Blue Waters Annual Report, pp 274-275, 2019


Deborah A. Levin: "Modal Decompositions of Shock Interactions", 2019 Blue Waters Annual Report, pp 44-45, 2019


Deborah A. Levin: "Plume Plasma Spacecraft Interactions", 2019 Blue Waters Annual Report, pp 46-47, 2019


Yi-Hsin Liu, Michael Hesse, William Daughton, Tak Chu Li: "The Spreading of Three-Dimensional Magnetic Reconnection in Asymmetric Geometry", 2019 Blue Waters Annual Report, pp 48-49, 2019


Rafael Tinoco Lopez, Paul Fischer, Som Dutta, Pallav Ranjan: "Investigation of Sediment Transport through Aquatic Vegetation using Large-Scale High-Fidelity Turbulence Simulations", 2019 Blue Waters Annual Report, pp 184-185, 2019


Paul Morin, Claire Porter, Ian Howat, Myoung–Jong Noh, Charles Nguyen, Cathleen Williamson, Charles Crittenden: "Petascale Polar Topography Production", 2019 Blue Waters Annual Report, pp 94-95, 2019


Felipe Menanteau, Robert Gruendl, Donald Petravick, Erin Sheldon: "Assembling a Map of the Universe: Shapes and Mass Distribution for the Dark Energy Survey", 2019 Blue Waters Annual Report, pp 50-51, 2019


Moshe Matalon, Shikhar Mohan: "Outwardly Propagating Turbulent Flames", 2019 Blue Waters Annual Report, pp 168-169, 2019


Arif Masud, Soonpil Kang: "A New Stabilized Fluid–Structure Interaction Method: Coupled System of Anisotropic Viscoelastic Model for Artery and Non-Newtonian Model for Blood", 2019 Blue Waters Annual Report, pp 276-277, 2019


Philipp Mösta, David Radice, Roland Haas, Erik Schnetter, Sebastiano Bernuzzi: "Petascale Simulations of Binary Neutron Star Mergers", 2019 Blue Waters Annual Report, pp 52-53, 2019


Farzad Mashayek, Jonathan Komperda, Dongru Li, Ahmad Peyvan: "Compressibility Effects on Spatially Developing Plane Free Shear Layer", 2019 Blue Waters Annual Report, pp 166-167, 2019


Kara Marsac: "Extending the Longevity of Produced Water Disposal Wells: Evaluation using Reactive Transport Simulation", 2019 Blue Waters Annual Report, pp 358-359, 2019


Mahmoud Moradi: "Activation Mechanisms of the Mechanosensitive Channel of Large Conductance: Employing Loosely Coupled Molecular Dynamics Simulations to Characterize Protein Structural Dynamics", 2019 Blue Waters Annual Report, pp 282-283, 2019


Mahmoud Moradi: "Transport Mechanism of POT Transporters: Employing Loosely Coupled Molecular Dynamics Simulations to Characterize Protein Structural Dynamics", 2019 Blue Waters Annual Report, pp 280-281, 2019


Jeffery S. Moore, Giuseppe Licari, Xing Jiang, Andres Arango, Jimmy Do: "Atomic Scale Simulation of Amyloid Beta with Dismantling Peptide-Based Inhibitors", 2019 Blue Waters Annual Report, pp 278-279, 2019


Luke Olson, Amanda Bienz, Andrew Reisner: "Scalable Line and Plane Solvers", 2019 Blue Waters Annual Report, pp 226-227, 2019


Luke Olson, Amanda Bienz, William Gropp: "Improved Scalability through Node-Aware Communicators", 2019 Blue Waters Annual Report, pp 224-225, 2019


Michael L. Norman, James Bordner: "Development of a Scalable Gravity Solver for ENZO–E", 2019 Blue Waters Annual Report, pp 54-55, 2019


Mark Neubauer, Robert Gardner, Dewen Zhong: "Deep Learning for Higgs Boson Identification and Searches for New Physics at the Large Hadron Collider", 2019 Blue Waters Annual Report, pp 170-171, 2019


Stephen W. Nesbitt, Itinderjot Singh: "High-Resolution Numerical Simulations of Convection Initiation over the Sierras de Córdoba Mountains in Argentina", 2019 Blue Waters Annual Report, pp 96-97, 2019


Kimberly Prather, Rommie Amaro: "Investigating the Climate-Relevant Impacts of Chemical Complexity in Marine Aerosols", 2019 Blue Waters Annual Report, pp 288-289, 2019


Donald Petravick, Eric Morganson, Monika Adamow, Doug Friedel, Robert Gruendl, Michael Johnson: "Processing Dark Energy Camera Data to Make the World’s Best Map of the Night Sky", 2019 Blue Waters Annual Report, pp 58-59, 2019


Joseph R. Peterson, John A. Cole, Tyler M. Earnest, Michael J. Hallock: "Calibrating the SimBioSys TumorScope for the Fight on Cancer: A Scenario Analysis Engine for Determining Optimal Therapy Choice", 2019 Blue Waters Annual Report, pp 286-287, 2019


Juan Perilla: "Molecular Mechanisms of Infection by Chlamydia", 2019 Blue Waters Annual Report, pp 284-285, 2019


Nikolaos Pavlis, Weijia Kuang: "Prediction of Geomagnetic Secular Variation with Large-Ensemble Geomagnetic Data Assimilation", 2019 Blue Waters Annual Report, pp 100-101, 2019


Brian O’Shea, David C. Collins, John H. Wise, Cameron J. Hummels, Britton D. Smith, Molly S. Peeples, John D. Regan, Jason Tumlinson, Lauren Corlies: "Simulating Galaxy Formation across Cosmic Time", 2019 Blue Waters Annual Report, pp 56-57, 2019


Leigh G. Orf, Catherine Finley, Kelton Halbert, Eric Savory: "Simulations of Violently Tornadic Supercells and Damaging Thunderstorms", 2019 Blue Waters Annual Report, pp 98-99, 2019


Nikolai Pogorelov, Jacob Heerikhuisen, Sergey Borovikov, Tae Kim, Mehmet Sarp Yalim: "Coupling the Solar Wind and Local Interstellar Medium in the Era of the New Horizons, Interstellar Boundary Explorer, Parker Solar Probe, Ulysses, and Voyager Spacecraft", 2019 Blue Waters Annual Report, pp 60-61, 2019


Taras V. Pogorelov, Chad Rienstra, Martin Burke: "Amphotericin-Driven Sterol Extraction: Probing the Mechanism", 2019 Blue Waters Annual Report, pp 316, 2019


Caroline Riedl, Riccardo Longo, Matthias Grosse Perdekamp, Marco Meyer, Robert Heitz, April Futch, Charles Naim, Angelo Maggiora, Andrei Gridin, Nicolas Pierre, Anatolii Koval, Celso Franco, Po–Ju Lin, Florian Kaspar, Henri Pekeler, Bakur Parsamyan: "Mapping Proton Quark Structure: Looking Inside the Proton—How Do Quarks Spin?", 2019 Blue Waters Annual Report, pp 176-177, 2019


Venkat Raman: "Simulation of Rotating Detonation Engines", 2019 Blue Waters Annual Report, pp 174-175, 2019


Rajib Rahman, Andrew S. Dzurak: "Designing Quantum Logic Gates on Silicon Chips with Large-Scale Multiphysics Simulations", 2019 Blue Waters Annual Report, pp 172-173, 2019


Thomas Quinn, Fabio Governato, Michael Tremmel, Arif Babul, Iryna Butsky: "Modeling of Galaxy Populations", 2019 Blue Waters Annual Report, pp 64-65, 2019


Jane Pratt, Isabelle Baraffe, Tom Goffrey: "Interior Dynamics of Young Stars Revealed by 3-D Hydrodynamic Simulations", 2019 Blue Waters Annual Report, pp 62-63, 2019


Paul Ricker, Yinghe Lü: "Effects of Active Galaxy Feedback on the Intracluster Medium", 2019 Blue Waters Annual Report, pp 66-67, 2019


Diwakar Shukla, Erik Procko: "Simulations Uncover the Mechanism of Serotonin Transport in the Brain", 2019 Blue Waters Annual Report, pp 294-295, 2019


Olufemi Emmanuel Kadri, Migle Surblyte, Vishnu Deep Chandran, and Roman S. Voronov: "Is the endothelial cell responsible for the thrombus core and shell architecture?", Medical Hypotheses, Elsevier Ltd., Vol 129, pp 109244, 2019, doi:10.1016/j.mehy.2019.109244


Nicole Riemer: "Machine Learning for Error Quantification in Simulating the Climate Impacts of Atmospheric Aerosols", 2019 Blue Waters Annual Report, pp 102-103, 2019


André Schleife, Ethan Shapera: "Discovery of New Plasmonic Materials via High-Throughput Machine Learning", 2019 Blue Waters Annual Report, pp 180-181, 2019


André Schleife, Alina Kononov: "Electron Dynamics of Ion-Irradiated Two-Dimensional Materials", 2019 Blue Waters Annual Report, pp 178-179, 2019


Benoit Roux, Chris Boughter, Prithviraj Nandigrami, Jonathan Thirman: "Molecular Dynamics Binding Free Energy Calculations Offer a Window to Understand Protein–Protein Binding Specificity", 2019 Blue Waters Annual Report, pp 290-291, 2019


Nicole Rosato: "Improved Trumpet Initial Lapse and Shift for Binary Black Hole Simulations", 2019 Blue Waters Annual Report, pp 360, 2019


Stuart Shapiro, Milton Ruiz, Antonios Tsokaros, Lunan Sun: "Gravitational and Electromagnetic Signatures from Binary Black Hole–Neutron Star Mergers: A Jet Engine for Short Gamma-Ray Bursts", 2019 Blue Waters Annual Report, pp 68-69, 2019


Phiala Shanahan, Balint Joo, David Murphy, William Detmold, Michael Wagman: "Constraining the Properties and Interactions of Dark Matter", 2019 Blue Waters Annual Report, pp 208, 2019


Ivan Soltesz, Ivan Raikov, Aaron Milstein, Darian Hadjiabadi: "Full-Scale Biophysical Modeling of Hippocampal Networks during Spatial Navigation", 2019 Blue Waters Annual Report, pp 298-299, 2019


Diwakar Shukla, Aditi Das: "Elucidating the Ligand Selectivity and Activation Mechanisms of Cannabinoid Receptors", 2019 Blue Waters Annual Report, pp 296-297, 2019


Edgar Solomonik: "Pushing the Boundaries of Large-Scale Tensor Computations", 2019 Blue Waters Annual Report, pp 230-231, 2019


Micheline Soley: "Escaping From an Ultracold Inferno: The Ultracold KRb Dimer Reaction", 2019 Blue Waters Annual Report, pp 362-363, 2019


Marc Snir, Franck Cappello: "Detection of Silent Data Corruptions using Machine Learning", 2019 Blue Waters Annual Report, pp 228-229, 2019


Justin Sirignano, Jonathan B. Freund, Jonathan F. MacArt: "HPC Development of Deep Learning Models in Scientific Computing and Finance", 2019 Blue Waters Annual Report, pp 234, 2019


Diwakar Shukla: "Molecular Basis of the Nitrate Transport Mechanism in Plants", 2019 Blue Waters Annual Report, pp 292-293, 2019


Emad Tajkhorshid, Soumyo Sen, Eric Shinn, Aaron Chan, Hyun Park: "Modeling of a Zika Virus Envelope at Atomic Resolution", 2019 Blue Waters Annual Report, pp 310-311, 2019


Clay Tabor, Isabel Montañez, Marcus Löfverström, Jessica Oster, Barbara Wortham, Cameron de Wet: "Simulating Hydroclimate Change in Southwest North America at 21,000 Years Ago", 2019 Blue Waters Annual Report, pp 104-105, 2019


Brad Sutton, Alex Cerjanic, Aaron Anderson, Curtis Johnson: "MRI-Based Biomarkers through High-Performance Computing", 2019 Blue Waters Annual Report, pp 304-305, 2019


Ronald Stenz: "The Impacts of Hydrometeor Centrifuging on Tornado Dynamics: Improving the Realism of Tornado Simulations", 2019 Blue Waters Annual Report, pp 364-365, 2019


Marcos Sotomayor: "Desmosomal Cadherins Beating under Tension", 2019 Blue Waters Annual Report, pp 300-301, 2019


Ashok Srinivasan, Sirish Namilae, Anuj Mubayi, Matthew Scotch, Robert Pahle, Sudheer Chunduri: "Simulation of Viral Infection Propagation during Air Travel", 2019 Blue Waters Annual Report, pp 302-303, 2019


Emad Tajkhorshid: "Atomistic Simulation of a Protocell", 2019 Blue Waters Annual Report, pp 308-309, 2019


Emad Tajkhorshid, Rafael C. Bernardi, James C. Phillips, John Stone, Hermann E. Gaub, Michael A. Nash, Edward A. Bayer: "Mechanobiology: Using Blue Waters to Decipher the Physical Principles of Protein Mechanics", 2019 Blue Waters Annual Report, pp 306-307, 2019


David E. Taflin: "Optimization of a Field Data Parallel Output Library", 2019 Blue Waters Annual Report, pp 235, 2019


Gabor Toth, Hongyang Zhou: "Scaling the BATS–R–US MHD Model to Over 100,000 Cores with Efficient Hybrid OpenMP and MPI Parallelization", 2019 Blue Waters Annual Report, pp 72-73, 2019


Darius Teo: "Unraveling Functional Hole Hopping Pathways in the [Fe4S4]-Containing DNA Primase", 2019 Blue Waters Annual Report, pp 366-367, 2019


Brian G. Thomas, Seong–Mook Cho, Hyunjin Yang, Surya Pratap Vanka, Matthew Zappulla, Seid Koric, Ahmed Taha: "Turbulent Multiphase Thermal Flow Modeling of Defect Formation Mechanisms and Electromagnetic Force Effects in Continuous Steel Casting", 2019 Blue Waters Annual Report, pp 182-183, 2019


Saul A. Teukolsky: "Merging Black Holes and Neutron Stars", 2019 Blue Waters Annual Report, pp 75, 2019


Alexander Tchekhovskoy, Matthew Liska, Casper Hesp, Adam Ingram, Michiel van der Klis, Sera Markoff, Koushik Chatterjee, Zack Andalman, Nicholas Stone, Eric Coughlin: "Feeding Black Holes: Tilt with a Twist", 2019 Blue Waters Annual Report, pp 70-71, 2019


Walter Torres: "The Transport and Dynamics of Wave-Driven Reef Jets under the Influence of Rotation and Bottom Friction", 2019 Blue Waters Annual Report, pp 368-369, 2019


Kimani Toussaint: "Machine Learning-Assisted High-Throughput Computational Design of Solvents for Liquid-Exfoliation", 2019 Blue Waters Annual Report, pp 186-187, 2019


Zhi Jian Wang: "Supersonic Jet Noise Prediction using High-Order Large-Eddy Simulation", 2019 Blue Waters Annual Report, pp 194-195, 2019


Lucas Wagner, Daniel Shoemaker, Greg MacDougall: "Accurate Effective Interactions in Quantum Materials", 2019 Blue Waters Annual Report, pp 192-193, 2019


Lela Vuković, Markita Landry: "Detecting Neurotransmitters with DNA-Wrapped Nanotube Sensors", 2019 Blue Waters Annual Report, pp 190-191, 2019


Gregory Voth: "Multiscale Simulations of Complex Self-Assembling Biomolecules: Targeting HIV-1", 2019 Blue Waters Annual Report, pp 312-313, 2019


Matthew Turk, Wei–Ting Liao, Hsi–Yu Schive: "Numerical Study on the Fragmentation Condition in a Primordial Accretion Disk", 2019 Blue Waters Annual Report, pp 74, 2019


Dallas R. Trinkle, Dan Katz, Joshua Vita: "High-Throughput Materials Modeling Optimization", 2019 Blue Waters Annual Report, pp 188-189, 2019


John Vidale, Yifeng Cui, Philip Maechling, Kim Olsen, Ricardo Taborda, Thomas H. Jordan, Jacobo Bielak, Alexander Breuer, Scott Callaghan, Jacquelyn Gilchrist, Christine A. Goulet, R. W. Graves, Xiaofeng Meng, Dawei Mu, Dmitry Pekurovsky, Daniel Roten, William Savran, Bruce Shaw, Qian Yao: "Simulating Large California Earthquakes before They Occur", 2019 Blue Waters Annual Report, pp 108-109, 2019


Robert J. Trapp: "Implementation and Use of a Global, Nonhydrostatic Model for Extended-Range Weather Prediction during the RELAMPAGO Field Campaign", 2019 Blue Waters Annual Report, pp 106-107, 2019


Tandy Warnow, William Gropp, Erin Molloy, Pranjal Vachaspati: "Algorithms for Large-Scale Evolutionary Tree Construction: Improving Scalability and Accuracy through Divide-and-Conquer", 2019 Blue Waters Annual Report, pp 232-233, 2019


Donald J. Wuebbles, Xin-Zhong Liang, Swarnali Sanyal: "Evolving Air Quality under the Changing Climate", 2019 Blue Waters Annual Report, pp 114-115, 2019


Samuel Whitman: "Simulation of Bluff Body Stabilized Flames with PeleC: Adaptively Resolving Turbulence–Combustion Interactions in Real-World Engineering Problems", 2019 Blue Waters Annual Report, pp 370-371, 2019


Matthew West, Jeffrey Curtis: "Simulating Aerosol Impacts on Climate, One Particle at a Time: A Regional-Scale, Particle-Resolved Aerosol Model to Quantify and Reduce Uncertainties in Aerosol–Atmosphere Interactions", 2019 Blue Waters Annual Report, pp 112-113, 2019


Renata Wentzcovitch, Dong–Bo Zhang, Kei Hirose: "Materials Simulations in Geophysics", 2019 Blue Waters Annual Report, pp 110-111, 2019


Zhen Xu, Mauro Rodriguez, Shahaboddin Alahyari Beig: "Numerical Simulations of a Collapsing Cavitation Bubble Near an Elastically Deformable Object", 2019 Blue Waters Annual Report, pp 198-199, 2019


Pui–Kuen Yeung, K.R. Sreenivasan: "New Insights on Intermittency and Circulation Statistics Obtained from a Massive Turbulence Simulation Database", 2019 Blue Waters Annual Report, pp 204-205, 2019


Xiangdong Zhang, Liran Peng, Jing Zhang: "Sensitivity of Arctic Sea Ice Thickness Distribution to Sea Ice Internal Dynamics in a Changing Climate", 2019 Blue Waters Annual Report, pp 116-117, 2019


Mao Ye: "High-Frequency Trading in Nanoseconds: Analysis, Modeling, and Policy Implications", 2019 Blue Waters Annual Report, pp 324-325, 2019


Jinhui Yan: "Free-Surface Flow Modeling of Multiple Tidal Turbines", 2019 Blue Waters Annual Report, pp 202-203, 2019


Bin Xu, Laurent Bellaiche, Bertrand Dupé, Wojtek Morawiec: "Spin Spirals in Multiferroic Bismuth Ferrite and at Metal Surface: From Fully First Principles", 2019 Blue Waters Annual Report, pp 196-197, 2019


Yonghua Yan, Yong Yang: "Numerical Study on Shock Wave–Boundary Layer Interaction and Its Control", 2019 Blue Waters Annual Report, pp 200-201, 2019


Yang Zhang: "Effects of Surface Defects on Hydrophobicity at Rare-Earth Oxide Interfaces using Molecular Dynamics Simulations Driven by Ab-Initio-Based Deep Neural Network Potentials", 2019 Blue Waters Annual Report, pp 206-207, 2019


Kartik P. Iyer, Katepalli R. Sreenivasan, and P. K. Yeung: "Circulation in High Reynolds Number Isotropic Turbulence is a Bifractal", Physical Review X, American Physical Society, Vol 9, Num 4, pp 041006, 2019, doi:10.1103/PhysRevX.9.041006


X. M. Zhai, K. R. Sreenivasan, and P. K. Yeung: "Cancellation exponents in isotropic turbulence and magnetohydrodynamic turbulence", Physical Review E, American Physical Society, Vol 99, Num 2, pp 023102, 2019, doi:10.1103/PhysRevE.99.023102


W. H. Savran and K. B. Olsen: "Ground motion simulation and validation of the 2008 Chino Hills earthquake in scattering media", Geophysical Journal International, The Royal Astronomical Society, Vol 219, Num 3, pp 1836-1850, 2019, doi:10.1093/gji/ggz399


Bruce E. Shaw: "Beyond Backslip: Improvement of Earthquake Simulators from New Hybrid Loading Conditions", Bulletin of the Seismological Society of America, Seismological Society of America, Vol 109, Num 6, pp 2159-2167, 2019, doi:10.1785/0120180128


Kyle B. Withers, Kim B. Olsen, Steven M. Day, and Zheqiang Shi: "Ground Motion and Intraevent Variability from 3D Deterministic Broadband (0-7.5 Hz) Simulations along a Nonplanar Strike‐Slip Fault", Bulletin of the Seismological Society of America, Seismological Society of America, Vol 109, Num 1, pp 229-250, 2019, doi:10.1785/0120180006


Kuai Yu, Tao Jiang, YuanYuan Cui, Emad Tajkhorshid, and H. Criss Hartzell: "A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca2+-activated Cl− channel ANO1 (TMEM16A)", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 116, Num 40, pp 19952-19962, 2019, doi:10.1073/pnas.1904012116


Xing Jiang, Abigail J. Halmes, Giuseppe Licari, John W. Smith, Yang Song, Edwin G. Moore, Qian Chen, Emad Tajkhorshid, Chad M. Rienstra, and Jeffrey S. Moore: "Multivalent Polymer-Peptide Conjugates: A General Platform for Inhibiting Amyloid Beta Peptide Aggregation", ACS Macro Letters, American Chemical Society, Vol 8, Num 10, pp 1365-1371, 2019, doi:10.1021/acsmacrolett.9b00559


A. Bazavov, C. Bernard, C. DeTar, Daping Du, A.  X. El-Khadra, E.  D. Freeland, E. Gámiz, Steven Gottlieb, U.  M. Heller, J. Komijani, A.  S. Kronfeld, J. Laiho, P.  B. Mackenzie, E. T. Neil, T. Primer, J.  N. Simone, R. Sugar, D. Toussaint, and R. S. Van de Water: "vertical bar V-us vertical bar from K-l3 decay and four-flavor lattice QCD", Physical Review D, American Physical Society, Vol 99, Num 11, pp 114509, 2019, doi:10.1103/PhysRevD.99.114509


A. Bazavov, C. Bernard, C. DeTar, Daping Du, A. X. El-Khadra, E. D. Freeland, E. Gámiz, Z. Gelzer, Steven Gottlieb, U. M. Heller, A. S. Kronfeld, J. Laiho, Yuzhi Liu, P. B. Mackenzie, Y. Meurice, E. T. Neil, J. N. Simone, R. Sugar, D. Toussaint, R. S. Van de Water, and Ran Zhou: "B-s -> Kl nu decay from lattice QCD", Physical Review D, American Physical Society, Vol 100, Num 3, pp 034501, 2019, doi:10.1103/PhysRevD.100.034501


Ruijie D. Teo, Elizabeth R. Smithwick, Agostino Migliore, and David N. Beratan: "A single AT-GC exchange can modulate charge transfer-induced p53-DNA dissociation", Chemical Communications, The Royal Society of Chemistry, Vol 55, Num 2, pp 206-209, 2019, doi:10.1039/C8CC09048C


Ruijie D. Teo, Ruobing Wang, Elizabeth R. Smithwick, Agostino Migliore, Michael J. Therien, and David N. Beratan: "Mapping hole hopping escape routes in proteins", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 116, Num 32, pp 15811-15816, 2019, doi:10.1073/pnas.1906394116


Yaping Cai, Kaiyu Guan, David Lobell, Andries B. Potgieter, Shaowen Wang, Jian Peng, Tianfang Xu, Senthold Asseng, Yongguang Zhang, Liangzhi You, and Bin Peng: "Integrating satellite and climate data to predict wheat yield in Australia using machine learning approaches", Agricultural and Forest Meteorology, Elsevier B.V., Vol 274, pp 144-159, 2019, doi:10.1016/j.agrformet.2019.03.010


Carleton DeTar, Andreas S. Kronfeld, Song-haeng Lee, Daniel Mohler, and James N. Simone (Fermilab Lattice and MILC Collaborations): "Splittings of low-lying charmonium masses at the physical point", Physical Review D, American Physical Society, Vol 99, Num 3, pp 034509, 2019, doi:10.1103/PhysRevD.99.034509


Andrew C. Kirby, Michael J. Brazell, Zhi Yang, Rajib Roy, Behzad R. Ahrabi, Michael K. Stoellinger, Jay Sitaraman, and Dimitri J. Mavriplis: "Wind farm simulations using an overset hp-adaptive approach with blade-resolved turbine models", International Journal of High Performance Computing Applications, SAGE Publishing, Vol 33, Num 5, pp 897-923, 2019, doi:10.1177/1094342019832960


Robert B. Baker, Jerry P. Draayer, Grigor H. Sargsyan, Alison C. Dreyfuss, Tomáš Dytrych, David Kekejian, Kristina D. Launey, and Alexis Mercenne: "A 21st Century View of Nuclear Structure", EDP Sciences, EPJ Web of Conferences (IV International Conference on Nuclear Structure and Dynamics, NSD 2019), Vol 223, pp 01004, Venice, Italy, 2019, doi:10.1051/epjconf/201922301004


Christine A. Shields, Nan Rosenbloom, Susan Bates, Cecile Hannay, Aixue Hu, Ashley E. Payne, Jonathan J. Rutz, and John Truesdale: "Meridional Heat Transport During Atmospheric Rivers in High-Resolution CESM Climate Projections", Geophysical Research Letters, American Geophysical Union, Vol 46, Num 24, pp 14702-14712, 2019, doi:10.1029/2019GL085565


Asaf Inbal, Qingkai Kong, William Savran, and Richard M. Allen: "On the Feasibility of Using the Dense MyShake Smartphone Array for Earthquake Location", Seismological Research Letters, Seismological Society of America, Vol 90, Num 3, pp 1209–1218, 2019, doi:10.1785/0220180349


Asad Khan, E. A. Huerta, Sibo Wang, Robert Gruendl, Elise Jennings, and Huihuo Zheng: "Deep learning at scale for the construction of galaxy catalogs in the Dark Energy Survey", Physics Letters B, Elsevier B.V., Vol 795, pp 248-258, 2019, doi:10.1016/j.physletb.2019.06.009


Parth Chaturvedi and Lela Vuković: "Structural Properties of Small Single-Stranded Circular Nucleic Acids", Journal of Physical Chemistry B, American Chemical Society, Vol 123, Num 39, pp 8216-8221, 2019, doi:10.1021/acs.jpcb.9b06831


Ankita Sarkar, Pancham Lal Gupta, and Adrian E. Roitberg: "pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase", Journal of Physical Chemistry B, American Chemical Society, Vol 123, Num 27, pp 5742-5754, 2019, doi:10.1021/acs.jpcb.9b03816


Kevin J. Cheng, Balaji Selvam, Li-Qing Chen, and Diwakar Shukla: "Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters", Journal of Physical Chemistry B, American Chemical Society, Vol 123, Num 40, pp 8411-8418, 2019, doi:10.1021/acs.jpcb.9b08257


Jiayong Zhang, Yongqiang Cheng, Wenchang Lu, Emil Briggs, Anibal J. Ramirez-Cuesta, and J. Bernholc: "Large-Scale Phonon Calculations Using the Real-Space Multigrid Method", Journal of Chemical Theory and Computation, American Chemical Society, Vol 15, Num 12, pp 6859-6864, 2019, doi:10.1021/acs.jctc.9b00802


2018

Alexandra L. Jones and Larry Di Girolamo: "Design and Verification of a New Monochromatic Thermal Emission Component for the I3RC Community Monte Carlo Model", Journal of the Atmospheric Sciences, American Meteorological Society, Vol 75, Num 3, pp 885-906, 2018, doi:10.1175/jas-d-17-0251.1


Jon Calhoun, Franck Cappello, Luke N. Olson, Marc Snir, and William D. Gropp: "Exploring the Feasibility of Lossy Compression for PDE Simulations", International Journal of High Performance Computing Applications, SAGE Publications, Vol 33, Num 2, pp 397-410, 2018, doi:10.1177/1094342018762036


Hui Li and Ryan L. Sriver: "Tropical Cyclone Activity in the High-Resolution Community Earth System Model and the Impact of Ocean Coupling", Journal of Advances in Modeling Earth Systems, Wiley-Blackwell, Vol 10, Num 1, pp 165-186, 2018, doi:10.1002/2017ms001199


Hotaka Shiokawa, Roseanne M. Cheng, Scott C. Noble, and Julian H. Krolik: "PATCHWORK: A Multipatch Infrastructure for Multiphysics/Multiscale/Multiframe Fluid Simulations", Astrophysical Journal, The American Astronomical Society, Vol 861, Num 1, 2018, doi:10.3847/1538-4357/aac2dd


Kai Jin, Surya P. Vanka, and Brian G. Thomas: "Large Eddy Simulations of Electromagnetic Braking Effects on Argon Bubble Transport and Capture in a Steel Continuous Casting Mold", Metallurgical and Materials Transactions B, Springer Nature, Vol 49, Num 3, pp 1360-1377, 2018, doi:10.1007/s11663-018-1191-1


Cain, Bruce E., Wendy K. Tam Cho, Yan Y. Liu, and Emily Zhang: "A Reasonable Bias Approach to Gerrymandering: Using Automated Plan Generation to Evaluate Redistricting Proposals", William & Mary Law School, William & Mary Law Review, Vol 59, Num 5, pp 1521, 2018


Yu Chen, Yaofa Li, Albert J. Valocchi, and Kenneth T. Christensen: "Lattice Boltzmann simulations of liquid CO2 displacing water in a 2D heterogeneous micromodel at reservoir pressure conditions", Journal of Contaminant Hydrology, Elsevier B.V., Vol 212, pp 14-27, 2018, doi:10.1016/j.jconhyd.2017.09.005


Daniel George and E. A. Huerta: "Deep Neural Networks to Enable Real-Time Multimessenger Astrophysics", Physical Review D, American Physical Society, Vol 97, Num 4, pp 044039, 2018, doi:10.1103/physrevd.97.044039


Aklant K. Bhowmick, Tiziana Di Matteo, Yu Feng, Francois Lanusse: "The clustering of z > 7 galaxies: predictions from the BLUETIDES simulation", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 474, Num 4, pp 5393-5405, 2018, doi:10.1093/mnras/stx3149


Matthew Liska, Casper Hesp, Alexander Tchekhovskoy, Adam Ingram, Michiel van der Klis, and Sera Markoff: "Formation of Precessing Jets by Tilted Black-hole Discs in 3D General Relativistic MHD Simulations", Monthly Notices of the Royal Astronomical Society: Letters, Oxford University Press, Vol 474, Num 1, pp L81-L85, 2018, doi:10.1093/mnrasl/slx174


Giovanni Rillo, Miguel A. Morales, David M. Ceperley, and Carlo Pierleoni: "Coupled Electron-Ion Monte Carlo Simulation of Hydrogen Molecular Crystals", Journal of Chemical Physics, AIP Publishing, Vol 148, Num 10, pp 102314, 2018, doi:10.1063/1.5001387


C. Ritter, R. Andrassy, B. Côté, F. Herwig, P. R. Woodward, M. Pignatari, and S. Jones: "Convective-reactive nucleosynthesis of K, Sc, Cl and p-process isotopes in O-C shell mergers", Monthly Notices of the Royal Astronomical Society: Letters, Royal Astronomical Society, Vol 474, Num 1, pp L1–L6, 2018, doi:10.1093/mnrasl/slx126


Balaji Selvam, Zahra Shamsi, and Diwakar Shukla: "Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors", Angewandte Chemie International Edition, Wiley-Blackwell, Vol 57, Num 12, pp 3048-3053, 2018, doi:10.1002/anie.201708889


David M. Bianchi, Joseph R. Peterson, Tyler M. Earnest, Michael J. Hallock, and Zaida Luthey-Schulten: "Hybrid CME-ODE Method for Efficient Simulation of the Galactose Switch in Yeast", IET Systems Biology, Institution of Engineering and Technology (IET), Vol 12, Num 4, pp 170-176, 2018, doi:10.1049/iet-syb.2017.0070


Bin Peng, Kaiyu Guan, Min Chen, David M. Lawrence, Yadu Pokhrel, Andrew Suyker, Timothy Arkebauer, and Yaqiong Lu: "Improving Maize Growth Processes in the Community Land Model: Implementation and Evaluation", Agricultural and Forest Meteorology, Elsevier BV, Vol 250-251, pp 64-89, 2018, doi:10.1016/j.agrformet.2017.11.012


Santosh Pokhrel, Miguel Rodriguez, Alireza Samimi, Gerd Heber, and Jamesina J. Simpson: "Parallel I/O for 3-D global FDTD Earth-ionosphere waveguide models at resolutions on the order of ~1 km and higher using HDF5", IEEE Transactions on Antennas and Propagation, Institute of Electrical and Electronics Engineers, Vol 66, Num 7, pp 3548-3555, 2018, doi:10.1109/tap.2018.2835163


Bach T. Nguyen, Alireza Samimi, Stephen Wiechecki Vergara, Costas D. Sarris, and Jamesina J. Simpson: "Analysis of Electromagnetic Wave Propagation in Variable Magnetized Plasma via Polynomial Chaos Expansion", IEEE Transactions on Antennas and Propagation, Institute of Electrical and Electronics Engineers, Vol 67, Num 1, pp 438-449, 2018, doi:10.1109/tap.2018.2879676


Bach T. Nguyen, Stephen Wiechecki Vergara, Costas D. Sarris, and Jamesina J. Simpson: "Ionospheric Variability Effects on Impulsive ELF Antipodal Propagation About the Earth-Sphere", IEEE Transactions on Antennas and Propagation, Institute of Electrical and Electronics Engineers, Vol 66, Num 11, pp 6244-6254, 2018, doi:10.1109/tap.2018.2874478


H. Sahasrabudhe, B. Novakovic, J. Nakamura, S. Fallahi, M. Povolotskyi, G. Klimeck, R. Rahman, and M. J. Manfra: "Optimization of Edge State Velocity in the Integer Quantum Hall Regime", Physical Review B, American Physical Society, Vol 97, Num 8, pp 085302, 2018, doi:10.1103/physrevb.97.085302


Daniel Valencia, Evan Wilson, Zhengping Jiang, Gustavo A. Valencia-Zapata, Kuang-Chung Wang, Gerhard Klimeck, and Michael Povolotskyi: "Grain-Boundary Resistance in Copper Interconnects: From an Atomistic Model to a Neural Network", Physical Review Applied, American Physical Society, Vol 9, Num 4, pp 044005, 2018, doi:10.1103/physrevapplied.9.044005


JaeHyuk Kwack and Gregory H. Bauer: "HPCG and HPGMG benchmark tests on Multiple Program, Multiple Data (MPMD) mode on Blue Waters", Concurrency and Computation: Practice and Experience, John Wiley & Sons, Inc., Vol 30, Num 1 (Special issue of the Cray User Group, CUG 2017), pp e4298, Redmond, Washington, U.S.A., 2018, doi:10.1002/cpe.4298


Reuben Budiardja, Timothy Bouvet, and Galen Arnold: "Application-level regression testing framework using Jenkins", Concurrency and Computation: Practice and Experience, John Wiley & Sons, Inc., Vol 30, Num 1 (Special issue of the Cray User Group, CUG 2017), pp e4339, Redmond, Washington, U.S.A., 2018, doi:10.1002/cpe.4339


Cole M. Johnson, Alexander E. Doran, Seiichiro L. Ten-no, and So Hirata: "Monte Carlo Explicitly Correlated Many-Body Green's Function Theory", Journal of Chemical Physics, AIP Publishing, Vol 149, Num 17, pp 174112, 2018, doi:10.1063/1.5054610


Nancy Makri: "Quantum-Classical Path Integral Simulation of Charge Transfer Reactions", 2017 Blue Waters Annual Report, pp 222-223, 2018


Daniel George and E.A. Huerta: "Deep Learning for Real-Time Gravitational Wave Detection and Parameter Estimation: Results with Advanced LIGO Data", Physics Letters B, Elsevier BV, Vol 778, pp 64-70, 2018, doi:10.1016/j.physletb.2017.12.053


Lauren Foster and Reed Maxwell: "Sensitivity analysis of hydraulic conductivity and Manning's n parameters lead to new method to scale effective hydraulic conductivity across model resolutions", Hydrological Processes, Wiley, Vol 33, Num 3, pp 332-349, 2018, doi:10.1002/hyp.13327


Matthew S. Clement, Nathan A. Kaib, Sean N. Raymond, and Kevin J. Walsh: "Mars' Growth Stunted by an Early Giant Planet Instability", Icarus, Elsevier BV, Vol 311, Num 33, pp 340-356, 2018, doi:10.1016/j.icarus.2018.04.008


M. Gazzola, L. H. Dudte, A. G. McCormick, and L. Mahadevan: "Forward and Inverse Problems in the Mechanics of Soft Filaments", Royal Society Open Science, The Royal Society, Vol 5, Num 6, pp 171628, 2018, doi:10.1098/rsos.171628


Saurabh S. Sawant, Ozgur Tumuklu, Revathi Jambunathan, and Deborah A. Levin: "Application of Adaptively Refined Unstructured Grids in DSMC to Shock Wave Simulations", Computers & Fluids, Elsevier BV, Vol 170, pp 197-212, 2018, doi:10.1016/j.compfluid.2018.04.026


Michael Nute, Ehsan Saleh, and Tandy Warnow: "Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets", Systematic Biology, Society of Systematic Biologists, Vol 68, Num 3, pp 396-411, 2018, doi:10.1093/sysbio/syy068


Michael Nute, Jed Chou, Erin K. Molloy, and Tandy Warnow: "The Performance of Coalescent-Based Species Tree Estimation Methods Under Models of Missing Data", BMC Genomics, Springer Nature, Vol 19, Num S5, pp 80, 2018, doi:10.1186/s12864-018-4619-8


Wendy K. Tam Cho and Yan Y. Liu: "Sampling from complicated and unknown distributions: Monte Carlo and Markov Chain Monte Carlo methods for redistricting", Physica A: Statistical Mechanics and its Applications, Elsevier BV, Vol 506, pp 170-178, 2018, doi:10.1016/j.physa.2018.03.096


Gelson J. Pagan-Diaz, Xiaotian Zhang, Lauren Grant, Yongdeok Kim, Onur Aydin, Caroline Cvetkovic, Eunkyung Ko, Emilia Solomon, Jennifer Hollis, Hyunjoon Kong, Taher Saif, Mattia Gazzola, and Rashid Bashir: "Simulation and Fabrication of Stronger, Larger, and Faster Walking Biohybrid Machines", Advanced Functional Materials, Wiley, pp 1801145, 2018, doi:10.1002/adfm.201801145


Chakraborty, B., Davies, C. T. H., DeTar, C., El-Khadra, A. X., Gámiz, E., Gottlieb, Steven, Hatton, D., Koponen, J., Kronfeld, A. S., Laiho, J., Lepage, G. P., Liu, Yuzhi, Mackenzie, P. B., McNeile, C., Neil, E. T., Simone, J. N., Sugar, R., Toussaint, D., Van de Water, R. S., and Vaquero, A.: "Strong-Isospin-Breaking Correction to the Muon Anomalous Magnetic Moment from Lattice QCD at the Physical Point", Physical Review Letters, American Physical Society, Vol 120, Num 15, pp 152001, 2018, doi:10.1103/physrevlett.120.152001


Benjamin Villalonga, Xiongjie Yu, David J. Luitz, and Bryan K. Clark: "Exploring One-Particle Orbitals in Large Many-Body Localized Systems", Physical Review B, American Physical Society, Vol 97, Num 10, pp 104406, 2018, doi:10.1103/physrevb.97.104406


Eli Chertkov and Bryan K. Clark: "Computational Inverse Method for Constructing Spaces of Quantum Models from Wave Functions", Physical Review X, American Physical Society, Vol 8, Num 3, pp 031029, 2018, doi:10.1103/physrevx.8.031029


Molloy, Erin K. and Warnow, Tandy: "To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods", Systematic Biology, Oxford University Press, Vol 67, Num 2, pp 285-303, 2018, doi:10.1093/sysbio/syx077


Yunan Luo, Kaiyu Guan, and Jian Peng: "STAIR: A Generic and Fully-Automated Method to Fuse Multiple Sources of Optical Satellite Data to Generate a High-Resolution, Daily and Cloud-/Gap-Free Surface Reflectance Product", Remote Sensing of Environment, Elsevier BV, Vol 214, pp 87-99, 2018, doi:10.1016/j.rse.2018.04.042


Yaping Cai, Kaiyu Guan, Jian Peng, Shaowen Wang, Christopher Seifert, Brian Wardlow, and Zhan Li: "A High-Performance and In-Season Classification System of Field-Level Crop Types Using Time-Series Landsat Data and a Machine Learning Approach", Remote Sensing of Environment, Elsevier BV, Vol 210, pp 35-47, 2018, doi:10.1016/j.rse.2018.02.045


Michael P. Howard, Athanassios Z. Panagiotopoulos, and Arash Nikoubashman: "Efficient Mesoscale Hydrodynamics: Multiparticle Collision Dynamics with Massively Parallel GPU Acceleration", Computer Physics Communications, Elsevier BV, Vol 230, pp 10-20, 2018, doi:10.1016/j.cpc.2018.04.009


Rachael A. Mansbach and Andrew L. Ferguson: "Patchy Particle Model of the Hierarchical Self-Assembly of pi-Conjugated Optoelectronic Peptides", Journal of Physical Chemistry B, American Chemical Society, Vol 122, Num 44, pp 10219-10236, 2018, doi:10.1021/acs.jpcb.8b05781


Maureen T. Brooks, V. J. Coles, R. R. Hood, and J. F. R. Gower: "Factors Controlling the Seasonal Distribution of Pelagic Sargassum", Marine Ecology Progress Series, Inter-Research Science Center, Vol 599, pp 1-18, 2018, doi:10.3354/meps12646


Jiashun Hu, Lijun Liu, Manuele Faccenda, Quan Zhou, Karen M. Fischer, Stephen Marshak, and Craig Lundstrom: "Modification of the Western Gondwana Craton by Plume-Lithosphere Interaction", Nature Geoscience, Springer Nature, Vol 11, pp 203–210, 2018, doi:10.1038/s41561-018-0064-1


Andrew Reisner, Luke N. Olson, and J. David Moulton: "Scaling Structured Multigrid to 500K+ Cores Through Coarse-Grid Redistribution", SIAM Journal on Scientific Computing, Society for Industrial & Applied Mathematics, Vol 40, Num 4, pp C581-C604, 2018, doi:10.1137/17m1146440


Jiangyan Feng and Diwakar Shukla: "Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings", Journal of Physical Chemistry B, American Chemical Society, Vol 122, Num 3, pp 1017-1025, 2018, doi:10.1021/acs.jpcb.7b07529


Shriyaa Mittal and Diwakar Shukla: "Recruiting Machine Learning Methods for Molecular Simulations of Proteins", Molecular Simulation, Informa UK Limited, pp 1-14, 2018, doi:10.1080/08927022.2018.1448976


Balaji Selvam, Shriyaa Mittal, and Diwakar Shukla: "Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter", ACS Central Science, American Chemical Society, Vol 4, Num 9, pp 1146-1154, 2018, doi:10.1021/acscentsci.8b00330


Zahra Shamsi, Kevin J. Cheng, and Diwakar Shukla: "Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes", Journal of Physical Chemistry B, American Chemical Society, Vol 122, Num 35, pp 8386-8395, 2018, doi:10.1021/acs.jpcb.8b06521


Yingxue Ren, Joseph S. Reddy, Cyril Pottier, Vivekananda Sarangi, Shulan Tian, Jason P. Sinnwell, Shannon K. McDonnell, Joanna M. Biernacka, Minerva M. Carrasquillo, Owen A. Ross, Nilüfer Ertekin-Taner, Rosa Rademakers, Matthew Hudson, Liudmila Sergeevna Mainzer, and Yan W. Asmann: "Identification of Missing Variants by Combining Multiple Analytic Pipelines", BMC Bioinformatics, Springer Nature, Vol 19, Num 1, pp 139, 2018, doi:10.1186/s12859-018-2151-0


Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, and Tandy Warnow: "OCTAL: Optimal Completion of Gene Trees in Polynomial Time", Algorithms for Molecular Biology, Springer Nature, Vol 13, Num 1, pp 6, 2018, doi:10.1186/s13015-018-0124-5


M. P. Clay, D. Buaria, P. K. Yeung, and T. Gotoh: "GPU Acceleration of a Petascale Application for Turbulent Mixing at High Schmidt Number Using OpenMP 4.5", Computer Physics Communications, Elsevier BV, Vol 228, pp 100-114, 2018, doi:10.1016/j.cpc.2018.02.020


Marcelo C. R. Melo, Rafael C. Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C. Phillips, Julio D. C. Maia, Gerd B. Rocha, João V. Ribeiro, John E. Stone, Frank Neese, Klaus Schulten, and Zaida Luthey-Schulten: "NAMD Goes Quantum: An Integrative Suite for Hybrid Simulations", Nature Methods, Springer Nature, Vol 15, pp 351-354, 2018, doi:10.1038/nmeth.4638


Yuzhi Liu, Jon A. Bailey, A. Bazavov, C. Bernard, C. M. Bouchard, C. DeTar, Daping Du, A. X. El-Khadra, E. D. Freeland, E. Gámiz, Z. Gelzer, Steven Gottlieb, U. M. Heller, A. S. Kronfeld, J. Laiho, P. B. Mackenzie, Y. Meurice, E. T. Neil, J. N. Simone, R. Sugar, D. Toussaint, R. S. Van de Water, and Ran Zhou: "Bs. Klv. Form Factors with 2+1 Flavors", EDP Sciences, EPJ Web of Conferences (35th International Symposium on Lattice Field Theory, Lattice 2017), Vol 175, pp 13008, Granada, Spain, 2018, doi:10.1051/epjconf/201817513008


Christian D. Ott, Luke F. Roberts, André da Silva Schneider, Joseph M. Fedrow, Roland Haas, and Erik Schnetter: "The Progenitor Dependence of Core-collapse Supernovae from Three-dimensional Simulations with Progenitor Models of 12-40 M-circle dot", Astrophysical Journal Letters, The American Astronomical Society, Vol 855, Num 1, pp L3, 2018, doi:10.3847/2041-8213/aaa967


Lukas F. Milles, Klaus Schulten, Hermann E. Gaub, and Rafael C. Bernardi: "Molecular Mechanism of Extreme Mechanostability in a Pathogen Adhesin", Science, American Association for the Advancement of Science, Vol 359, Num 6383, pp 1527-1533, 2018, doi:10.1126/science.aar2094


Tarek A. Ameen, Hesameddin Ilatikhameneh, Archana Tankasala, Yuling Hsueh, James Charles, Jim Fonseca, Michael Povolotskyi, Jun Oh Kim, Sanjay Krishna, Monica S. Allen, Jeffery W. Allen, Rajib Rahman, and Gerhard Klimeck: "Theoretical Study of Strain-Dependent Optical Absorption in a Doped Self-Assembled InAs/InGaAs/GaAs/AlGaAs Quantum Dot", Beilstein Journal of Nanotechnology, Beilstein Institut, Vol 9, pp 1075-1084, 2018, doi:10.3762/bjnano.9.99


Rinat Khaziev and Davide Curreli: "hPIC: A Scalable Electrostatic Particle-in-Cell for Plasma-Material Interactions", Computer Physics Communications, Elsevier BV, Vol 229, pp 87-98, 2018, doi:10.1016/j.cpc.2018.03.028


O. E. B. Messer, J. A. Harris, W. R. Hix, E. J. Lentz, S. W. Bruenn, and A. Mezzacappa: "Multi-Dimensional Simulations of Core-Collapse Supernova Explosions with CHIMERA ", American Institute of Physics, AIP Conference Proceedings (14th International Symposium on Origin of Matter and Evolution of Galaxies, OMEG 2017), Vol 1947, Num 1, pp 020017, Daejeon, Korea, 2018, doi:10.1063/1.5030821


Pablo Villanueva-Domingo, Nickolay Y. Gnedin, and Olga Mena: "Warm Dark Matter and Cosmic Reionization", Astrophysical Journal, The American Astronomical Society, Vol 852, Num 2, pp 139, 2018, doi:10.3847/1538-4357/aa9ff5


Abid Khan, Vasileios Paschalidis, Milton Ruiz, and Stuart L. Shapiro: "Disks Around Merging Binary Black Holes: From GW150914 to Supermassive Black Holes", Physical Review D, The American Physical Society, Vol 97, Num 4, pp 044036, 2018, doi:10.1103/physrevd.97.044036


Curtis L. Johnson, Hillary Schwarb, Kevin M. Horecka, Matthew D.J. McGarry, Charles H. Hillman, Arthur F. Kramer, Neal J. Cohen, and Aron K. Barbey: "Double Dissociation of Structure-Function Relationships in Memory and Fluid Intelligence Observed with Magnetic Resonance Elastography", NeuroImage, Elsevier BV, Vol 171, pp 99-106, 2018, doi:10.1016/j.neuroimage.2018.01.007


Pierrot Derjany and Sirish Namilae: "Computational Model for Pedestrian Movement and Infectious Diseases Spread During Air Travel", American Institute of Aeronautics and Astronautics, 2018 AIAA Modeling and Simulation Technologies Conference, Kissimmee, Florida, U.S.A., 2018, doi:10.2514/6.2018-0419


Doriam Restrepo and Ricardo Taborda: "Multiaxial Cyclic Plasticity in Accordance with 1D Hyperbolic Models and Masing Criteria", International Journal for Numerical and Analytical Methods in Geomechanics, Wiley, Vol 42, Num 17, pp 2095-2108, 2018, doi:10.1002/nag.2845


Alberto Perez, Florian Sittel, Gerhard Stock, and Ken Dill: "MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths", Journal of Chemical Theory and Computation, American Chemical Society, Vol 14, Num 4, pp 2109-2116, 2018, doi:10.1021/acs.jctc.7b01294


Amir Barati Farimani, Mohammad Heiranian, and Narayana R. Aluru: "Identification of Amino Acids with Sensitive Nanoporous MoS2: Towards Machine Learning-Based Prediction", npj 2D Materials and Applications, Springer Nature, Vol 2, Num 1, pp 14, 2018, doi:10.1038/s41699-018-0060-8


Alexander Ohmann, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N. Baumann, Kerstin Göpfrich, Jejoong Yoo, Ulrich F. Keyser, and Aleksei Aksimentiev: "A synthetic enzyme built from DNA flips 10^7 lipids per second in biological membranes", Nature Communications, Springer Nature Limited, Vol 9, Num 1, pp 2426, 2018, doi:10.1038/s41467-018-04821-5


M. Burrows, Ch. Elster, G. Popa, K. D. Launey, A. Nogga, and P. Maris: "Ab Initio Translationally Invariant Nonlocal One-Body Densities from No-Core Shell-Model Theory", Physical Review C, American Physical Society, Vol 97, Num 2, pp 024325, 2018, doi:10.1103/physrevc.97.024325


Jerry P. Draayer, Kristina D. Launey, Tomáš Dytrych, Alison C. Dreyfuss, Grigor H. Sargsyan, and Robert B. Baker: "Untangling Simple Patterns in Intricate Atomic Nuclei", World Scientific, Walter Greiner Memorial Volume, pp 97-121, 2018, doi:10.1142/9789813234284_0008


Tremmel, M. Governato, F., Volonteri, M., Quinn, T. R., and Pontzen, A.: "Dancing to CHANGA: a self-consistent prediction for close SMBH pair formation time-scales following galaxy mergers", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 475, Num 4, pp 4967-4977, 2018, doi:10.1093/mnras/sty139


Michael Tremmel, Fabio Governato, Marta Volonteri, Andrew Pontzen, and Thomas R. Quinn: "Wandering Supermassive Black Holes in Milky-Way-mass Halos", Astrophysical Journal Letters, The American Astronomical Society, Vol 857, Num 2, pp L22, 2018, doi:10.3847/2041-8213/aabc0a


Dennis B. Bowen, Vassilios Mewes, Manuela Campanelli, Scott C. Noble, Julian H. Krolik, and Miguel Zilhão: "Quasi-periodic Behavior of Mini-disks in Binary Black Holes Approaching Merger", Astrophysical Journal Letters, The American Astronomical Society, Vol 853, Num 1, pp L17, 2018, doi:10.3847/2041-8213/aaa756


Alexander Lindsay, Gavin Ridley, Andrei Rykhlevskii, and Kathryn Huff: "Introduction to Moltres: An application for simulation of Molten Salt Reactors", Annals of Nuclear Energy, Elsevier B.V., Vol 114, pp 530 - 540, 2018, doi:10.1016/j.anucene.2017.12.025


Alexander Lindsay and Kathryn Huff: "Moltres: Finite Element Based Simulation of Molten Salt Reactors", Journal of Open Source Software, The Open Journal, Vol 3, Num 21, pp 298, 2018, doi:10.21105/joss.00298


Alex Lindsay; Gavin Ridley; Cody Permann; Katy Huff; John W. Peterson; Andrew E Slaughter; Derek Gaston; David Andrs; Robert Carlsen; and Andrei Rykhlevskii: "arfc/moltres: Add CHI\_D; some minor changes for publication", Zenodo, Zenodo (website), Num 3.0, 2018, doi:10.5281/zenodo.1137726


Hui Li and Ryan L. Sriver: "Impact of Tropical Cyclones on the Global Ocean: Results from Multidecadal Global Ocean Simulations Isolating Tropical Cyclone Forcing", Journal of Climate, American Meteorological Society, Vol 31, Num 21, pp 8761-8784, 2018, doi:10.1175/jcli-d-18-0221.1


Kuan-Wei Huang, Tiziana Di Matteo, Aklant K. Bhowmick, Yu Feng, and Chung-Pei Ma: "BlueTides simulation: establishing black hole-galaxy relations at high-redshift", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 478, Num 4, pp 5063–5073, 2018, doi:10.1093/mnras/sty1329


Wilkins, Stephen M., Feng, Yu, Di Matteo, Tiziana, Croft, Rupert, Lovell, Christopher C., and Thomas, Peter: "Dust-obscured star-forming galaxies in the early universe", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 473, Num 4, pp 5363-5369, 2018, doi:10.1093/mnras/stx2588


Tenneti, Ananth, Di Matteo, Tiziana, Croft, Rupert, Garcia, ThomasJae, and Feng, Yu: "The descendants of the first quasars in the BlueTides simulation", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 474, Num 1, pp 597-603, 2018, doi:10.1093/mnras/stx2788


Yueying Ni, Tiziana Di Matteo, Yu Feng, Rupert A. C. Croft, and Ananth Tenneti: "Gas outflows from the z = 7.54 quasar: Predictions from the BLUETIDES simulation", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 481, Num 4, pp 4877-4884, 2018, doi:10.1093/mnras/sty2616


Hitesh J. Changlani, Dmitrii Kochkov, Krishna Kumar, Bryan K. Clark, and Eduardo Fradkin: "Macroscopically Degenerate Exactly Solvable Point in the Spin-1/2 Kagome Quantum Antiferromagnet", Physical Review Letters, American Physical Society, Vol 120, Num 11, pp 117202, 2018, doi:10.1103/physrevlett.120.117202


Xiongjie Yu, Di Luo, and Bryan K. Clark: "Beyond Many-Body Localized States in a Spin-Disordered Hubbard Model", Physical Review B, American Physical Society, Vol 98, Num 11, pp 115106, 2018, doi:10.1103/physrevb.98.115106


S. A. Beig, B. Aboulhasanzadeh, and E. Johnsen: "Temperatures Produced by Inertially Collapsing Bubbles Near Rigid Surfaces", Journal of Fluid Mechanics, Cambridge University Press, Vol 852, pp 105-125, 2018, doi:10.1017/jfm.2018.525


Jodi A. Hadden, Juan R. Perilla, Christopher John Schlicksup, Balasubramanian Venkatakrishnan, Adam Zlotnick, and Klaus Schulten: "All-Atom Molecular Dynamics of the HBV Capsid Reveals Insights Into Biological Function and Cryo-EM Resolution Limits", eLife, eLife Sciences Organisation, Ltd., Vol 7, 2018, doi:10.7554/elife.32478


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Chenglin Yi, Soumendu Bagchi, Christopher M. Dmuchowski, Feilin Gou, Xiaoming Chen, Cheol Park, Huck Beng Chew, and Changhong Ke: "Direct Nanomechanical Characterization of Carbon Nanotubes - Titanium Interfaces", Carbon, Elsevier BV, Vol 132, pp 548-555, 2018, doi:10.1016/j.carbon.2018.02.069


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Iryna S. Butsky and Thomas R. Quinn: "The Role of Cosmic Ray Transport in Shaping the Simulated Circumgalactic Medium", Astrophysical Journal, The American Astronomical Society, Vol 868, Num 2, pp 108, 2018, doi:10.3847/1538-4357/aaeac2


William D. Gropp: "Using Node Information to Implement MPI Cartesian Topologies", ACM Press, Proceedings of the 25th European MPI Users' Group Meeting (EuroMPI '18), pp 18:1-18:9, Barcelona, Spain, 2018, doi:10.1145/3236367.3236377


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Astrid Lamberts, Shea Garrison-Kimmel, Philip Hopkins, Eliot Quataert, James Bullock, Claude-André Faucher-Giguère, Andrew Wetzel, Dusan Kereš, Kaliden Drango, and Robyn Sanderson: "Predicting the binary black hole population of the Milky Way with cosmological simulations", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 480, Num 2, pp 2704-2718, 2018, doi:10.1093/mnras/sty2035


Robyn E. Sanderson, Shea Garrison-Kimmel, Andrew Wetzel, Tsang Keung Chan, Philip F. Hopkins, Dušan Kereš, Ivanna Escala, Claude-André Faucher-Giguère, and Xiangcheng Ma: "Reconciling Observed and Simulated Stellar Halo Masses", Astrophysical Journal, The American Astronomical Society, Vol 869, Num 1, pp 12, 2018, doi:10.3847/1538-4357/aaeb33


Shea Garrison-Kimmel, Philip F. Hopkins, Andrew Wetzel, Kareem El-Badry, Robyn E. Sanderson, James S. Bullock, Xiangcheng Ma, Freeke van de Voort, Zachary Hafen, Claude-André Faucher-Giguère, Christopher C. Hayward, Eliot Quataert, Dusan Keres, and Michael Boylan-Kolchin: "The origin of the diverse morphologies and kinematics of Milky Way-mass galaxies in the FIRE-2 simulations", Monthly Notices of the Royal Astronomical Society, Tthe Royal Astronomical Society, Vol 481, Num 3, pp 4133-4157, 2018, doi:10.1093/mnras/sty2513


James Healy, Jacob Lange, Richard O'Shaughnessy, Carlos Lousto, Manuela Campanelli, Andrew Williamson, Yosef Zlochower, Juan Calderon Bustillo, James Clark, Christopher Evans, D. Ferguson, Sudarshan Ghonge, Karan Jani, Bhavesh Khamesra, Pablo Laguna, Deirdre M. Shoemaker, Alyssa Garcia, Michael Boyle, Daniel Hemberger, Lawrence Kidder, Prayush Kumar, Geoffrey Lovelace, Harald Pfeiffer, Mark Scheel, and Saul Teukolsky: "Targeted Numerical Simulations of Binary Black Holes for GW170104", Physical Review D, American Physical Society, Vol 97, Num 6, pp 064027, 2018, doi:10.1103/physrevd.97.064027


Wei-dong Sun, Li-jun Liu, Yong-bing Hu, Wei Ding, Ji-qiang Liu, Ming-xing Ling, Xing Ding, Zhao-feng Zhang, Xin-lei Sun, Cong-ying Li, He Li, and Wei-ming Fan: "Post-Ridge-Subduction Acceleration of the Indian Plate Induced by Slab Rollback", Solid Earth Sciences, Elsevier BV, Vol 3, Num 1, pp 1-7, 2018, doi:10.1016/j.sesci.2017.12.003


Feng Pan, Xiaoxue Ding, Kristina D. Launey, and J. P. Draayer: "A simple procedure for construction of the orthonormal basis vectors of irreducible representations of 0(5) in the 0(T)(3) 0(N)(2) basis", Nuclear Physics A, Elsevier BV, Vol 974, pp 86-105, 2018, doi:10.1016/j.nuclphysa.2018.03.011


Feng Pan, Xiaoxue Ding, Kristina D. Launey, Lianrong Dai, and Jerry P. Draayer: "Exact Solution of Mean-Field Plus an Extended T = 1 Nuclear Pairing Hamiltonian in the Seniority-Zero Symmetric Subspace", Physics Letters B, Elsevier BV, Vol 780, pp 1-6, 2018, doi:10.1016/j.physletb.2018.02.054


Justin A. Drake and B. Montgomery Pettitt: "Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model", Biophysical Journal, Elsevier BV, Vol 114, Num 12, pp 2799-2810, 2018, doi:10.1016/j.bpj.2018.04.027


Andrew C. Kirby, Arash Hassanzadeh, Dimitri J. Mavriplis, and Jonathan W. Naughton: "Wind Turbine Wake Dynamics Analysis Using a High-Fidelity Simulation Framework with Blade-Resolved Turbine Models", American Institute of Aeronautics and Astronautics, 2018 Wind Energy Symposium, Kissimmee, Florida, U.S.A., 2018, doi:10.2514/6.2018-0256


Andrew C. Kirby, Zhi Yang, Dimitri J. Mavriplis, Earl P. Duque, and Brad J. Whitlock: "Visualization and Data Analytics Challenges of Large-Scale High-Fidelity Numerical Simulations of Wind Energy Applications", American Institute of Aeronautics and Astronautics, 2018 AIAA Aerospace Sciences Meeting, Kissimmee, Florida, U.S.A., 2018, doi:10.2514/6.2018-1171


Amanda Bienz, William D. Gropp, and Luke N. Olson: "Improving Performance Models for Irregular Point-to-Point Communication", ACM Press, Proceedings of the 25th European MPI Users' Group Meeting (EuroMPI '18), pp 7:1-7:8, Barcelona, Spain, 2018, doi:10.1145/3236367.3236368


Alireza Moradzadeh, Mohammad H. Motevaselian, Sikandar Y. Mashayak, and Narayana R. Aluru: "Coarse-Grained Force Field for Imidazolium-Based Ionic Liquids", Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 14, Num 6, pp 3252-3261, 2018, doi:10.1021/acs.jctc.7b01293


Jumana Dakka, Kristof Farkas-Pall, Matteo Turilli, David W. Wright, Peter V. Coveney, and Shantenu Jha: "Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations", Institute of Electrical & Electronics Engineers, 2018 IEEE 14th International Conference on e-Science (e-Science), pp 189-200, Amsterdam, Netherlands, 2018, doi:10.1109/eScience.2018.00034


Britton D. Smith, John A. Regan, Turlough P. Downes, Michael L. Norman, Brian W. O’Shea, and John H Wise: "The growth of black holes from Population III remnants in the Renaissance simulations", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 480, Num 3, pp 3762-3773, 2018, doi:10.1093/mnras/sty2103


Samuel R. Totorica, Frederico Fiuza, and Tom Abel: "A New Method for Analyzing and Visualizing Plasma Simulations Using a Phase-Space Tessellation", Physics of Plasmas, AIP Publishing, Vol 25, Num 7, pp 072109, 2018, doi:10.1063/1.5037348


Lian Duan, Meelan M. Choudhari, Amanda Chou, Federico Munoz, S.R.C. Ail, Rolf Radespiel, Thomas Schilden, Wolfgang Schroeder, Eric C. Marineau, Katya M. Casper, Ross S. Chaudhry, Graham V. Candler, Kathryn A. Gray, Cameron J. Sweeney, and Steven P. Schneider: "Characterization of Freestream Disturbances in Conventional Hypersonic Wind Tunnels", American Institute of Aeronautics and Astronautics, 2018 AIAA Aerospace Sciences Meeting, Kissimmee, Florida, U.S.A., 2018, doi:10.2514/6.2018-0347


Mohammed El-Kebir: "SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error", Bioinformatics, Oxford University Press, Vol 34, Num 17, pp i671-i679, 2018, doi:10.1093/bioinformatics/bty589


P. K. Yeung, K. R. Sreenivasan, and S. B. Pope: "Effects of Finite Spatial and Temporal Resolution in Direct Numerical Simulations of Incompressible Isotropic Turbulence", Physical Review Fluids, American Physical Society, Vol 3, Num 6, pp 064603, 2018, doi:10.1103/physrevfluids.3.064603


Pengyu Long, Jun Z. Huang, Michael Povolotskyi, Prasad Sarangapani, Gustavo A. Valencia-Zapata, Tillmann Kubis, Mark J. W. Rodwell, and Gerhard Klimeck: "Atomistic Modeling Trap-Assisted Tunneling in Hole Tunnel Field Effect Transistors", Journal of Applied Physics, AIP Publishing, Vol 123, Num 17, pp 174504, 2018, doi:10.1063/1.5018737


Yi-Hsin Liu, M. Hesse, T. C. Li, M. Kuznetsova, and A. Le: "Orientation and Stability of Asymmetric Magnetic Reconnection X Line", Journal of Geophysical Research: Space Physics, American Geophysical Union, Vol 123, Num 6, pp 4908-4920, 2018, doi:10.1029/2018ja025410


A. Le, W. Daughton, O. Ohia, L.-J. Chen, Y.-H. Liu, S. Wang, W. D. Nystrom, and R. Bird: "Drift Turbulence, Particle Transport, and Anomalous Dissipation at the Reconnecting Magnetopause", Physics of Plasmas, AIP Publishing, Vol 25, Num 6, pp 062103, 2018, doi:10.1063/1.5027086


G. R. Marion and R. J. Trapp: "The Dynamical Coupling of Convective Updrafts, Downdrafts, and Cold Pools in Simulated Supercell Thunderstorms", Journal of Geophysical Research: Atmospheres, American Geophysical Union, Vol 124, Num 2, pp 664-683, 2018, doi:10.1029/2018jd029055


Jing Li, Jared Ostmeyer, Luis G. Cuello, Eduardo Perozo, and Benoît Roux: "Rapid constriction of the selectivity filter underlies C-type inactivation in the KcsA potassium channel", Journal of General Physiology, Rockefeller University Press, Vol 150, Num 10, pp 1408-1420, 2018, doi:10.1085/jgp.201812082


Huan Rui, Avisek Das, Robert Nakamoto, and Benoît Roux: "Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump", Journal of Molecular Biology, Elsevier BV, Vol 430, Num 24, pp 5050-5065, 2018, doi:10.1016/j.jmb.2018.10.014


Lawrence R. Frank, Vitaly L. Galinsky, Leigh Orf, and Joshua Wurman: "Dynamic Multiscale Modes of Severe Storm Structure Detected in Mobile Doppler Radar Data by Entropy Field Decomposition", Journal of the Atmospheric Sciences, American Meteorological Society, Vol 75, Num 3, pp 709-730, 2018, doi:10.1175/jas-d-17-0117.1


R. Borrell, J.C. Cajas, D. Mira, A. Taha, S. Koric, M. Vázquez, and G. Houzeaux: "Parallel Mesh Partitioning Based on Space Filling Curves", Computers & Fluids, Elsevier BV, Vol 173, pp 264-272, 2018, doi:10.1016/j.compfluid.2018.01.040


Alexandra L. Jones: "Alexandraljones/Mcbrat3D: Initial Public Release", Zenodo, Zenodo (website), 2018, doi:10.5281/zenodo.1313839


Ui-Han Zhang, Hsi-Yu Schive, and Tzihong Chiueh: "Magnetohydrodynamics with GAMER", Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 236, Num 2, pp 50, 2018, doi:10.3847/1538-4365/aac49e


Hsi-Yu Schive, John A. ZuHone, Nathan J. Goldbaum, Matthew J. Turk, Massimo Gaspari, and Chin-Yu Cheng: "GAMER-2: a GPU-accelerated adaptive mesh refinement code -- accuracy, performance, and scalability", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 481, Num 4, pp 4815-4840, 2018, doi:10.1093/mnras/sty2586


Larissa J. Reames and David J. Stensrud: "Influence of a Great Plains Urban Environment on a Simulated Supercell", Monthly Weather Review, American Meteorological Society, Vol 146, Num 5, pp 1437-1462, 2018, doi:10.1175/mwr-d-17-0284.1


Falk Herwig, Robert Andrassy, Nic Annau, Ondrea Clarkson, Benoit Côté, Aaron D’Sa, Sam Jones, Belaid Moa, Jericho O’Connell, David Porter, Christian Ritter, and Paul Woodward: "Cyberhubs: Virtual Research Environments for Astronomy", Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 236, Num 1, pp 2, 2018, doi:10.3847/1538-4365/aab777


Paul R. Woodward, Falk Herwig, and Ted Wetherbee: "Simulating Stellar Hydrodynamics at Extreme Scale", Computing in Science & Engineering, Institute of Electrical and Electronics Engineers, Vol 20, Num 5, pp 8-17, 2018, doi:10.1109/mcse.2018.05329811


Justin Sirignano and Konstantinos Spiliopoulos: "DGM: A Deep Learning Algorithm for Solving Partial Differential Equations", Journal of Computational Physics, Elsevier BV, Vol 375, pp 1339-1364, 2018, doi:10.1016/j.jcp.2018.08.029


Justin Sirignano and Rama Cont: "Universal Features of Price Formation in Financial Markets: Perspectives from Deep Learning", Quantitative Finance, Routledge, Vol 19, Num 9, pp 1449-1459, 2018, doi:10.1080/14697688.2019.1622295


Revathi Jambunathan and Deborah A. Levin: "CHAOS: An Octree-Based PIC-DSMC Code for Modeling of Electron Kinetic Properties in a Plasma Plume Using MPI-CUDA Parallelization", Journal of Computational Physics, Elsevier BV, Vol 373, pp 571-604, 2018, doi:10.1016/j.jcp.2018.07.005


Vincenzo Carnevale: "Protonation Underlies Tonic vs. Use-Dependent Block", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 115, Num 14, pp 3512-3514, 2018, doi:10.1073/pnas.1802178115


Marina A. Kasimova, Aysenur Yazici, Yevgen Yudin, Daniele Granata, Michael L. Klein, Tibor Rohacs, and Vincenzo Carnevale: "Ion Channel Sensing: Are Fluctuations the Crux of the Matter?", Journal of Physical Chemistry Letters, American Chemical Society, Vol 9, Num 6, pp 1260-1264, 2018, doi:10.1021/acs.jpclett.7b03396


Chuanxu Ma, Zhongcan Xiao, Alex A. Puretzky, Arthur P. Baddorf, Wenchang Lu, Kunlun Hong, J. Bernholc, and An-Ping Li: "Oxidization Stability of Atomically Precise Graphene Nanoribbons", Physical Review Materials, American Physical Society, Vol 2, Num 1, pp 014006, 2018, doi:10.1103/physrevmaterials.2.014006


Kirk S. S. Barrow, John H. Wise, Aycin Aykutalp, Brian W. O'Shea, Michael L. Norman, and Hao Xu: "First light – II. Emission line extinction, population III stars, and X-ray binaries", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 474, Num 2, pp 2617-2634, 2018, doi:10.1093/mnras/stx2973


Sudheer Chunduri, Meysam Ghaffari, Mehran Sadeghi Lahijani, Ashok Srinivasan, and Sirish Namilae: "Parallel Low Discrepancy Parameter Sweep for Public Health Policy", Institute of Electrical & Electronics Engineers, 2018 18th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), pp 291-300, Washington, D.C., U.S.A., 2018, doi:10.1109/ccgrid.2018.00044


Dinshaw S. Balsara, Sudip Garain, Allen Taflove, and Gino Montecinos: "Computational Electrodynamics in Material Media with Constraint-Preservation, Multidimensional Riemann Solvers and Sub-Cell Resolution - Part II, Higher Order FVTD Schemes", Journal of Computational Physics, Elsevier BV, Vol 354, pp 613-645, 2018, doi:10.1016/j.jcp.2017.10.013


Chang Sun, Samir Benlekbir, Padmaja Venkatakrishnan, Yuhang Wang, Sangjin Hong, Jonathan Hosler, Emad Tajkhorshid, John L. Rubinstein, and Robert B. Gennis: "Structure of the Alternative Complex III in a Supercomplex with Cytochrome Oxidase", Nature, Springer Nature, Vol 557, Num 7703, pp 123-126, 2018, doi:10.1038/s41586-018-0061-y


Ethan P. Shapera and André Schleife: "Database-Driven Materials Selection for Semiconductor Heterojunction Design", Advanced Theory and Simulations, Wiley, pp 1800075, 2018, doi:10.1002/adts.201800075


Michael R. Lawson, Wen Ma, Michael J. Bellecourt, Irina Artsimovitch, Andreas Martin, Robert Landick, Klaus Schulten, and James M. Berger: "Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein", Molecular Cell, Elsevier BV, Vol 71, Num 6, pp 911-922.e4, 2018, doi:10.1016/j.molcel.2018.07.014


Yuhang Wang, Mrinal Shekhar, Darren Thifault, Christopher J. Williams, Ryan McGreevy, Jane Richardson, Abhishek Singharoy, and Emad Tajkhorshid: "Constructing Atomic Structural Models Into Cryo-EM Densities Using Molecular Dynamics - Pros and Cons", Journal of Structural Biology, Elsevier BV, Vol 204, Num 2, pp 319-328, 2018, doi:10.1016/j.jsb.2018.08.003


Ozgur Tumuklu and Deborah A. Levin: "Particle Simulations of the Effects of Atomic Oxygen on Ion Thruster Plumes", Journal of Spacecraft and Rockets, American Institute of Aeronautics and Astronautics, pp 1-12, 2018, doi:10.2514/1.a34053


Zhuolei Zhang, Richard C. Remsing, Himanshu Chakraborty, Wenxiu Gao, Guoliang Yuan, Michael L. Klein, and Shenqiang Ren: "Light-Induced Dilation in Nanosheets of Charge-Transfer Complexes", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 115, Num 15, pp 3776-3781, 2018, doi:10.1073/pnas.1800234115


Hongwei Niu, Yuhang Jing, Yi Sun, and Narayana R. Aluru: "Ab Initio Based Interionic Potential for Silver Iodide", Solid State Ionics, Elsevier BV, Vol 325, pp 102-111, 2018, doi:10.1016/j.ssi.2018.07.027


Ketan Mittal and Paul Fischer: "Mesh Smoothing for the Spectral Element Method", Journal of Scientific Computing, Springer Nature America, Inc, Vol 78, Num 2, pp 1152–1173, 2018, doi:10.1007/s10915-018-0812-9


James Wilson and Aleksei Aksimentiev: "Water-Compression Gating of Nanopore Transport", Physical Review Letters, American Physical Society, Vol 120, Num 26, pp 268101, 2018, doi:10.1103/physrevlett.120.268101


Daniel H. Moser and Sonia Lasher-Trapp: "Cloud-Spacing Effects Upon Entrainment and Rainfall Along a Convective Line", Journal of Applied Meteorology and Climatology, American Meteorological Society, Vol 57, Num 8, pp 1865-1882, 2018, doi:10.1175/jamc-d-17-0363.1


Priyanka Samanta, Yitang Wang, Shadi Fuladi, Jinjing Zou, Ye Li, Le Shen, Christopher Weber, and Fatemeh Khalili-Araghi: "Molecular Determination of Claudin-15 Organization and Channel Selectivity", Journal of General Physiology, Rockefeller University Press, pp jgp.201711868, 2018, doi:10.1085/jgp.201711868


James W. Mazzuca and Nathaniel K. Haut: "Theoretical Description of Quantum Mechanical Permeation of Graphene Membranes by Charged Hydrogen Isotopes", Journal of Chemical Physics, AIP Publishing, Vol 148, Num 22, pp 224301, 2018, doi:10.1063/1.5027821


Som Dutta, Mark W. Van Moer, Paul Fischer, and Marcelo H. Garcia: "Visualization of the Bulle-Effect at River Bifurcations", ACM Press, PEARC '18: Proceedings of the Practice and Experience on Advanced Research Computing, pp 107:1-107:4, Pittsburgh, Pennsylvania, U.S.A., 2018, doi:10.1145/3219104.3229433


Maxim Belkin, Roland Haas, Galen Wesley Arnold, Hon Wai Leong, Eliu A. Huerta, David Lesny, and Mark Neubauer: "Container Solutions for HPC Systems", ACM Press, PEARC '18: Proceedings of the Practice and Experience on Advanced Research Computing, pp 43:1-43:8, Pittsburgh, Pennsylvania, U.S.A., 2018, doi:10.1145/3219104.3219145


Rajkumar Kettimuthu, Zhengchun Liu, David Wheeler, Ian Foster, Katrin Heitmann, and Franck Cappello: "Transferring a Petabyte in a Day", Future Generation Computer Systems-The International Journal of eScience, Elsevier BV, Vol 88, pp 191-198, 2018, doi:10.1016/j.future.2018.05.051


Santosh Pokhrel, Bach Nguyen, Miguel Rodriguez, Emanuel Bernabeu, and Jamesina J. Simpson: "A Finite Difference Time Domain Investigation of Electric Field Enhancements Along Ocean-Continent Boundaries During Space Weather Events", Journal of Geophysical Research: Space Physics, American Geophysical Union, Vol 123, Num 6, pp 5033-5046, 2018, doi:10.1029/2017ja024648


Lu Ruan, Jodi A. Hadden, and Adam Zlotnick: "Assembly Properties of Hepatitis B Virus Core Protein Mutants Correlate with Their Resistance to Assembly-Directed Antivirals", Journal of Virology, American Society for Microbiology, pp JVI.01082-18, 2018, doi:10.1128/jvi.01082-18


Sean P. Cornillie, Benjamin J. Bruno, Carol S. Lim, and Thomas E. Cheatham: "Computational Modeling of Stapled Peptides Toward a Treatment Strategy for CML and Broader Implications in the Design of Lengthy Peptide Therapeutics", Journal of Physical Chemistry B, American Chemical Society, Vol 122, Num 14, pp 3864-3875, 2018, doi:10.1021/acs.jpcb.8b01014


Rodrigo Galindo-Murillo, Thomas E. Cheatham, and Robert C. Hopkins: "Exploring Potentially Alternative Non-Canonical DNA Duplex Structures Through Simulation", Journal of Biomolecular Structure and Dynamics, Taylor & Francis, Vol 37, Num 9, pp 2201-2210, 2018, doi:10.1080/07391102.2018.1483839


Bin Peng, Kaiyu Guan, Ming Pan, and Yan Li: "Benefits of Seasonal Climate Prediction and Satellite Data for Forecasting U.S. Maize Yield", Geophysical Research Letters, The American Geophysical Union, Vol 45, Num 18, pp 9662-9671, 2018, doi:10.1029/2018gl079291


Grace McIlvain, Hillary Schwarb, Neal J. Cohen, Eva H. Telzer, and Curtis L. Johnson: "Mechanical Properties of the in Vivo Adolescent Human Brain", Developmental Cognitive Neuroscience, Elsevier BV, Vol 34, pp 27-33, 2018, doi:10.1016/j.dcn.2018.06.001


Aditya Sarathy, Nagendra B. Athreya, Lav R. Varshney, and Jean-Pierre Leburton: "Classification of Epigenetic Biomarkers with Atomically Thin Nanopores", Journal of Physical Chemistry Letters, American Chemical Society, Vol 9, pp 5718-5725, 2018, doi:10.1021/acs.jpclett.8b02200


Yingjie Zhang, Mohammad Heiranian, Blanka Janicek, Zoe Budrikis, Stefano Zapperi, Pinshane Y. Huang, Harley T. Johnson, Narayana R. Aluru, Joseph W. Lyding, and Nadya Mason: "Strain Modulation of Graphene by Nanoscale Substrate Curvatures: A Molecular View", Nano Letters, American Chemical Society, Vol 18, Num 3, pp 2098-2104, 2018, doi:10.1021/acs.nanolett.8b00273


Jianrong Bai, Fengjie Sun, Minglei Wang, Liang Su, Rui Li, and Gustavo Caetano-Anollés: "Genome-Wide Analysis of the MYB-CC Gene Family of Maize", Genetica, Springer Nature America, Inc, Vol 147, Num 1, pp 1-9, 2018, doi:10.1007/s10709-018-0042-y


Quan Zhou, Jiashun Hu, Lijun Liu, Thomas Chaparro, Dave R. Stegman, and Manuele Faccenda: "Western U.S. Seismic Anisotropy Revealing Complex Mantle Dynamics", Earth and Planetary Science Letters, Elsevier BV, Vol 500, pp 156-167, 2018, doi:10.1016/j.epsl.2018.08.015


Bruce E. Shaw, Kevin R. Milner, Edward H. Field, Keith Richards-Dinger, Jacquelyn J. Gilchrist, James H. Dieterich, and Thomas H. Jordan: "A Physics-Based Earthquake Simulator Replicates Seismic Hazard Statistics Across California", Science Advances, American Association for the Advancement of Science (AAAS), Vol 4, Num 8, pp eaau0688, 2018, doi:10.1126/sciadv.aau0688


Robert Gerstenberger, Maciej Besta, and Torsten Hoefler: "Enabling Highly Scalable Remote Memory Access Programming with MPI-3 One Sided", Communications of the ACM, Association for Computing Machinery, Vol 61, Num 10, pp 106-113, 2018, doi:10.1145/3264413


Molloy, Erin K. and Warnow, Tandy: "NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees", University of Illinois at Urbana-Champaign, Illinois Data Bank, 2018, doi:10.13012/b2idb-1424746_v1


Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi Zhang, Satish Rao, and Tandy Warnow: "Using INC Within Divide-and-Conquer Phylogeny Estimation", Springer International Publishing, Algorithms for Computational Biology (International Conference on Algorithms for Computational Biology, AlCoB 2019), Vol 11488, pp 167-178, Berkeley, California, U.S.A.,, 2018, doi:10.1007/978-3-030-18174-1_12


Daniel R. Roe and Thomas E. Cheatham: "Parallelization of CPPTRAJ Enables Large Scale Analysis of Molecular Dynamics Trajectory Data", Journal of Computational Chemistry, Wiley, Vol 39, Num 25, pp 2110-2117, 2018, doi:10.1002/jcc.25382


Joshua J. Goings, Clorice R. Reinhardt, and Sharon Hammes-Schiffer: "Propensity for Proton Relay and Electrostatic Impact of Protein Reorganization in Slr1694 BLUF Photoreceptor", Journal of the American Chemical Society, American Chemical Society, Vol 140, Num 45, pp 15241-15251, 2018, doi:10.1021/jacs.8b07456


Xiao Zhang and André Schleife: "Nonequilibrium BN-ZnO: Optical Properties and Excitonic Effects from First Principles", Physical Review B, American Physical Society, Vol 97, Num 12, pp 125201, 2018, doi:10.1103/physrevb.97.125201


Hopkins, Philip F. and Wetzel, Andrew and Kereš, Dušan and Faucher-Giguère, Claude-André and Quataert, Eliot and Boylan-Kolchin, Michael and Murray, Norman and Hayward, Christopher C. and Garrison-Kimmel, Shea and Hummels, Cameron and Feldmann, Robert and Torrey, Paul and Ma, Xiangcheng and Anglés-Alcázar, Daniel and Su, Kung-Yi and Orr, Matthew and Schmitz, Denise and Escala, Ivanna and Sanderson, Robyn and Grudić, Michael Y and Hafen, Zachary and Kim, Ji-Hoon and Fitts, Alex and Bullock, James S and Wheeler, Coral and Chan, T. K. and Elbert, Oliver D. and Narayanan, Desika: "FIRE-2 simulations: physics versus numerics in galaxy formation", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 480, Num 1, pp 800-863, 2018, doi:10.1093/mnras/sty1690


Hyunjin Yang, Surya P. Vanka, and Brian G. Thomas: "Modeling Argon Gas Behavior in Continuous Casting of Steel", JOM, Springer Nature America, Inc, Vol 70, Num 10, pp 2148-2156, 2018, doi:10.1007/s11837-018-2997-7


Steffen M. Sedlak, Leonard C. Schendel, Marcelo C. R. Melo, Diana A. Pippig, Zaida Luthey-Schulten, Hermann E. Gaub, and Rafael C. Bernardi: "Direction Matters: Monovalent Streptavidin/Biotin Complex Under Load", Nano Letters, The American Chemical Society, Vol 19, Num 6, pp 3415-3421, 2018, doi:10.1021/acs.nanolett.8b04045


Chenglin Yi, Soumendu Bagchi, Feilin Gou, Christopher M. Dmuchowski, Cheol Park, Catharine C. Fay, Huck Beng Chew, and Changhong Ke: "Direct nanomechanical measurements of boron nitride nanotube—ceramic interfaces", Nanotechnology, IOP Publishing Ltd., Vol 30, Num 2, pp 025706, 2018, doi:10.1088/1361-6528/aae874


K. D. Launey, A. Mercenne, G. H. Sargsyan, H. Shows, R. B. Baker, M. E. Miora, T. Dytrych, and J. P. Draayer: "Emergent Clustering Phenomena in the Framework of the Ab Initio Symmetry-Adapted No-Core Shell Model ", AIP Publishing, AIP Conference Proceedings (Proceedings of the 4th International Workshop on "State of the Art in Nuclear Cluster Physics", SOTANCP4), Vol 2038, Num 1, pp 020004, Galveston, Texas, U.S.A., 2018, doi:10.1063/1.5078823


R. B. Baker, K. D. Launey, N. Nevo Dinur, S. Bacca, J. P. Draayer, and T. Dytrych: "Electromagnetic Excitations and Responses in Nuclei from First Principles ", AIP Publishing, AIP Conference Proceedings (Proceedings of the 4th International Workshop on "State of the Art in Nuclear Cluster Physics'', SOTANCP4), Vol 2038, Num 1, pp 020006, Galveston, Texas, U.S.A., 2018, doi:10.1063/1.5078825


Robert J. Trapp, Geoffrey R. Marion, and Stephen W. Nesbitt: "Reply to "Comments on `The Regulation of Tornado Intensity by Updraft Width'"", Journal of the Atmospheric Sciences, American Meteorological Society, Vol 75, Num 11, pp 4057-4061, 2018, doi:10.1175/jas-d-18-0276.1


Evan N. Feinberg, Debnil Sur, Zhenqin Wu, Brooke E. Husic, Huanghao Mai, Yang Li, Saisai Sun, Jianyi Yang, Bharath Ramsundar, and Vijay S. Pande: "PotentialNet for Molecular Property Prediction", ACS Central Science, American Chemical Society, Vol 4, Num 11, pp 1520-1530, 2018, doi:10.1021/acscentsci.8b00507


Vadim Roytershteyn, Stanislav Boldyrev, Gian Luca Delzanno, Christopher H. K. Chen, Daniel Groselj, and Nuno F. Loureiro: "Numerical Study of Inertial Kinetic-Alfven Turbulence", Harvard Dataverse, Plasma Science and Fusion Center Dataverse, Num 1.0, 2018, doi:10.7910/DVN/C5U78M


Kuang-Chung Wang, Yuanchen Chu, Daniel Valencia, Junzhe Geng, James Charles, Prasad Sarangapani, and Tillmann Kubis: "Nonequilibrium Green's Function Method: Buttiker Probes for Carrier Generation and Recombination", Institute of Electrical & Electronics Engineers, 2018 International Conference on Simulation of Semiconductor Processes and Devices (SISPAD), pp 5-8, Austin, Texas, U.S.A., 2018, doi:10.1109/sispad.2018.8551714


Huanqing Chen and Nickolay Y. Gnedin: "Constraints on the Duty Cycles of Quasars at z ∼ 6", Astrophysical Journal, The American Astronomical Society, Vol 868, Num 2, pp 126, 2018, doi:10.3847/1538-4357/aae8e8


Talwinder Singh, Mehmet Sarp Yalim, and Nikolai V. Pogorelov: "Data-constrained Model for Coronal Mass Ejections Using Graduated Cylindrical Shell Method", Astrophysical Journal, American Astronomical Society, Vol 864, Num 1, pp 18, 2018, doi:10.3847/1538-4357/aad3b4


E. J. Zirnstein, J. Heerikhuisen, D. J. McComas, N. V. Pogorelov, D. B. Reisenfeld, and J. R. Szalay: "Simulation of the Solar Wind Dynamic Pressure Increase in 2014 and Its Effect on Energetic Neutral Atom Fluxes from the Heliosphere", Astrophysical Journal, American Astronomical Society, Vol 859, Num 2, pp 104, 2018, doi:10.3847/1538-4357/aac016


JaeHyuk Kwack, Galen Arnold, Celso Mendes, and Gregory H. Bauer: "Roofline Analysis with Cray Performance Analysis Tools (CrayPat) and Roofline-Based Performance Projections for a Future Architecture", Concurrency and Computation: Practice and Experience, John Wiley & Sons, Inc., Vol 31, Num 16 (Special Issue of the Cray User Group, CUG 2018), pp e4963, 2018, doi:10.1002/cpe.4963


Chuankai Zhao and Diwakar Shukla: "SAXS-Guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes", Scientific Reports, Springer Nature, Vol 8, Num 1, 2018, doi:10.1038/s41598-018-36090-z


Gustavo Caetano-Anollés, Frauke Graeter, Edmond Lau, and Fizza Mughal: "Untangling the Origins of Protein Flexibility and Biological Functions", 2018 Blue Waters Annual Report, pp 208-209, 2018


Iryna Butsky: "Simulating the Circumgalactic Medium: The Need for Robust Cosmic Ray Transport", 2018 Blue Waters Annual Report, pp 274-275, 2018


Maureen Brooks: "Multiscale Biophysical Interactions: Inertia, Growth, and Sargassum Seed Populations", 2018 Blue Waters Annual Report, pp 272-273, 2018


Daniel Bodony: "Running PlasCom2 on Blue Waters with OpenMP Offloading", 2018 Blue Waters Annual Report, pp 174-175, 2018


Jerry Bernholc, Emil L. Briggs, Miroslav Hodak, Carl T. Kelley, Wenchang Lu, Zhongcan Xiao: "Petascale Simulations of Graphene Nanoribbon Device Structures", 2018 Blue Waters Annual Report, pp 168-169, 2018


Gregory Bauer, Victor Anisimov, Manish Parashar, Melissa Romanus: "Improving NWChem Scalability using the DataSpaces Framework", 2018 Blue Waters Annual Report, pp 214, 2018


Dinshaw S. Balsara, Alexandre Lazarian, Blakesley Burkhart: "Simulating Two-Fluid MHD Turbulence and Dynamos in Star-Forming Molecular Clouds", 2018 Blue Waters Annual Report, pp 56-57, 2018


Maciej Balajewicz, Francisco Gonzalez: "Learning Low-Dimensional Feature Dynamics of Turbulent Flows using Deep Convolutional Recurrent Autoencoders", 2018 Blue Waters Annual Report, pp 106-107, 2018


Elizabeth Agee: "Quantifying Forest Drought Resistance", 2018 Blue Waters Annual Report, pp 270-271, 2018


Sumanta Acharya, Yousef Kanani: "High-Fidelity Numerical Simulations of Turbine Vane Heat Transfer under Freestream Turbulence", 2018 Blue Waters Annual Report, pp 162-163, 2018


Narayana Aluru: "Mechanistic Insights into Hydration of Solid Oxides", 2018 Blue Waters Annual Report, pp 164-165, 2018


Narayana Aluru: "Detection of Amino Acids with Highly Sensitive MoS2 Nanopores: Toward Machine Learning-Based Predictive Models", 2018 Blue Waters Annual Report, pp 206-207, 2018


Narayana Aluru: "Coarse-Grained Force Field for Ionic Liquids", 2018 Blue Waters Annual Report, pp 160-161, 2018


Aleksei Aksimentiev, Alexander Ohmann, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin Baumann, Kerstin Göpfrich, Jejoong Yoo, Ulrich F. Keyser: "Outperforming Nature: Synthetic Enzyme Built from DNA Flips Lipids of Biological Membranes at Record Rates", 2018 Blue Waters Annual Report, pp 204-205, 2018


Aleksei Aksimentiev, David Winogradoff: "DNA “Breathing” Captured in All-Atom Detail", 2018 Blue Waters Annual Report, pp 202-203, 2018


Larry Di Girolamo, John Towns, Shaowen Wang, Guangyu Zhao, Kent Yang, Yan Liu: "The Terra Data Fusion Project", 2018 Blue Waters Annual Report, pp 86-87, 2018


Donna Cox, Robert Patterson, Kalina Borkiewicz, A.J. Christensen, Stuart Levy, Jeffrey Carpenter, Thomas Lucas, Melih Sener, John Stone, Robin Canup: "Cinematic Scientific Data Visualization for CADENS", 2018 Blue Waters Annual Report, pp 182-183, 2018


Jennifer Corcoran, Brian Huberty, James Klassen, Keith Pelletier, Paul Morin, Joe Knight, Laura Bourgeau-Chavez: "Image Processing to Build a Multi-Temporal Vegetation Elevation Ecosystem Model of the Great Lakes Basin", 2018 Blue Waters Annual Report, pp 90-91, 2018


Salme Cook: "Sediment Transport in Estuaries: Estimating Bed Shear Stress Distribution from Numerically Modeled Tides in an Energetic Estuary", 2018 Blue Waters Annual Report, pp 278-279, 2018


Matthew Clement: "How the Solar System Survived a Violent Epoch of Dynamical Instability", 2018 Blue Waters Annual Report, pp 276-277, 2018


Bryan Clark, Xiongjie Yu, Di Luo, Eli Chertkov, Benjamin Villalonga, Dmitrii Kochkov, Jahan Claese, Krishna Kumar, Eduardo Fradkin, Hitesh Changlani, Vadim Oganesyan, Gil Rafeal, David Luitz: "Simulating the Emergent Phenomena Arising from Strongly Correlated Systems", 2018 Blue Waters Annual Report, pp 148-149, 2018


Wendy Cho, Yan Liu, Bruce Cain: "Enabling Redistricting Reform: A Computational Study of Zoning Optimization", 2018 Blue Waters Annual Report, pp 264-267, 2018


Huck Beng Chew: "Interfacial Load Transfer Mechanisms in Carbon Nanotube-Polymer Nanocomposites", 2018 Blue Waters Annual Report, pp 170-171, 2018


Chi-Hing Cheng: "Structural Basis for Extreme Cold Tolerance in the Eye Lenses of Teleost Fishes", 2018 Blue Waters Annual Report, pp 216-217, 2018


Thomas Cheatham, Adrian Roitberg, Carlos Simmerling, David Case, Darrin York, Rodrigo Galindo Murillo, Daniel Roe, Christina Bergonzo, Niel Henriksen, Hamed Hayatshahi: "Using Large Ensembles of AMBER Molecular Dynamics Simulations to Reproducibly and Reliably Converge the Conformational Distributions of Nucleic Acids", 2018 Blue Waters Annual Report, pp 212-215, 2018


David Ceperley, Carlo Pierleoni, Marcus Holzmann, Yubo Yang: "Properties of Dense Hydrogen", 2018 Blue Waters Annual Report, pp 142-143, 2018


Matias Carrasco Kind, Robert Gramillano, Thomas Kirsh, Francisco Paz-Chinchon: "The Evolution of the Halo Mass Function in an Accelerated Universe", 2018 Blue Waters Annual Report, pp 58-59, 2018


Vincenzo Carnevale, Michael Klein, Giacomo Fiorin, Tibor Rohacs: "Molecular Dynamics Simulations Unveil the Mechanism of the Sensitivity to Heat of an Ion Channel", 2018 Blue Waters Annual Report, pp 210-211, 2018


Roy H Campbell, Sayed Hadi Hashemi, William Gropp: "Accelerating Deep Neural Network Training with Model-Aware Network Scheduling", 2018 Blue Waters Annual Report, pp 180-181, 2018


Yongyang Cai, Kenneth Judd, William Brock, Thomas Hertel, Simon Scheidegger, T.J. Canann, Carlos Rangel: "Policy Responses to Climate Change", 2018 Blue Waters Annual Report, pp 266-267, 2018


Mohammed El-Kebir: "Algorithms for Reconstructing the Life History of Tumors from Genomics Data", 2018 Blue Waters Annual Report, pp 220-221, 2018


Zachary Goldsmith: "Electronic Structure of NiFe Oxyhydroxide Active Sites: Understanding an Effective Oxygen-Evolving Catalyst at a Quantum-Mechanical Level", 2018 Blue Waters Annual Report, pp 284-285, 2018


Nickolay Gnedin: "Cosmic Reionization on Computers", 2018 Blue Waters Annual Report, pp 64-65, 2018


Mattia Gazzola: "Modeling and Simulations of Complex Dynamic Musculoskeletal Architectures", 2018 Blue Waters Annual Report, pp 224-225, 2018


Marcelo García, Paul Fischer, Dimitrios K. Fytanidis, Jose M. Mier Lopez: "High-Resolution Modeling of Turbulence in Wave Boundary Layers", 2018 Blue Waters Annual Report, pp 158-159, 2018


Lauren Foster: "Scaling Relationships across Modeling Resolutions in Mountain Headwaters: Understanding Climate Change Impacts on Rocky Mountain Hydrology in a Numerical Modeling Context", 2018 Blue Waters Annual Report, pp 282-283, 2018


Paul Fischer, Som Dutta, Ketan Mittal: "High-Order Methods for Turbulent Transport in Engineering and Geosciences", 2018 Blue Waters Annual Report, pp 140-141, 2018


Andrew Ferguson and Greg Hart: "In Silico Vaccine Design through Empirical Fitness Landscapes and Population Dynamics", 2018 Blue Waters Annual Report, pp 222-223, 2018


Evan N. Feinberg: "Machine Learning Harnesses Molecular Dynamics to Develop Therapeutic Strategies for Alzheimer's Disease and Chronic Pain", 2018 Blue Waters Annual Report, pp 280-281, 2018


Claude-André Faucher-Giguère, Daniel Anglés-Alcázar, Philip Hopkins, Eliot Quataert, Dušan Kereš, Robert Feldmann, Blakesley Burkhart: "Simulating the Co-Evolution of Galaxies and their Supermassive Black Holes", 2018 Blue Waters Annual Report, pp 68-69, 2018


Lian Duan, Meelan Choudhari: "Pressure Fluctuations Induced by Supersonic Turbulent Boundary Layers", 2018 Blue Waters Annual Report, pp 150-151, 2018


J. P. Draayer, W. M. Tang, K. D. Launey, T. Dytrych, B. Wang, D. Langr, M. Kocourek, T. Oberhuber, R. Baker, G. Sargsyan, A. Mercenne: "Collaborative Research: Advancing First-Principle Symmetry-Guided Nuclear Modeling for Studies of Nucleosynthesis and Fundamental Symmetries in Nature", 2018 Blue Waters Annual Report, pp 136-137, 2018


Tiziana Di Matteo, Yu Feng, Rupert Croft, Ananth Tenneti, Steven Wilkins: "Tiny Galaxies Host the First Giant Black Holes: BlueTides Simulation Makes Contact with the First 700 Million Years of Cosmic History", 2018 Blue Waters Annual Report, pp 30-31, 2018


Ken Dill, Alberto Perez: "Combining Physics and Supercomputers to Predict Protein Structures from Sequences", 2018 Blue Waters Annual Report, pp 218-219, 2018


Kathryn Huff, Alexander Lindsay: "Coupled Multiphysics of Advanced Molten-Salt Nuclear Reactors", 2018 Blue Waters Annual Report, pp 104-105, 2018


Eliu Huerta, Roland Haas, Daniel S. Katz, Timothy Bouvet, Jeremy Enos, William T.C. Kramer, Hon Wai Leong, David Wheeler, Edgar Fajardo, Stuart Anderson, Peter Couvares, Joshua Willis: "Multimessenger Astrophysics with the Blue Waters Supercomputer", 2018 Blue Waters Annual Report, pp 22-23, 2018


Eliu Huerta, Daniel George: "Deep Learning for Multimessenger Astrophysics: Real-Time Discovery at Scale", 2018 Blue Waters Annual Report, pp 28-29, 2018


Michael Howard: "Designing Materials in Flow: Multiscale Simulations of Complex Fluid Rheology", 2018 Blue Waters Annual Report, pp 288-289, 2018


Philip Hopkins, Claude-Andre Faucher-Giguere, Dusan Keres, Eliot Quataert, Norman Murray, Mike Boylan-Kolchin, James Bullock, Andrew Wetzel, Robyn Sanderson, Chris Hayward, Robert Feldman, Christine Corbett-Moran: "Using Blue Waters to Understand the Origins of Galaxies and the Nature of Dark Matter", 2018 Blue Waters Annual Report, pp 66-67, 2018


Benjamin Hooberman, Amir Farbin, Ryan Reece, Matt Zhang: "Machine Learning for High-Energy Physics: Particle Identification and Regression using Deep Neural Networks", 2018 Blue Waters Annual Report, pp 166-167, 2018


So Hirata, Cole M. Johnson, Alexander E. Doran: "Toward Predictive Computational Design of Precision Molecular Optoelectronics", 2018 Blue Waters Annual Report, pp 228-229, 2018


Paul Hime: "Genomic Perspectives on the Amphibian Tree of Life", 2018 Blue Waters Annual Report, pp 316-317, 2018


Jennifer Hays: "Refining the Conformational Ensembles of Flexible Proteins using Simulation-Guided Spectroscopy", 2018 Blue Waters Annual Report, pp 286-287, 2018


John Hawley, Julian Krolik: "Elucidating the Alignment Mechanism for Black Hole Accretion Disks Subjected to Lense-Thirring Torques", 2018 Blue Waters Annual Report, pp 52-53, 2018


Roland Haas, Edward Seidel, Luke Roberts, Philipp Moesta, Eliu Huerta, Erik Schnetter, Christian Ott: "Core-Collapse Supernova Simulations: Simulating the Brightest Objects in the Sky and the Source of Life's Building Blocks", 2018 Blue Waters Annual Report, pp 26-27, 2018


Indranil Gupta: "Topology-Aware Distributed Graph Processing for Tightly Coupled Clusters", 2018 Blue Waters Annual Report, pp 186, 2018


Kaiyu Guan, Jian Peng, Bin Peng, Yunan Luo, Sibo Wang: "Forecasting Global Crop Productivity through Integrating Novel Satellite Data and Process-Based Models", 2018 Blue Waters Annual Report, pp 82-83, 2018


William Gropp, Erin Molloy, Tandy Warnow: "Constructing Large Evolutionary Trees on Supercomputers", 2018 Blue Waters Annual Report, pp 226-227, 2018


William Gropp, Luke Olson, Amanda Bienz, Paul Eller, Ed Karrels: "Algorithms for Extreme Scale Systems", 2018 Blue Waters Annual Report, pp 184-185, 2018


Rachel Kurchin: "Toward Quantitative Prediction of Defect Tolerance In Semiconductors: Leveraging HPC and Physical Insights to Design Radically Cheaper Energy Materials", 2018 Blue Waters Annual Report, pp 296-297, 2018


Ethan Kruse: "Discovering Hundreds of New Exoplanets with K2", 2018 Blue Waters Annual Report, pp 294-295, 2018


Seid Koriċ, Guillaume Houzeaux, Paula Córdoba, Anshul Gupta: "Toward Robust and High-Fidelity Multiphysics Modeling on Petascale Architecture", 2018 Blue Waters Annual Report, pp 192-193, 2018


Seid Koriċ, Robert F. Lucas, Erman Guleryuz: "Improving Virtually Guided Product Certification with Implicit Finite Element Analysis at Scale", 2018 Blue Waters Annual Report, pp 172-173, 2018


Gerhard Klimeck, Tillmann Kubis, James Charles, Fan Chen, Jim Fonseca, Junzhe Geng, Xinchen Guo, Hesameddin Ilatikhameneh, Daniel Mejia, Bozidar Novakovic, Michael Povolotskyi, Rajib Rahman, Prasad Sarangapani, Archana Tankasala, Yu Wang: "Leading Future Electronics into the Nano Regime using Quantum Atomistic Simulations in NEMO5", 2018 Blue Waters Annual Report, pp 144-147, 2018


Andrew Kirby: "High-Fidelity Blade-Resolved Wind Farm Simulations", 2018 Blue Waters Annual Report, pp 292-293, 2018


Alexandra Jones: "High Accuracy Radiative Transfer in Cloudy Atmospheres", 2018 Blue Waters Annual Report, pp 290-291, 2018


Harley Johnson: "Modeling Millions of Atoms and their Electrons: Tight-Binding using a Spectral Projection Purification Method", 2018 Blue Waters Annual Report, pp 146, 2018


Eric Johnsen, Shahaboddin Alahyari Beig, Mauro Rodriguez: "Numerical Simulations of the Inertial Collapse of Individual Gas Bubbles Near a Rigid Surface", 2018 Blue Waters Annual Report, pp 156-157, 2018


Shantenu Jha: "RADICAL-Cybertools: A Building-Blocks Approach to Harnessing the Power of Many", 2018 Blue Waters Annual Report, pp 190-191, 2018


Iwona Jasiuk, Erman Guleryuz: "Novel Metal-Carbon Materials", 2018 Blue Waters Annual Report, pp 138-139, 2018


Prashant K. Jain, Sudhakar Pamidighantam, Daniel Dumett Torres: "Topologies of Electronic States of Nanocrystalline Materials", 2018 Blue Waters Annual Report, pp 152-153, 2018


Ravishankar Iyer, Zbigniew Kalbarczyk, Saurabh Jha, Benjamin Lim, and Wen Shih: "Holistic Monitoring and Diagnosis of Large-Scale Application Performance Degradation", 2018 Blue Waters Annual Report, pp 188-189, 2018


Sohrab Ismail-Beigi, Glenn Martyna, Laxmikant Kale: "Understanding Hydrogen Storage in Metal-Organic Frameworks using Massively Parallel Electronic Structure Calculations", 2018 Blue Waters Annual Report, pp 154-155, 2018


Raluca Ilie: "Inductive E Fields in Earth's Magnetosphere", 2018 Blue Waters Annual Report, pp 60-61, 2018


Rakesh Nagi, Ketan Date: "Parallel Algorithms for Solving Large Multidimensional Assignment Problems with Decomposable Costs", 2018 Blue Waters Annual Report, pp 194-195, 2018


Paul Morin, Charles Nguyen, Claire Porter, Ian Howat, M.J. Noh, Michael Willis, Brian Bates, Cathleen Williamson, Andrew Johnson: "Enhanced Digital Elevation Model for the Arctic", 2018 Blue Waters Annual Report, pp 88-89, 2018


Warren Mori, Frank S. Tsung, L. O. Silva, R. A. Fonseca: "Petascale Simulation of High-Energy-Density (HED) Plasmas", 2018 Blue Waters Annual Report, pp 112-113, 2018


Arif Masud, Soonpil Kang, and Elizabeth R. Livingston: "Blood-Artery Interaction and Simulation-Based Analysis of Aortic Aneurysm", 2018 Blue Waters Annual Report, pp 236-237, 2018


Rachael Mansbach: "Wires Within Wires: A Multiscale Model for Computational Investigation of Bioelectronic Protein Design", 2018 Blue Waters Annual Report, pp 298-299, 2018


Nancy Makri: "Quantum-Classical Path Integral Simulation of Electronic Transitions", 2018 Blue Waters Annual Report, pp 234-235, 2018


Liudmila Mainzer, Yan Asmann, Matthew Hudson: "Identification of Missing Variants in Alzheimer's Disease, and the New Standards for Genomic Variant Identification in Large Cohorts", 2018 Blue Waters Annual Report, pp 232-233, 2018


Paul Mackenzie, Norman Christ, Robert Sugar, Alexei Bazavov, Peter Boyle, Carleton DeTar, Steven Gottlieb, Doug Toussaint, Chulwoo Jung, Yuzhi Liu: "High-Energy Physics on Blue Waters", 2018 Blue Waters Annual Report, pp 130-131, 2018


Zaida Luthey-Schulten, David Bianchi, Tyler Earnest, Joseph Peterson, Michael Hallock: "An Efficient Hybrid Stochastic-Deterministic Simulation Technique for Living Cells", 2018 Blue Waters Annual Report, pp 230-231, 2018


Lijun Liu, Manuele Faccenda: "Modeling 4D Earth Evolution: From Continental Cratons to the Yellowstone Supervolcano", 2018 Blue Waters Annual Report, pp 96-97, 2018


Yi-Hsin Liu, Michael Hesse, William Daughton, Tak Chu Li, Ari Le, Shan Wang: "3D Nature of Collisionless Magnetic Reconnection at Earth's Magnetopause", 2018 Blue Waters Annual Report, pp 38-39, 2018


Deborah Levin: "Fully Three-Dimensional Kinetic Simulations of Unsteady Shock-Boundary Layer Interactions", 2018 Blue Waters Annual Report, pp 124-125, 2018


Deborah Levin: "Modeling Plasma Flows with Kinetic Approaches using Hybrid CPU-GPU Computing", 2018 Blue Waters Annual Report, pp 42-43, 2018


Jean-Pierre Leburton, Lav Varshney, Nagendra Athreya, Aditya Sarathy: "Epigenetic Identification and Mapping using Solid-State 2D Nanopores", 2018 Blue Waters Annual Report, pp 132-133, 2018


Sonia Lasher-Trapp: ""Breathing" Clouds and Storms: Inflow and Entrainment, Precipitation and Outflow", 2018 Blue Waters Annual Report, pp 84-85, 2018


Caroline Riedl, Matthias Perdekamp, Naomi Makins, Vincent Andrieux, Robert Heitz, Riccardo Longo, Angelo Maggiora, Artem Petrosyan: "Mapping proton Quark Structure—Looking Inside the Proton: How Do Quarks Spin?", 2018 Blue Waters Annual Report, pp 126-127, 2018


Sherwood Richers: "General Relativistic Neutrino Radiation Transport: Understanding the Driving Force behind Cosmic Explosions", 2018 Blue Waters Annual Report, pp 304-305, 2018


Larissa Reames: "Factor Separation Analysis of Urban Impacts on a Simulated Supercell", 2018 Blue Waters Annual Report, pp 302-303, 2018


Sarma Rani: "Direct Numerical Simulations of the Relative Motion of High-Inertia Particles in Isotropic Turbulence", 2018 Blue Waters Annual Report, pp 94-95, 2018


Venkat Raman: "Computational Modeling of Rotating Detonation Engines", 2018 Blue Waters Annual Report, pp 134-135, 2018


Thomas Quinn, Fabio Governato, Michael Tremmel, Arif Babul, Iryna Butsky: "Unified Modeling of Galaxy Populations in Clusters", 2018 Blue Waters Annual Report, pp 44-45, 2018


Nikolai Pogorelov, Jacob Heerikhuisen, Sergey Borovikov, Tae Kim, Mehmet Sarp Yalim: "Modeling Physical Processes in the Solar Wind and Local Interstellar Medium with a Multiscale Fluid-Kinetic Simulation Suite: Connecting Solar, Heliospheric, and Astrophysical Scales", 2018 Blue Waters Annual Report, pp 54-55, 2018


Juan R. Perilla, Jodi A. Hadden, Adam Zlotnick, Louis M. Mansky, Peijun Zhang, Tatyana Polenova, Angela M. Gronenborn, Christopher R. Aiken, Tuli Mukhopadhyay: "Unveiling the Functions of Virus Capsids through the Computational Microscope", 2018 Blue Waters Annual Report, pp 238-239, 2018


William Payne: "Computer-Aided Formulation Design for Improved Nanoformulation of Anticancer Therapeutics: Using Simulation to Improve the Effectiveness of Cancer Drugs", 2018 Blue Waters Annual Report, pp 300-301, 2018


Brian O'Shea, David C. Collins, John H. Wise, Cameron J. Hummels, Britton D. Smith, Molly Peeples, Jason Tumlinson, Lauren Corlines: "Simulating Galaxy Formation across Cosmic Time", 2018 Blue Waters Annual Report, pp 50-51, 2018


Leigh Orf, Catherine Finley, Bruce Lee, Robert Wilhelmson: "Simulating the Most Devastating Thunderstorms: Big Tornadoes and Big Data", 2018 Blue Waters Annual Report, pp 72-73, 2018


Luke Olson, Amanda Bienz, Andrew Reisner, Lukas Spies: "Scaling Elliptic Solvers via Data Redistribution", 2018 Blue Waters Annual Report, pp 196-197, 2018


Michael Norman, James Bordner, David Tytler: "Realistic Simulations of the Intergalactic Medium: The Need for Enzo-P/Cello", 2018 Blue Waters Annual Report, pp 24-25, 2018


Scott Noble, Manuela Campanelli, Julian Krolik, Stephane d'Ascoli, Mark Avara, Dennis Bowen, Vassilios Mewes: "Shedding Light on Inspiraling Binary Black Holes with Magnetized Mini-Disks", 2018 Blue Waters Annual Report, pp 32-33, 2018


Mark Neubauer, Robert Gardner, David Lesny, Dewen Zhong: "Enabling Discovery at the Large Hadron Collider through Data-Intensive Computation and Machine Learning", 2018 Blue Waters Annual Report, pp 128-129, 2018


Ryan Sriver, Hui Li: "The Response of Tropical Cyclone Activity to Global Warming in the Community Earth System Model", 2018 Blue Waters Annual Report, pp 78-79, 2018


Ryan Sriver: "Atmospheric Rivers: Potential Drought Busters", 2018 Blue Waters Annual Report, pp 80-81, 2018


Ryan Sriver, Hui Li: "Analyzing Tropical Cyclone-Climate Interactions using the High-Resolution Community Earth System Model", 2018 Blue Waters Annual Report, pp 76-77, 2018


Ashok Srinivasan, Sirish Namilae, Anuj Mubayi, Matthew Scotch, Robert Pahle, Sudheer Chunduri: "Simulation of Viral Infection Propagation through Air Travel", 2018 Blue Waters Annual Report, pp 248-249, 2018


Ivan Soltesz, Aaron Milstein, Grace Ng, Darian Hadjiabadi: "Data-Driven, Biologically Constrained Computational Model of the Hippocampal Network at Scale", 2018 Blue Waters Annual Report, pp 246-247, 2018


Justin Sirignano: "Topology-Aware Distributed Graph Processing for Tightly Coupled Clusters", 2018 Blue Waters Annual Report, pp 187, 2018


Diwakar Shukla: "Unraveling the Molecular Magic of Witchweed", 2018 Blue Waters Annual Report, pp 242-243, 2018


Diwakar Shukla, Li-Qing Chen: "Molecular Simulations on Blue Waters Aid the Understanding of How Plants Transport Sugars between Cells", 2018 Blue Waters Annual Report, pp 244-245, 2018


Stuart Shapiro, Milton Ruiz, Antonios Tsokaros, Abid Khan, Vasileios Paschalidis: "Disks around Merging Binary Black Holes: From GW150914 to Supermassive Black Holes", 2018 Blue Waters Annual Report, pp 20-21, 2018


Sean Seyler: "Beyond Navier–Stokes and Molecular Dynamics: Understanding Biomacromolecular Dynamics through the Development of Multiscale Hybrid and Hydrodynamic Simulation", 2018 Blue Waters Annual Report, pp 306-307, 2018


André Schleife, Kisung Kang: "Magneto-Optical Kerr Effect of Antiferromagnetic Materials in External Magnetic Fields", 2018 Blue Waters Annual Report, pp 110-111, 2018


André Schleife, Alina Kononov: "Electron Dynamics of Ion-Irradiated Graphene", 2018 Blue Waters Annual Report, pp 108-109, 2018


Hsi-Yu Schive, Matthew Turk, John ZuHone, Nathan Goldbaum, Massimo Gaspari, Chin-Yu Chen, Ui-Han Zhang: "Astrophysics on Graphical Processing Units", 2018 Blue Waters Annual Report, pp 46-47, 2018


Vadim Roytershteyn, Yuri Omelchnko, Kai Germaschewski, John Podesta, Stansilav Boldyrev; Gian Luca Delzanno, William Matthaeus: "Kinetic Simulations of Plasma Turbulence", 2018 Blue Waters Annual Report, pp 40-41, 2018


Benoit Roux: "The Free Energy Landscapes Governing the Function of Complex Biomolecular Machines", 2018 Blue Waters Annual Report, pp 240-241, 2018


Robert J. Trapp: "Extreme Convective Storms under Climate Change", 2018 Blue Waters Annual Report, pp 100, 2018


Sam Totorica: "Magnetic Reconnection in Laser-Driven Plasmas: From Astrophysics to the Laboratory in silico", 2018 Blue Waters Annual Report, pp 312-313, 2018


Gabor Toth, Ward Manchester IV, Bart van der Holst, Yuxi Chen, Hongyang Zhou: "Multiscale Space Weather Simulations", 2018 Blue Waters Annual Report, pp 62-63, 2018


Rafael Tinoco Lopez, Paul Fischer, Som Dutta, Pallav Ranjan: "High-Resolution Numerical Simulation of Flow and Sediment Transport through Aquatic Vegetation", 2018 Blue Waters Annual Report, pp 120-121, 2018


Brian G. Thomas, Seong-Mook Cho, Surya Pratap Vanka, Seid Koric, Ahmed Taha, Hyunjin Yang, Matthew Zappulla: "Multiphase Turbulent Flow Modeling of Gas Injection into Molten Metal to Minimize Surface Defects in Continuous-Cast Steel", 2018 Blue Waters Annual Report, pp 118-119, 2018


Saul A. Teukolsky, Larry Kidder, Mark Scheel, Francois Foucart, Matt Duez, Harald Pfeiffer, Geoffrey Lovelace, Scott Field, Erik Schnetter, Peter Diener: "Petascale Simulations of Merging Black Holes and Neutron Stars", 2018 Blue Waters Annual Report, pp 48, 2018


Erin Teich: "Dynamics of Colloidal Glass-Formers", 2018 Blue Waters Annual Report, pp 310-311, 2018


Alexander Tchekhovskoy, Nicholas Stone, Matthew Liska, Casper Hesp, Adam Ingram, Michiel van der Klis, Sera Markoff, Koushik Chatterjee, Zack Andalman: "Feeding Black Holes: Tilt with a Twist", 2018 Blue Waters Annual Report, pp 34-35, 2018


Emad Tajkhorshid, Tao Jiang, H. Criss Hartzell, Kuai Yu: "Molecular Mechanism of Lipid and Ion Transport in Phospholipid Scrambling", 2018 Blue Waters Annual Report, pp 254-255, 2018


Emad Tajkhorshid, James C. Phillips, John E. Stone, Rafael C. Bernardi, Keith Cassidy, Peijun Zhang, John S. Parkinson, Ariane Briegel: "Structure and Function of Bacterial Chemosensory Arrays", 2018 Blue Waters Annual Report, pp 256-257, 2018


Ahmed Taha, Seid Koric, Sudhakar Parmidighantam, Narayan Aluru, Gabrielle Allen, Ashraf Idkaidek, Shantanu Shahane, Fereshteh A. Sabet, Ethan Shapera: "Advanced Digital Technology for Materials and Manufacturing", 2018 Blue Waters Annual Report, pp 116-117, 2018


Ahmed Taha, Seid Koric, Daniel Mira, Oriol Lehmkuhl, Ricard Borrel, Albert Coca, Samuel Gómez, Mariano Vázquez, Guillaume Houzeaux, Madhu Vellakal: "High-Fidelity Numerical Simulations of the Reacting Flow Field of an Annular Combustor Model of an Aircraft Engine", 2018 Blue Waters Annual Report, pp 122-123, 2018


Ilias Tagkopoulos: "Automatic Knowledge Base Construction and Hypothesis Generation: Antibiotic Resistance Mechanisms for Escherichia Coli", 2018 Blue Waters Annual Report, pp 252-253, 2018


Brad Sutton, Curtis L. Johnson, Alex Cerjanic, Aaron T. Anderson: "HPC-Based High-Resolution Quantitative MRI", 2018 Blue Waters Annual Report, pp 250-251, 2018


Ronald Stenz: "The Impacts of Hydrometeor Centrifuging on Tornado Dynamics: Improving the Realism of Tornado Simulations", 2018 Blue Waters Annual Report, pp 308-309, 2018


Varvara Zemskova: "Energetic Dynamics of Ocean Basin Model with Rotation, Surface Wind, and Buoyancy Forcing", 2018 Blue Waters Annual Report, pp 314-315, 2018


Pui-Kuen Yeung, K.R. Sreenivasan, S.B. Pope: "Resolution Effects and Extreme Events in Petascale Turbulence Simulations", 2018 Blue Waters Annual Report, pp 114-115, 2018


Donald J. Wuebbles, Xin-Zhong Liang: "Particulate Matter Prediction and Source Attribution for U.S. Air Quality Management in a Changing World", 2018 Blue Waters Annual Report, pp 92-93, 2018


Paul R. Woodward, Falk Herwig: "3D Stellar Hydrodynamics of H-Ingestion Flashes and Shell Mergers", 2018 Blue Waters Annual Report, pp 36-37, 2018


Matthew West, Chenchao Shou: "An Efficient Optimization Algorithm for Automatic Tuning of Machine-Learning Models", 2018 Blue Waters Annual Report, pp 198-199, 2018


Matthew West and Nicole Riemer: "Using a 3D Particle-Resolved Aerosol Model to Quantify and Reduce Uncertainties in Aerosol-Atmosphere Interactions", 2018 Blue Waters Annual Report, pp 74-75, 2018


Tandy Warnow, Erin Molloy, Michael Nute, Ehsan Saleh, Kodi Collins: "Improving Accuracy and Scalability for Core Bioinformatics Analyses", 2018 Blue Waters Annual Report, pp 260-261, 2018


Lucas Wagner, Elif Ertekin, Gregory MacDougall: "Quantum Magnets and Models", 2018 Blue Waters Annual Report, pp 176, 2018


Gregory Voth: "Large-Scale Coarse-Grained Simulations of HIV-1: New Therapeutic Targets", 2018 Blue Waters Annual Report, pp 258-259, 2018


John Vidale, Thomas Jordan, Yifeng Cui, Philip Maechling, Kim Olsen, Ricardo Taborda, Jacobo Bielak, Md Monsurul Huda, Naeem Khoshnevis, Andrea C. Riaño-Escandón, Alexander Breuer, Scott Callaghan, Jacquelyn Gilchrist, Christine A. Goulet, R.W. Graves, Dawei Mu, Dmitry Pekurovsky, Daniel Roten, Bruce Shaw, Qian Yao: "Simulating Alternative California Earthquake Histories using Rate and State Friction", 2018 Blue Waters Annual Report, pp 98-101, 2018


Matthew Turk: "Chemistry and the Early Universe", 2018 Blue Waters Annual Report, pp 49, 2018


John F. Hawley and Julian H. Krolik: "Sound Speed Dependence of Alignment in Accretion Disks Subjected to Lense-Thirring Torques", Astrophysical Journal, The American Astronomical Society, Vol 866, Num 1, pp 5, 2018, doi:10.3847/1538-4357/aadf90


Soumendu Bagchi, Changhong Ke, and Huck Beng Chew: "Oxidation effect on the shear strength of graphene on aluminum and titanium surfaces", Physical Review B, American Physical Society, Vol 98, Num 17, pp 174106, 2018, doi:10.1103/PhysRevB.98.174106


Yi Wang, Souichiro Hioki, Ping Yang, Michael D. King, Larry Di Girolamo, Dongwei Fu, and Bryan A. Baum: "Inference of an optimal ice particle model through latitudinal analysis of MISR and MODIS data", Remote Sensing, Multidisciplinary Digital Publishing Institute, Vol 10, Num 12, pp 1981, 2018, doi:10.3390/rs10121981


Yizhe Zhan, Larry Di Girolamo, Roger Davies, and Catherine Moroney: "Instantaneous Top-of-Atmosphere Albedo Comparison between CERES and MISR over the Arctic", Remote Sensing, Multidisciplinary Digital Publishing Institute, Vol 10, Num 12, pp 1882, 2018, doi:10.3390/rs10121882


Stéphane d'Ascoli, Scott C. Noble, Dennis B. Bowen, Manuela Campanelli, Julian H. Krolik, and Vassilios Mewes: "Electromagnetic Emission from Supermassive Binary Black Holes Approaching Merger", Astrophysical Journal, The American Astronomical Society, Vol 865, Num 2, pp 140, 2018, doi:10.3847/1538-4357/aad8b4


Huihuo Zheng, Hitesh J. Changlani, Kiel T. Williams, Brian Busemeyer, and Lucas K. Wagner: "From Real Materials to Model Hamiltonians With Density Matrix Downfolding", Frontiers in Physics, Frontiers Media, Vol 6, pp 43, 2018, doi:10.3389/fphy.2018.00043


J. Henderson, G. Hackman, P. Ruotsalainen, S. R. Stroberg, K. D. Launey, J. D. Holt, F. A. Ali, N. Bernier, M. A. Bentley, M. Bowry, R. Caballero-Folch, L. J. Evitts, R. Frederick, A. B. Garnsworthy, P. E. Garrett, B. Jigmeddorj, A. I. Kilic, J. Lassen, J. Measures, D. Muecher, B. Olaizola, E. O'Sullivan, O. Paetkau, J. Park, J. Smallcombe, C. E. Svensson, R. Wadsworth, and C. Y. Wu: "Testing microscopically derived descriptions of nuclear collectivity: Coulomb excitation of 22Mg", Physics Letters B, Elsevier B. V., Vol 782, pp 468-473, 2018, doi:10.1016/j.physletb.2018.05.064


Hyunjin Yang, Surya P. Vanka, Brian G. Thomas: "A Hybrid Eulerian–Eulerian Discrete-Phase Model of Turbulent Bubbly Flow", Journal of Fluids Engineering, The American Society of Mechanical Engineers, Vol 140, Num 10, pp 101202, 2018, doi:10.1115/1.4039793


Hyunjin Yang, Surya Pratap Vanka, Brian G. Thomas: "Modeling of Argon Gas Behavior in Continuous Casting of Steel", Springer International Publishing, CFD Modeling and Simulation in Materials Processing 2018, Vol Minerals, Metals and Materials Series, pp 119-131, Phoenix, Ariz., U.S.A., 2018, doi:10.1007/978-3-319-72059-3_12


Chao Zhang, Lian Duan, and Meelan M. Choudhari: "Direct Numerical Simulation Database for Supersonic and Hypersonic Turbulent Boundary Layers", AIAA Journal, American Institute of Aeronautics and Astronautics, Vol 56, Num 11, pp 4297-4311, 2018, doi:10.2514/1.J057296


Jyotisman Sahoo, Dmitrii Kochkov, Bryan K. Clark, and Rebecca Flint: "Classical phase diagram of the stuffed honeycomb lattice", Physical Review B, The American Physical Society, Vol 98, Num 13, pp 134419, 2018, doi:10.1103/PhysRevB.98.134419


Carlo Pierleoni, Giovanni Rillo, David M. Ceperley, and Markus Holzmann: "Electron localization properties in high pressure hydrogen at the liquid-liquid phase transition by Coupled Electron-Ion Monte Carlo", IOP Publishing Ltd, Journal of Physics: Conference Series (XXIXth IUPAP Conference on Computational Physics, CCP2017), Vol 1136, Num 1, pp 012005, Paris, France, 2018, doi:10.1088/1742-6596/1136/1/012005


Wendy K. Tam Cho: "Algorithms can foster a more democratic society", Nature, Springer Nature, Vol 558, Num 7711, pp 487, 2018, doi:10.1038/d41586-018-05498-y


Shahaboddin A. Beig and Eric Johnsen: "Bubble-Bubble Interactions and Wall Pressures Produced by the Collapse of a Bubble Pair near a Rigid Surface", ASME Press, Proceedings of the 10th International Symposium on Cavitation (CAV2018), Baltimore, Maryland, U.S.A., 2018, doi:10.1115/1.861851_ch30


Andrei Rykhlevskii, Jin Whan Bae, and Kathryn Huff: "arfc/saltproc: Code for online reprocessing simulation of molten salt reactor with external depletion solver SERPENT", Zenodo, Zenodo (website), 2018, doi:10.5281/zenodo.1306628


Katy Huff and Gavin Ridley: "arfc/uiuc-arfc-2017-01: uiuc-arfc-2017-01", Zenodo, Zenodo (website), Vol 1.0, 2018, doi:10.5281/zenodo.1145437


Abraham G. Beyene, Ali A. Alizadehmojarad, Gabriel Dorlhiac, Natalie Goh, Aaron M. Streets, Petr Král, Lela Vuković, and Markita P. Landry: "Ultralarge Modulation of Fluorescence by Neuromodulators in Carbon Nanotubes Functionalized with Self-Assembled Oligonucleotide Rings", Nano Letters, American Chemical Society, Vol 18, Num 11, pp 6995-7003, 2018, doi:10.1021/acs.nanolett.8b02937


A. Burrows, D. Vartanyan, J. C. Dolence, M. A. Skinner, and D. Radice: "Crucial Physical Dependencies of the Core-Collapse Supernova Mechanism", Space Science Reviews, Springer Netherlands, Vol 214, Num 33, 2018, doi:10.1007/s11214-017-0450-9


Wen Ma, Kevin D Whitley, Yann R Chemla, Zaida Luthey-Schulten, and Klaus Schulten: "Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase", eLife, eLife Sciences Publications, Ltd., Vol 7, pp e34186, 2018, doi:10.7554/eLife.34186


David Radice, Albino Perego, Kenta Hotokezaka, Sebastiano Bernuzzi, Steven A. Fromm, and Luke F. Roberts: "Viscous-Dynamical Ejecta from Binary Neutron Star Mergers", Astrophysical Journal, The American Astronomical Society, Vol 869, Num 2, pp L35, 2018, doi:10.3847/2041-8213/aaf053


David Radice, Albino Perego, Kenta Hotokezaka, Steven A. Fromm, Sebastiano Bernuzzi, and Luke F. Roberts: "Binary Neutron Star Mergers: Mass Ejection, Electromagnetic Counterparts and Nucleosynthesis", Astrophysical Journal, The American Astronomical Society, Vol 869, Num 2, pp 130, 2018, doi:10.3847/1538-4357/aaf054


Chunyuan Diao and Le Wang: "Landsat time series-based multiyear spectral angle clustering (MSAC) model to monitor the inter-annual leaf senescence of exotic saltcedar", Remote Sensing of Environment, Elsevier B.V., Vol 209, pp 581-593, 2018, doi:10.1016/j.rse.2018.02.036


Erin K. Molloy and Tandy Warnow: "NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees", Springer International Publishing, Lecture Notes in Computer Science: Comparative Genomics (RECOMB International conference on Comparative Genomics, RECOMB-CG 2018), Vol 11183, pp 260-276, Magog-Orford, Quebec City, Canada, 2018, doi:10.1007/978-3-030-00834-5_15


Ian Howat, Paul Morin, Claire Porter, and Myong-Jong Noh: "The Reference Elevation Model of Antarctica", The President & Fellows of Harvard College, Harvard Dataverse, Vol 1, 2018, doi:10.7910/DVN/SAIK8B


Porter, Claire and Morin, Paul and Howat, Ian and Noh, Myoung-Jon and Bates, Brian and Peterman, Kenneth and Keesey, Scott and Schlenk, Matthew and Gardiner, Judith and Tomko, Karen and Willis, Michael and Kelleher, Cole and Cloutier, Michael and Husby, Eric and Foga, Steven and Nakamura, Hitomi and Platson, Melisa and Wethington, Michael, Jr. and Williamson, Cathleen and Bauer, Gregory and Enos, Jeremy and Arnold, Galen and Kramer, William and Becker, Peter and Doshi, Abhijit and D'Souza, Cristelle and Cummens, Pat and Laurier, Fabien and Bojesen, Mikkel: "ArcticDEM", The President & Fellows of Harvard College, Harvard Dataverse, Vol 1, 2018, doi:10.7910/DVN/OHHUKH


Milton Ruiz, Stuart L. Shapiro, and Antonios Tsokaros: "Jet launching from binary black hole-neutron star mergers: Dependence on black hole spin, binary mass ratio and magnetic field orientation", Physical Review D, The American Physical Society, Vol 98, Num 12, pp 123017, 2018, doi:10.1103/PhysRevD.98.123017


Lunan Sun, Milton Ruiz, and Stuart L. Shapiro: "Simulating the Magnetorotational Collapse of Supermassive Stars: Incorporating Gas Pressure Perturbations and Different Rotation Profiles", Physical Review D, The American Physical Society, Vol 98, Num 10, pp 103008, 2018, doi:10.1103/PhysRevD.98.103008


Qihua Chen, Jiangyan Feng, Shriyaa Mittal, and Diwakar Shukla: "Automatic Feature Selection in Markov State Models Using Genetic Algorithm", Journal of Computational Science Education, Shodor Education Foundation, Vol 9, Num 2, pp 14-22, 2018, doi:10.22369/issn.2153-4136/9/2/2


Vassilios Mewes, Yosef Zlochower, Manuela Campanelli, Ian Ruchlin, Zachariah B. Etienne, and Thomas W. Baumgarte: "Numerical relativity in spherical coordinates with the Einstein Toolkit", Physical Review D, American Physical Society, Vol 97, Num 8, pp 084059, 2018, doi:10.1103/PhysRevD.97.084059


A. C. Dreyfuss, K. D. Launey, J. E. Escher, R. B. Baker, J. P. Draayer, and T. Dytrych: "Clustering and alpha-capture reaction rates from first-principle structure calculations for nucleosynthesis", AIP Publishing, AIP Conference Proceedings (Proceedings of the 4th International Workshop on "State of the Art in Nuclear Cluster Physics", SOTANCP4), Vol 2038, Num 1, pp 020013, Galveston, Texas, U.S.A., 2018, doi:10.1063/1.5078832


James C. Robertson, Alberto Perez, and Ken A. Dill: "MELD x MD Folds Nonthreadables, Giving Native Structures and Populations", Journal of Chemical Theory and Computation, American Chemical Society, Vol 14, Num 12, pp 6734-6740, 2018, doi:10.1021/acs.jctc.8b00886


Junzhe Geng, Prasad Sarangapani, Kuang‐Chung Wang, Erik Nelson, Ben Browne, Carl Wordelman, James Charles, Yuanchen Chu, Tillmann Kubis, and Gerhard Klimeck: "Quantitative Multi-Scale, Multi-Physics Quantum Transport Modeling of GaN-Based Light Emitting Diodes", Physica Status Solidi A: Applications and Materials Science, John Wiley and Sons, Inc., Vol 215, Num 9, pp 1700662, 2018, doi:10.1002/pssa.201700662


Yuanchen Chu, Prasad Sarangapani, James Charles, Gerhard Klimeck, and Tillmann Kubis: "Explicit screening full band quantum transport model for semiconductor nanodevices", Journal of Applied Physics, AIP Publishing LLC, Vol 123, Num 24, pp 244501, 2018, doi:10.1063/1.5031461


Yang Liu, Haibibu Aziguli, Bing Zhang, Wenhan Xu, Wenchang Lu, J. Bernholc, and Qing Wang: "Ferroelectric polymers exhibiting behaviour reminiscent of a morphotropic phase boundary", Nature, Springer Nature Limited, Vol 562, Num 7725, pp 96-100, 2018, doi:10.1038/s41586-018-0550-z


Marina A. Kasimova, Aysenur Torun Yazici, Yevgen Yudin, Daniele Granata, Michael L. Klein, Tibor Rohacs, and Vincenzo Carnevale: "A hypothetical molecular mechanism for TRPV1 activation that invokes rotation of an S6 asparagine", Journal of General Physiology, Rockefeller University Press, Vol 150, Num 11, pp 1554-1566, 2018, doi:10.1085/jgp.201812124


Vadim Roytershteyn and Gian Luca Delzanno: "Spectral Approach to Plasma Kinetic Simulations Based on Hermite Decomposition in the Velocity Space", Frontiers in Astronomy and Space Sciences, Frontiers Media S.A., Vol 5, 2018, doi:10.3389/fspas.2018.00027


JiaShun Hu, Lijun Liu, and Quan Zhou: "Reproducing past subduction and mantle flow using high‐resolution global convection models", Earth and Planetary Physics, John Wiley and Sons, Inc., Vol 2, Num 3, pp 189-207, 2018, doi:10.26464/epp2018019


Chaitanya Afle, Anuradha Gupta, Bhooshan Gadre, Prayush Kumar, Nick Demos, Geoffrey Lovelace, Han Gil Choi, Hyung Mok Lee, Sanjit Mitra, Michael Boyle, Daniel A. Hemberger, Lawrence E. Kidder, Harald P. Pfeiffer, Mark A. Scheel, and Bela Szilagyi: "Detection and characterization of spin-orbit resonances in the advanced gravitational wave detectors era", Physical Review D, American Physical Society, Vol 98, Num 8, pp 083014, 2018, doi:10.1103/PhysRevD.98.083014


Vinícius Wilian D. Cruzeiro, and Marcos S. Amaral, and Adrian E. Roitberg: "Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation", Journal of Chemical Physics, AIP Publishing LLC, Vol 149, Num 7, pp 072338, 2018, doi:10.1063/1.5027379


He Huang and Carlos Simmerling: "Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs", Journal of Chemical Theory and Computation, American Chemical Society, Vol 14, Num 11, pp 5797-5814, 2018, doi:10.1021/acs.jctc.8b00413


Tai-Sung Lee, David S. Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J. Giese, Adrian Roitberg. David A. Case, Ross C. Walker, and Darrin M. York: "GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features", Journal of Chemical Information and Modeling, American Chemical Society, Vol 58, Num 10, pp 2043-2050, 2018, doi:10.1021/acs.jcim.8b00462


Jinfeng Liu, and Jason Swails, and John Z. H. Zhang, and Xiao He, and Adrian E. Roitberg: "A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease", Journal of the American Chemical Society, American Chemical Society, Vol 140, Num 5, pp 1639-1648, 2018, doi:10.1021/jacs.7b08569


A. J. Christensen, Venkatraman Srinivasan, John C. Hart, and Amy Marshall-Colon: "Use of computational modeling combined with advanced visualization to develop strategies for the design of crop ideotypes to address food security", Nutrition Reviews, Vol 76, Num 5, pp 332-347, 2018, doi:10.1093/nutrit/nux076


Mert Hidayetoglu, Carl Pearson. Izzat El Hajj, Levent Gurel, Weng Cho Chew, and Wen-Mei Hwu: "A Fast and Massively-Parallel Inverse Solver for Multiple-Scattering Tomographic Image Reconstruction", Institute of Electrical & Electronics Engineers, 2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS), pp 64-74, Vancouver, British Columbia, Canada, 2018, doi:10.1109/IPDPS.2018.00017


David Vartanyan, Adam Burrows, David Radice, M. Aaron Skinner, and Joshua Dolence: "Revival of the fittest: exploding core-collapse supernovae from 12 to 25M(circle dot)", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 477, Num 3, pp 3091-3108, 2018, doi:10.1093/mnras/sty809


A. Le, V. Roytershteyn, H. Karimabadi, A. Stanier, L. Chacon, and K. Schneider: "Wavelet methods for studying the onset of strong plasma turbulence", Physics of Plasmas, AIP Publishing, Vol 25, Num 12, pp 122310, 2018, doi:10.1063/1.5062853


B. P. Abbott et al. (The LIGO Scientific Collaboration and the Virgo Collaboration): "GW170817: Measurements of Neutron Star Radii and Equation of State", Physical Review Letters, American Physical Society, Vol 121, Num 16, pp 161101, 2018, doi:10.1103/PhysRevLett.121.161101


B. P. Abbott et al. (LIGO Scientific Collaboration and Virgo Collaboration): "First Search for Nontensorial Gravitational Waves from Known Pulsars", Physical Review Letters, American Physical Society, Vol 120, Num 3, pp 031104, 2018, doi:10.1103/PhysRevLett.120.031104


Jam Sadiq, Yosef Zlochower, and Hiroyuki Nakano: "Comparing an analytical spacetime metric for a merging binary to a fully nonlinear numerical evolution using curvature scalars", Physical Review D, American Physical Society, Vol 97, Num 8, pp 084007, 2018, doi:10.1103/PhysRevD.97.084007


James Healy, Carlos O. Lousto, Ian Ruchlin, and Yosef Zlochower: "Evolutions of unequal mass, highly spinning black hole binaries", Physical Review D, American Physical Society, Vol 97, Num 10, pp 104026, 2018, doi:10.1103/PhysRevD.97.104026


Donghyuk Suh, Brian K. Radak, Christophe Chipot, and Benoît Roux: "Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator", Journal of Chemical Physics, AIP Publishing, Vol 148, Num 1, pp 014101, 2018, doi:10.1063/1.5004154


B. P. Abbott et al. (LIGO Scientific Collaboration and Virgo Collaboration): "Search for Subsolar-Mass Ultracompact Binaries in Advanced LIGO’s First Observing Run", Physical Review Letters, American Physical Society, Vol 121, Num 23, pp 231103, 2018, doi:10.1103/PhysRevLett.121.231103


Andrew C. Kirby: "Enabling High-Order Methods for Extreme-Scale Simulations", Mavriplis CFD Lab (website), Vol Doctoral dissertation, 2018


Ethan Kruse: "A New Transiting Planet Search Applied to Kepler and K2: Discovery of Hundreds of Planet Candidates, Eclipsing Binary Stars, and a Self-lensing Binary System", University of Washington, ResearchWorks Archive, Vol Dissertations and theses, 2018


Lauren Foster: "Modeling climate change impacts to Rocky Mountain headwater hydrology", Colorado School of Mines, Mountain Scholar, Vol Theses & Dissertations, 2018


Rachael Alexandra Mansbach: "Dimensionality reduction and multiscale modeling for the understanding of protein folding and hierarchical self-assembly", University of Illinois at Urbana-Champaign, Illinois Digital Environment for Access to Learning and Scholarship, Vol Doctoral dissertation, 2018


Sherwood Andrew Richers III: "Neutrino Radiation Transport and Other Topics in High Energy Density Astrophysics", California Institute of Technology Library Services, CaltechTHESIS, Vol Doctoral dissertation, 2018, doi:10.7907/Z9PC30JH


Michael Patrick Howard: "Structure and Dynamics in Colloid-Polymer Mixtures Out of Equilibrium", Princeton University, DataSpace at Princeton University, Vol Doctoral dissertation, 2018


B. Acun, D. J. Hardy, L. V. Kale, K. Li, J. C. Phillips, and J. E. Stone: "Scalable molecular dynamics with NAMD on the Summit system", IBM Journal of Research and Development, International Business Machines Research, Vol 62, Num 6, pp 4:1-4:9, 2018, doi:10.1147/JRD.2018.2888986


James C. Phillips: "What You Should Know About NAMD and Charm++ But Were Hoping to Ignore", Association for Computing Machinery, PEARC '18: Proceedings of the Practice and Experience on Advanced Research Computing, pp 55:1-55:8, Pittsburgh, Pennsylvania, U.S.A., 2018, doi:10.1145/3219104.3219134


Renjie Chen, Ryan Poling-Skutvik, Arash Nikoubashman, Michael P. Howard, Jacinta C. Conrad, and Jeremy C. Palmer: "Coupling of Nanoparticle Dynamics to Polymer Center-of-Mass Motion in Semidilute Polymer Solutions", Macromolecules, American Chemical Society, Vol 51, Num 5, pp 1865-1872, 2018, doi:10.1021/acs.macromol.7b02441


Evan N, Feinberg: "Artificial Intelligence Methods for Molecular Property Prediction", Stanford University Libraries, SearchWorks, Vol Doctoral dissertation, 2018


Shuai Zhang, Burkhard Militzer, Michelle C. Gregor, Kyle Caspersen, Lin H. Yang, Jim Gaffney, Tadashi Ogitsu, Damian Swift, Amy Lazicki, D. Erskine, Richard A. London, P. M. Celliers, Joseph Nilsen, Philip A. Sterne, and Heather D. Whitley: "Theoretical and experimental investigation of the equation of state of boron plasmas", Physical Review E, American Physical Society, Vol 98, Num 2, pp 023205, 2018, doi:10.1103/PhysRevE.98.023205


Shuai Zhang, Burkhard Militzer, Lorin X. Benedict, François Soubiran, Kevin P. Driver, and Philip A. Sterne: "Path integral Monte Carlo simulations of dense carbon-hydrogen plasmas", Journal of Chemical Physics, AIP Publishing, Vol 148, Num 10, pp 102318, 2018, doi:10.1063/1.5001208


Hon Wai Leong, Timothy A. Bouvet, Brett Bode, Jeremy J. Enos, and David A. King: "Installation, Configuration and Performance Tuning of Shifter V16 on Blue Waters", presented at CUG 2018, Stockholm, Sweden, 2018


Gregory H. Bauer, Brett Bode, Jeremy Enos, William T. Kramer, Scott Lathrop, Celso L. Mendes, and Roberto R. Sisneros: "Best Practices and Lessons from Deploying and Operating a Sustained-Petascale System: The Blue Waters Experience", SC '18: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, pp 53, Dallas, Texas, U.S.A., 2018, doi:10.5555/3291656.3291727


David W. Weisrock, Paul M. Hime, Schyler O. Nunziata, Kara S. Jones, Mason O. Murphy, Scott Hotaling, and Justin D. Kratovil: "Surmounting the Large-Genome Problem for Genomic Data Generation in Salamanders", Springer Nature, Population Genomics, 2018, doi:10.1007/13836_2018_36


Robert Sisneros, Jonathan Kim, Mohammad Raji, and Kalyana Chadalavada: "How Deep is Your I/O? Toward Practical Large-Scale I/O Optimization via Machine Learning Methods", presented at CUG 2018, Stockholm, Sweden, 2018


Allen Sanderson, Alan Humphrey, John Schmidt, and Robert Sisneros: "Coupling the Uintah Framework and the VisIt Toolkit for Parallel In Situ Data Analysis and Visualization and Computational Steering", Springer Nature, High Performance Computing: ISC High Performance 2018 International Workshops, pp 201-214, Third International Workshop on In Situ Visualization (WOIV 2018); Frankfurt, Germany, 2018, doi:10.1007/978-3-030-02465-9_14


Kodi Collins and Tandy Warnow: "PASTA for proteins", Bioinformatics, Oxford University Press, Vol 34, Num 22, pp 3939-3941, 2018, doi:10.1093/bioinformatics/bty495


Erin Teich: "Local Structure in Hard Particle Self-Assembly and Assembly Failure", Michigan Publishing and the University of Michigan Library, Deep Blue, Vol Dissertations and theses, 2018


Jeongnim Kim, Andrew Baczewski, Todd D. Beaudet, Anouar Benali, M. Chandler Bennett, Mark A. Berrill, Nick S. Blunt, Edgar Josue Landinez Borda, Michele Casula, David M. Ceperley, Simone Chiesa, Bryan K. Clark, Raymond C. Clay III, Kris T. Delaney, Mark Dewing, Kenneth P. Esler, Hongxia Hao, Olle Heinonen, Paul R. C. Kent, Jaron T. Krogel, Ilkka Kylanpaa, Ying Wai Li, M. Graham Lopez, Ye Luo, Fionn D. Malone, Richard M. Martin, Amrita Mathuriya, Jeremy McMinis, Cody A. Melton, Lubos Mitas, Miguel A. Morales, Eric Neuscamman, William D. Parker, Sergio D. Pineda Flores, Nichols A. Romero, Brenda M. Rubenstein, Jacqueline A. R. Shea, Hyeondeok Shin, Luke Shulenburger, Andreas Tillack, Joshua P. Townsend, Norm M. Tubman, Brett Van Der Goetz, Jordan E. Vincent, D. ChangMo Yang, Yubo Yang, Shuai Zhang, and Luning Zhao: "QMCPACK : An open source ab initio Quantum Monte Carlo package for the electronic structure of atoms, molecules, and solids", Journal of Physics: Condensed Matter, IOP Publishing Ltd., Vol 30, Num 19, pp 195901, 2018, doi:10.1088/1361-648x/aab9c3


Jesper J. Madsen, John M. A. Grime, Jeremy S. Rossman, and Gregory A. Voth: "Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 115, Num 37, pp E8595-E8603, 2018, doi:10.1073/pnas.1805443115


Tulasi N. Parashar, Alexandros Chasapis, Riddhi Bandyopadhyay, Rohit Chhiber, W. H. Matthaeus, B. Maruca, M. A. Shay, J. L. Burch, T. E. Moore, B. L. Giles, D. J. Gershman, C. J. Pollock, R. B. Torbert, C. T. Russell, R. J. Strangeway, and Vadim Roytershteyn: "Kinetic Range Spectral Features of Cross Helicity Using the Magnetospheric Multiscale Spacecraft", Physical Review Letters, American Physical Society, Vol 121, Num 26, pp 265101, 2018, doi:10.1103/PhysRevLett.121.265101


Madhu Vellakal, Muris Torlak, Seid Koric, and Ahmed Taha: "Comparison of Characteristics of Flow Around a Sphere With Trip Wire Using Different Turbulence Modeling Approaches", The American Society of Mechanical Engineers, ASME 2017 International Mechanical Engineering Congress and Exposition (IMECE 2017), Vol 1: Advances in Aerospace Technology, Tampa, Florida, U.S.A., 2018, doi:10.1115/IMECE2017-71667


Elisa A. Hemmig, Clare Fitzgerald, Christopher Maffeo, Lisa Hecker, Sarah E. Ochmann, Aleksei Aksimentiev, Philip Tinnefeld, and Ulrich F. Keyser: "Optical Voltage Sensing Using DNA Origami", Nano Letters, American Chemical Society, Vol 18, Num 3, pp 1962-1971, 2018, doi:10.1021/acs.nanolett.7b05354


Jejoong Yoo and Aleksei Aksimentiev: "New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions", Physical Chemistry Chemical Physics, The Royal Society of Chemistry, Vol 20, Num 13, pp 8432-8449, 2018, doi:10.1039/C7CP08185E


Hyunju Kang, Jejoong Yoo, Byeong-Kwon Sohn, Seung-Won Lee, Hong Soo Lee, Wenjie Ma, Jung-Min Kee, Aleksei Aksimentiev, and Hajin Kim: "Sequence-dependent DNA condensation as a driving force of DNA phase separation", Nucleic Acids Research, Oxford University Press, Vol 46, Num 18, pp 9401-9413, 2018, doi:10.1093/nar/gky639


Patrick M. Arnott, Himanshu Joshi, Aleksei Aksimentiev, and Stefan Howorka: "Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes", Langmuir, American Chemical Society, Vol 34, Num 49, pp 15084-15092, 2018, doi:10.1021/acs.langmuir.8b02271


Samuel Richard Totorica: "Novel methods and applications for kinetic plasma simulation", Stanford Libraries, SearchWorks, Vol doctotral dissertation, 2018


Joshua Leveillee, Claudine Katan, Liujiang Zhou, Aditya D. Mohite, Jacky Even, Sergei Tretiak, André Schleife, and Amanda J. Neukirch: "Influence of pi-conjugated cations and halogen substitution on the optoelectronic and excitonic properties of layered hybrid perovskites", Physical Review Materials, American Physical Society, Vol 2, Num 10, pp 105406, 2018, doi:10.1103/PhysRevMaterials.2.105406


André Schleife, Maciej D. Neumann, Norbert Esser, Zbigniew Galazka, Alexander Gottwald, Jakob Nixdorf, Rüdiger Goldhahn, and Martin Feneberg: "Optical properties of In2O3 from experiment and first-principles theory: influence of lattice screening", New Journal of Physics, IOP Publishing Ltd. on behalf of Deutsche Physikalische Gesellschaft, Vol 20, Num 5, pp 053016, 2018, doi:10.1088/1367-2630/aabeb0


Shivesh Pathaka and Lucas K. Wagner: "Non-orthogonal determinants in multi-Slater-Jastrow trial wave functions for fixed-node diffusion Monte Carlo", Journal of Chemical Physics, AIP Publishing LLC, Vol 149, Num 23, pp 234104, 2018, doi:10.1063/1.5052906


Taishan Zhu, Krishnan Swaminathan-Gopalan, Kelly Stephani, and Elif Ertekin: "Thermoelectric phonon-glass electron-crystal via ion beam patterning of silicon", Physical Review B, American Physical Society, Vol 97, Num 17, pp 174201, 2018, doi:10.1103/PhysRevB.97.174201


Heonjae Jeong, Edmund G. Seebauer and Elif Ertekin: "First-principles description of oxygen self-diffusion in rutile TiO2: assessment of uncertainties due to enthalpy and entropy contributions", Physical Chemistry Chemical Physics, The Royal Society of Chemistry, Vol 20, Num 25, pp 17448-17457, 2018, doi:10.1039/C8CP02741B


Laurie S. Huning and Steven A. Margulis: "Investigating the Variability of High-Elevation Seasonal Orographic Snowfall Enhancement and Its Drivers across Sierra Nevada, California", Journal of Hydrometeorology, American Meteorological Society, Vol 19, Num 1, pp 47-67, 2018, doi:10.1175/JHM-D-16-0254.1


D. Roten, K. B. Olsen, S. M. Day, and Y. Cui: "Quantification of Fault-Zone Plasticity Effects with Spontaneous Rupture Simulations", Springer International Publishing, Best Practices in Physics-based Fault Rupture Models for Seismic Hazard Assessment of Nuclear Installations, pp 45-67, 2018, doi:10.1007/978-3-319-72709-7_5


Maxwell Burnette, Rob Kooper, J. D. Maloney, Gareth S. Rohde, Jeffrey A. Terstriep, Craig Willis, Noah Fahlgren, Todd Mockler, Maria Newcomb, Vasit Sagan, Pedro Andrade-Sanchez, Nadia Shakoor, Paheding Sidike, Rick Ward, and David LeBauer: "TERRA-REF Data Processing Infrastructure", Association for Computing Machinery, PEARC '18: Proceedings of the Practice and Experience on Advanced Research Computing, pp 27, Pittsburgh, Pennsylvania, U.S.A., 2018, doi:10.1145/3219104.3219152


Jinho Kim, Dinshaw S. Balsara, Maxim Lyutikov, and Serguei S. Komissarov: "On the linear stability of sheared and magnetized jets without current sheets - relativistic case", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 474, Num 3, pp 3954-3966, 2018, doi:10.1093/mnras/stx3065


Abhilash Harpale, Saurabh Sawant, Rakesh Kumar, Deborah Levin, and Huck Beng Chew: "Ablative thermal protection systems: Pyrolysis modeling by scale-bridging molecular dynamics", Carbon, Elsevier Ltd., Vol 130, pp 315-324, 2018, doi:10.1016/j.carbon.2017.12.099


2017

Yan Zhan and Patricia M. Gregg: "Data Assimilation Strategies for Volcano Geodesy", Journal of Volcanology and Geothermal Research, Elsevier BV, Vol 344, Num Supplement C, pp 13-25, 2017, doi:10.1016/j.jvolgeores.2017.02.015


Weiming An, Wei Lu, Chengkun Huang, Xinlu Xu, Mark J. Hogan, Chan Joshi, and Warren B. Mori: "Ion Motion Induced Emittance Growth of Matched Electron Beams in Plasma Wakefields", Physical Review Letters, American Physical Society, Vol 118, Num 24, pp 244801, 2017, doi:10.1103/physrevlett.118.244801


Fei Li, Peicheng Yu, Xinlu Xu, Frederico Fiuza, Viktor K. Decyk, Thamine Dalichaouch, Asher Davidson, Adam Tableman, Weiming An, Frank S. Tsung, Ricardo A. Fonseca, Wei Lu, and Warren B. Mori: "Controlling the Numerical Cerenkov Instability in PIC Simulations Using a Customized Finite Difference Maxwell Solver and a Local FFT Based Current Correction", Computer Physics Communications, Elsevier BV, Vol 214, pp 6-17, 2017, doi:10.1016/j.cpc.2017.01.001


Asher Davidson, Adam Tableman, Peicheng Yu, Weiming An, Frank Tsung, Wei Lu, Ricardo A. Fonseca, and Warren B. Mori: "An Examination of the Scaling Laws for LWFA in the Self-Guided Nonlinear Blowout Regime ", American Institute of Physics, AIP Conference Proceedings (57th Annual Meeting of the APS Division of Plasma Physics), Vol 1812, Num 1, pp 040014, Savannah, Georgia, U.S.A., 2017, doi:10.1063/1.4975861


Larissa J. Reames: "Diurnal Variations in Severe Weather Forecast Parameters of Rapid Update Cycle-2 Tornado Proximity Environments", Weather and Forecasting, American Meteorological Society, Vol 32, Num 2, pp 743-761, 2017, doi:10.1175/waf-d-16-0029.1


Elif Ertekin: "QMCDB: A Living Database to Accelerate Worldwide Development & Usage of Quantum Monte Carlo Methods", 2017 Blue Waters Annual Report, pp 126-127, 2017


Rohit Dhariwal, Sarma L. Rani, and Donald L. Koch: "Stochastic Theory and Direct Numerical Simulations of the Relative Motion of High-Inertia Particle Pairs in Isotropic Turbulence", Journal of Fluid Mechanics, Cambridge University Press, Vol 813, pp 205-249, 2017, doi:10.1017/jfm.2016.859


Matthias Diener, Sam White, Laxmikant V. Kale, Michael Campbell, Daniel J. Bodony, and Jonathan B. Freund: "Improving the Memory Access Locality of Hybrid MPI Applications", ACM Press, Proceedings of the 24th European MPI Users' Group Meeting (EuroMPI '17), pp 11:1-11:10, Chicago, Illinois, U.S.A., 2017, doi:10.1145/3127024.3127038


F.A. Sabet, O. Jin, S. Koric, and I. Jasiuk: "Nonlinear Micro-CT Based FE Modeling of Trabecular Bone-Sensitivity of Apparent Response to Tissue Constitutive Law and Bone Volume Fraction", International Journal for Numerical Methods in Biomedical Engineering, Wiley-Blackwell, Vol 34, Num 4, pp e2941, 2017, doi:10.1002/cnm.2941


Alexander S. Moffett, Kyle W. Bender, Steven C. Huber, and Diwakar Shukla: "Molecular Dynamics Simulations Reveal the Conformational Dynamics of Arabidopsis thaliana BRI1 and BAK1 Receptor-Like Kinases", Journal of Biological Chemistry, American Society for Biochemistry & Molecular Biology (ASBMB), Vol 292, Num 30, pp 12643-12652, 2017, doi:10.1074/jbc.m117.792762


Saurabh Shukla, Zahra Shamsi, Alexander S. Moffett, Balaji Selvam, and Diwakar Shukla: "Application of Hidden Markov Models in Biomolecular Simulations", Springer New York, Hidden Markov Models: Methods and Protocols, pp 29-41, 2017, doi:10.1007/978-1-4939-6753-7_3


Pranjal Vachaspati and Tandy Warnow: "FastRFS: Fast and Accurate Robinson-Foulds Supertrees using Constrained Exact Optimization", Bioinformatics, Oxford University Press, Vol 33, Num 5, pp 631-639, 2017, doi:10.1093/bioinformatics/btw600


Jaehyung Yu, Lucas K. Wagner, and Elif Ertekin: "Fixed-node diffusion Monte Carlo description of nitrogen defects in zinc oxide", Physical Review B, American Physical Society, Vol 95, Num 7, pp 075209, 2017, doi:10.1103/PhysRevB.95.075209


A. C. Dreyfuss, K. D. Launey, T. Dytrych, J. P. Draayer, R. B. Baker, C. M. Deibel, and C. Bahri: "Understanding Emergent Collectivity and Clustering in Nuclei from a Symmetry-Based No-Core Shell-Model Perspective", Physical Review C, American Physical Society, Vol 95, Num 4, pp 044312, 2017, doi:10.1103/physrevc.95.044312


Amir Barati Farimani, Mohammad Heiranian, Kyoungmin Min, and Narayana R. Aluru: "Antibody Subclass Detection Using Graphene Nanopores", Journal of Physical Chemistry Letters, American Chemical Society, Vol 8, Num 7, pp 1670-1676, 2017, doi:10.1021/acs.jpclett.7b00385


M. P. Clay, D. Buaria, T. Gotoh, and P. K. Yeung: "A Dual Communicator and Dual Grid-Resolution Algorithm for Petascale Simulations of Turbulent Mixing at High Schmidt Number", Computer Physics Communications, Elsevier BV, Vol 219, pp 313-328, 2017, doi:10.1016/j.cpc.2017.06.009


Kartik P. Iyer, Katepalli R. Sreenivasan, and P. K. Yeung: "Reynolds Number Scaling of Velocity Increments in Isotropic Turbulence", Physical Review E, American Physical Society, Vol 95, Num 2, pp 021101, 2017, doi:10.1103/physreve.95.021101


K. Jin, S. P. Vanka, R. K. Agarwal, and B. G. Thomas: "GPU Accelerated Simulations of Three-Dimensional Flow of Power-Law Fluids in a Driven Cube", International Journal of Computational Fluid Dynamics, Informa UK Limited, Vol 31, Num 1, pp 36-56, 2017, doi:10.1080/10618562.2016.1270449


S. R. Totorica, T. Abel, and F. Fiuza: "Particle Acceleration in Laser-Driven Magnetic Reconnection", Physics of Plasmas, AIP Publishing, Vol 24, Num 4, pp 041408, 2017, doi:10.1063/1.4978627


Hillary Schwarb, Curtis L. Johnson, Ana M. Daugherty, Charles H. Hillman, Arthur F. Kramer, Neal J. Cohen, and Aron K. Barbey: "Aerobic Fitness, Hippocampal Viscoelasticity, and Relational Memory Performance", NeuroImage, Elsevier BV, Vol 153, pp 179-188, 2017, doi:10.1016/j.neuroimage.2017.03.061


Yongyang Cai, Kenneth Judd, and Jevgenijs Steinbuks: "A Nonlinear Certainty Equivalent Approximation Method for Dynamic Stochastic Problems", Quantitative Economics, The Econometric Society, Vol 8, Num 1, pp 117-147, 2017, doi:10.3982/qe533


Sevin Yeltekin, Yongyang Cai, and Kenneth L. Judd: "Computing Equilibria of Dynamic Games", Operations Research, Institute for Operations Research and the Management Sciences (INFORMS), Vol 65, Num 2, pp 337--356, 2017, doi:10.1287/opre.2016.1572


Alexandra L. Jones: "Alexandraljones/Imc-Emission: Code Base Plus Select Benchmark Results", Zenodo, Zenodo (website), 2017, doi:10.5281/zenodo.574872


Alexander J. Pak, John M. A. Grime, Prabuddha Sengupta, Antony K. Chen, Aleksander E. P. Durumeric, Anand Srivastava, Mark Yeager, John A. G. Briggs, Jennifer Lippincott-Schwartz, and Gregory A. Voth: "Immature HIV-1 Lattice Assembly Dynamics Are Regulated by Scaffolding from Nucleic Acid and the Plasma Membrane ", Proceedings of the National Academy of Sciences, National Academy of Sciences, 2017, doi:10.1073/pnas.1706600114


S. Namilae, A. Srinivasan, A. Mubayi, M. Scotch, and R. Pahle: "Self-Propelled Pedestrian Dynamics Model: Application to Passenger Movement and Infection Propagation in Airplanes", Physica A: Statistical Mechanics and its Applications, Elsevier BV, Vol 465, pp 248--260, 2017, doi:10.1016/j.physa.2016.08.028


Sirish Namilae, Pierrot Derjany, Anuj Mubayi, Mathew Scotch, and Ashok Srinivasan: "Multiscale Model for Pedestrian and Infection Dynamics During Air Travel", Physical Review E, American Physical Society, Vol 95, Num 5, pp 052320, 2017, doi:10.1103/physreve.95.052320


Jiashun Hu, Manuele Faccenda, and Lijun Liu: "Subduction-Controlled Mantle Flow and Seismic Anisotropy in South America", Earth and Planetary Science Letters, Elsevier BV, Vol 470, pp 13--24, 2017, doi:10.1016/j.epsl.2017.04.027


Sung Jun Lim, Andre Schleife, and Andrew M. Smith: "Optical Determination of Crystal Phase in Semiconductor Nanocrystals", Nature Communications, Springer Nature, Vol 8, pp 14849, 2017, doi:10.1038/ncomms14849


Matthew P. Harrigan, Keri A. McKiernan, Veerabahu Shanmugasundaram, Rajiah Aldrin Denny, and Vijay S. Pande: "Markov Modeling Reveals Novel Intracellular Modulation of the Human TREK-2 Selectivity Filter", Scientific Reports, Springer Nature, Vol 7, Num 1, 2017, doi:10.1038/s41598-017-00256-y


Stuart L. Shapiro: "Black Holes, Disks, and Jets Following Binary Mergers and Stellar Collapse: The Narrow Range of Electromagnetic Luminosities and Accretion Rates", Physical Review D, American Physical Society, Vol 95, Num 10, pp 101303, 2017, doi:10.1103/physrevd.95.101303


Antonios Tsokaros, Milton Ruiz, Vasileios Paschalidis, Stuart L. Shapiro, Luca Baiotti, and Koji Uryu: "Gravitational Wave Content and Stability of Uniformly, Rotating, Triaxial Neutron Stars in General Relativity", Physical Review D, American Physical Society, Vol 95, Num 12, pp 124057, 2017, doi:10.1103/physrevd.95.124057


Kurt R. Brorsen, Michael V. Pak, and Sharon Hammes-Schiffer: "Calculation of Positron Binding Energies and Electron-Positron Annihilation Rates for Atomic Systems with the Reduced Explicitly Correlated Hartree-Fock Method in the Nuclear-Electronic Orbital Framework", Journal of Physical Chemistry A, American Chemical Society, Vol 121, Num 2, pp 515-522, 2017, doi:10.1021/acs.jpca.6b10124


Kurt R. Brorsen, Yang Yang, Michael V. Pak, and Sharon Hammes-Schiffer: "Is the Accuracy of Density Functional Theory for Atomization Energies and Densities in Bonding Regions Correlated?", Journal of Physical Chemistry Letters, American Chemical Society, Vol 8, Num 9, pp 2076-2081, 2017, doi:10.1021/acs.jpclett.7b00774


Puja Goyal and Sharon Hammes-Schiffer: "Role of Active Site Conformational Changes in Photocycle Activation of the App A BLUF Photoreceptor", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 114, Num 7, pp 1480-1485, 2017, doi:10.1073/pnas.1621393114


Cole M. Johnson, So Hirata, and Seiichiro Ten-no: "Explicit Correlation Factors", Chemical Physics Letters, Elsevier BV, Vol 683, pp 247--252, 2017, doi:10.1016/j.cplett.2017.02.072


Daniel Dumett Torres, Progna Banerjee, Sudhakar Pamidighantam, and Prashant K. Jain: "A Non-Natural Wurtzite Polymorph of HgSe: A Potential 3D Topological Insulator", Chemistry of Materials, American Chemical Society, Vol 29, Num 15, pp 6356-6366, 2017, doi:10.1021/acs.chemmater.7b01674


Chao Zhang, Lian Duan, and Meelan M. Choudhari: "Effect of Wall Cooling on Boundary-Layer-Induced Pressure Fluctuations at Mach 6", Journal of Fluid Mechanics, Cambridge University Press, Vol 822, pp 5-30, 2017, doi:10.1017/jfm.2017.212


Joseph A. Morrone, Alberto Perez, Qiaolin Deng, Sookhee N. Ha, M. Katharine Holloway, Tomi K. Sawyer, Bradley S. Sherborne, Frank K. Brown, and Ken A. Dill: "Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled alpha-Helical Peptides to MDM2 and MDMX", Journal of Chemical Theory and Computation, American Chemical Society, Vol 13, Num 2, pp 863-869, 2017, doi:10.1021/acs.jctc.6b00978


Joseph A. Morrone, Alberto Perez, Justin MacCallum, and Ken A. Dill: "Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics", Journal of Chemical Theory and Computation, American Chemical Society, Vol 13, Num 2, pp 870-876, 2017, doi:10.1021/acs.jctc.6b00977


Sherwood Richers, Christian D. Ott, Ernazar Abdikamalov, Evan O'Connor, and Chris Sullivan: "Equation of State Effects on Gravitational Waves from Rotating Core Collapse", Physical Review D, American Physical Society, Vol 95, Num 6, pp 063019, 2017, doi:10.1103/physrevd.95.063019


Sherwood Richers, Hiroki Nagakura, Christian D. Ott, Joshua Dolence, Kohsuke Sumiyoshi, and Shoichi Yamada: "A Detailed Comparison of Multidimensional Boltzmann Neutrino Transport Methods in Core-collapse Supernovae", Astrophysical Journal, The American Astronomical Society, Vol 847, Num 2, pp 133, 2017, doi:10.3847/1538-4357/aa8bb2


D. Baumgardner, S. J. Abel, D. Axisa, R. Cotton, J. Crosier, P. Field, C. Gurganus, A. Heymsfield, A. Korolev, M. Krämer, P. Lawson, G. McFarquhar, Z. Ulanowski, and J. Um: "Cloud Ice Properties: In Situ Measurement Challenges", Meteorological Monographs, American Meteorological Society, Vol 58, pp 9.1-9.23, 2017, doi:10.1175/amsmonographs-d-16-0011.1


Andrew Huang, Hui Li, Ryan L. Sriver, Alexey V. Fedorov, and Chris M. Brierley: "Regional Variations in the Ocean Response to Tropical Cyclones: Ocean Mixing Versus Low Cloud Suppression", Geophysical Research Letters, Wiley-Blackwell, Vol 44, Num 4, pp 1947-1955, 2017, doi:10.1002/2016gl072023


Zachary Zobel, Jiali Wang, Donald J. Wuebbles, and V. Rao Kotamarthi: "Evaluations of High-Resolution Dynamically Downscaled Ensembles Over the Contiguous United States", Climate Dynamics, Springer Nature, Vol 50, Num 3, pp 863-884, 2017, doi:10.1007/s00382-017-3645-6


Lunan Sun, Vasileios Paschalidis, Milton Ruiz, and Stuart L. Shapiro: "Magnetorotational Collapse of Supermassive Stars: Black Hole Formation, Gravitational Waves, and Jets", Physical Review D, American Physical Society, Vol 96, Num 4, pp 043006, 2017, doi:10.1103/physrevd.96.043006


Dennis B. Bowen, Manuela Campanelli, Julian H. Krolik, Vassilios Mewes, and Scott C. Noble: "Relativistic Dynamics and Mass Exchange in Binary Black Hole Mini-disks", Astrophysical Journal, The American Astronomical Society, Vol 838, Num 1, pp 42, 2017, doi:10.3847/1538-4357/aa63f3


David J. Luitz and Yevgeny Bar Lev: "Information Propagation in Isolated Quantum Systems", Physical Review B, American Physical Society, Vol 96, Num 2, pp 020406, 2017, doi:10.1103/physrevb.96.020406


David J. Luitz and Yevgeny Bar Lev: "The Ergodic Side of the Many-Body Localization Transition", Annalen der Physik, Wiley-Blackwell, Vol 529, Num 7, pp 1600350, 2017, doi:10.1002/andp.201600350


Amir Barati Farimani, Payam Dibaeinia, and Narayana R. Aluru: "DNA Origami-Graphene Hybrid Nanopore for DNA Detection", ACS Applied Materials & Interfaces, American Chemical Society, Vol 9, Num 1, pp 92-100, 2017, doi:10.1021/acsami.6b11001


Karl Decker, Martin Page, Ashley Boyd, Irene MacAllister, Mark Ginsberg, and Aleksei Aksimentiev: "Selective Permeability of Truncated Aquaporin 1 in Silico", ACS Biomaterials Science & Engineering, American Chemical Society, Vol 3, Num 3, pp 342-348, 2017, doi:10.1021/acsbiomaterials.6b00583


Jahan Claes and Bryan K. Clark: "Finite-Temperature Properties of Strongly Correlated Systems via Variational Monte Carlo", Physical Review B, American Physical Society, Vol 95, Num 20, pp 205109, 2017, doi:10.1103/physrevb.95.205109


David Pekker, Bryan K. Clark, Vadim Oganesyan, and Gil Refael: "Fixed Points of Wegner-Wilson Flows and Many-Body Localization", Physical Review Letters, American Physical Society, Vol 119, Num 7, pp 075701, 2017, doi:10.1103/PhysRevLett.119.075701


Xiongjie Yu, David Pekker, and Bryan K. Clark: "Finding Matrix Product State Representations of Highly Excited Eigenstates of Many-Body Localized Hamiltonians", Physical Review Letters, American Physical Society, Vol 118, Num 1, pp 017201, 2017, doi:10.1103/physrevlett.118.017201


David Pekker and Bryan K. Clark: "Encoding the Structure of Many-Body Localization with Matrix Product Operators", Physical Review B, American Physical Society, Vol 95, Num 3, pp 035116, 2017, doi:10.1103/physrevb.95.035116


Puja Goyal and Sharon Hammes-Schiffer: "Tuning the Ultrafast Dynamics of Photoinduced Proton-Coupled Electron Transfer in Energy Conversion Processes", ACS Energy Letters, American Chemical Society, Vol 2, Num 2, pp 512-519, 2017, doi:10.1021/acsenergylett.6b00723


Revathi Jambunathan, and Deborah A. Levin: "Advanced Parallelization Strategies Using Hybrid MPI-CUDA Octree DSMC Method for Modeling Flow Through Porous Media", Computers & Fluids, Elsevier BV, Vol 149, pp 70--87, 2017, doi:10.1016/j.compfluid.2017.02.020


Jerry P. Draayer, Tomas Dytrych, and Kristina D. Launey: "Symmetry-adapted No-core Shell Model - the Ab Initio Picture of Nuclear Collectivity", World Scientific, Emergent Phenomena in Atomic Nuclei from Large-Scale Modeling, pp 229-263, 2017, doi:10.1142/9789813146051_0008


J. P. Draayer, K. D. Launey, T. Dytrych, A. C. Dreyfuss, R. B. Baker, and M. E. Miora.: "No-core Symplectic Model: Exploiting Hidden Symmetry in Atomic Nuclei", IOP Publishing Ltd, Journal of Physics: Conference Series (11th International Conference on Clustering Aspects of Nuclear Structure and Dynamics), Vol 863, Num 1, pp 012008, Naples, Italy, 2017, doi:10.1088/1742-6596/863/1/012008


James W. Mazzuca and Chase P. Schultz: "Quantum Mechanical Enhancement of Rate Constants and Kinetic Isotope Effects for Water-Mediated Proton Transfer in a Model Biological System", Journal of Physical Chemistry A, American Chemical Society, Vol 121, Num 4, pp 819-826, 2017, doi:10.1021/acs.jpca.6b10337


T. K. Kim, N. V. Pogorelov, and L. F. Burlaga: "Modeling Shocks Detected by Voyager 1 in the Local Interstellar Medium", Astrophysical Journal Letters, The American Astronomical Society, Vol 843, Num 2, pp L32, 2017, doi:10.3847/2041-8213/aa7b2b


V. López-Barquero, S. Xu, P. Desiati, A. Lazarian, N. V. Pogorelov, and H. Yan: "TeV Cosmic-Ray Anisotropy from the Magnetic Field at the Heliospheric Boundary", Astrophysical Journal, The American Astronomical Society, Vol 842, Num 1, pp 54, 2017, doi:10.3847/1538-4357/aa74d1


N. V. Pogorelov, S. N. Borovikov, I. A. Kryukov, S. T. Wu, M. S. Yalim, P. C. Colella, and B. Van Straalen: "Modeling Coronal Mass Ejections with the Multi-Scale Fluid-Kinetic Simulation Suite", IOP Publishing Ltd, Journal of Physics: Conference Series (11th International Conference on Numerical Modeling of Space Plasma Flows, ASTRONUM 2016), Vol 837, Num 1, pp 012014, Monterey, California, U.S.A., 2017, doi:10.1088/1742-6596/837/1/012014


N. V. Pogorelov, H. Fichtner, A. Czechowski, A. Lazarian, B. Lembege, J. A. le Roux, M. S. Potgieter, K. Scherer, E. C. Stone, R. D. Strauss, T. Wiengarten, P. Wurz, G. P. Zank, and M. Zhang: "Heliosheath Processes and the Structure of the Heliopause: Modeling Energetic Particles, Cosmic Rays, and Magnetic Fields", Space Science Reviews, Springer Nature, Vol 212, Num 1, pp 193--248, 2017, doi:10.1007/s11214-017-0354-8


Mehmet Sarp Yalim, Nikolai Pogorelov, and Yang Liu: "A data-driven MHD model of the global solar corona within Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS)", IOP Publishing Ltd, Journal of Physics: Conference Series (11th International Conference on Numerical Modeling of Space Plasma Flows, ASTRONUM 2016), Vol 837, Num 1, pp 012015, Monterey, California, U.S.A., 2017, doi:10.1088/1742-6596/837/1/012015


E. J. Zirnstein, J. Heerikhuisen, G. P. Zank, N. V. Pogorelov, H. O. Funsten, D. J. McComas, D. B. Reisenfeld, and N. A. Schwadron: "Structure of the Heliotail from Interstellar Boundary Explorer Observations: Implications for the 11-year Solar Cycle and Pickup Ions in the Heliosheath", Astrophysical Journal, American Astronomical Society, Vol 836, Num 2, pp 238, 2017, doi:10.3847/1538-4357/aa5cb2


Jon Calhoun, Marc Snir, Luke N. Olson, and William D. Gropp: "Towards a More Complete Understanding of SDC Propagation", ACM Press, Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing (HPDC '17), pp 131, Washington, D.C., U.S.A., 2017, doi:10.1145/3078597.3078617


Michael A. Lively, Brandon Holybee, Michael Toriyama, and Jean Paul Allain: "Massive-Scale Molecular Dynamics of Ion-Irradiated III-v Compound Semiconductors at the Onset of Nanopatterning", Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Elsevier BV, Vol 409, Num Supplement C, pp 282-287, 2017, doi:10.1016/j.nimb.2017.04.047


Andrew C. Kirby, Michael Brazell, Zhi Yang, Rajib Roy, Behzad Reza Ahrabi, Dimitri Mavriplis, Jay Sitaraman, and Michael K. Stoellinger: "Wind Farm Simulations Using an Overset Hp-Adaptive Approach with Blade-Resolved Turbine Models", American Institute of Aeronautics and Astronautics, 23rd AIAA Computational Fluid Dynamics Conference, Denver, Colorado, U.S.A., 2017, doi:10.2514/6.2017-3958


Michael J. Brazell, Andrew C. Kirby, and Dimitri Mavriplis: "A High-Order Discontinuous-Galerkin Octree-Based AMR Solver for Overset Simulations", American Institute of Aeronautics and Astronautics, 23rd AIAA Computational Fluid Dynamics Conference, Denver, Colorado, U.S.A., 2017, doi:10.2514/6.2017-3944


Abhilash Harpale and Huck Beng Chew: "Hydrogen-Plasma Patterning of Multilayer Graphene: Mechanisms and Modeling", Carbon, Elsevier BV, Vol 117, pp 82--91, 2017, doi:10.1016/j.carbon.2017.02.062


Shu-Ching Ou, Justin A. Drake, and B. Montgomery Pettitt: "Nonpolar Solvation Free Energy from Proximal Distribution Functions", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 15, pp 3555-3564, 2017, doi:10.1021/acs.jpcb.6b09528


David Radice, Sebastiano Bernuzzi, Walter Del Pozzo, Luke F. Roberts, and Christian D. Ott: "Probing Extreme-density Matter with Gravitational-wave Observations of Binary Neutron Star Merger Remnants", Astrophysical Journal Letters, The American Astronomical Society, Vol 842, Num 2, pp L10, 2017, doi:10.3847/2041-8213/aa775f


Jonathan Blackman, Scott E. Field, Mark A. Scheel, Chad R. Galley, Christian D. Ott, Michael Boyle, Lawrence E. Kidder, Harald P. Pfeiffer, and Béla Szilágyi: "Numerical Relativity Waveform Surrogate Model for Generically Precessing Binary Black Hole Mergers", Physical Review D, American Physical Society, Vol 96, Num 2, pp 024058, 2017, doi:10.1103/physrevd.96.024058


Shuai Zhang, Kevin P. Driver, François Soubiran, and Burkhard Militzer: "First-Principles Equation of State and Shock Compression Predictions of Warm Dense Hydrocarbons", Physical Review E, American Physical Society, Vol 96, Num 1, pp 013204, 2017, doi:10.1103/physreve.96.013204


K. P. Driver and B. Militzer: "First-Principles Simulations of Warm Dense Lithium Fluoride", Physical Review E, American Physical Society, Vol 95, Num 4, pp 043205, 2017, doi:10.1103/physreve.95.043205


K. P. Driver, François Soubiran, Shuai Zhang, and B. Militzer: "Comparison of Path Integral Monte Carlo Simulations of Helium, Carbon, Nitrogen, Oxygen, Water, Neon, and Silicon Plasmas", High Energy Density Physics, Elsevier BV, Vol 23, pp 81-89, 2017, doi:10.1016/j.hedp.2017.03.003


Shuai Zhang, Kevin P. Driver, François Soubiran, and Burkhard Militzer: "Equation of state and shock compression of warm dense sodium—A first-principles study", Journal of Chemical Physics, AIP Publishing, Vol 146, Num 7, pp 074505, 2017, doi:10.1063/1.4976559


Daniel H. Moser and Sonia Lasher-Trapp: "The Influence of Successive Thermals on Entrainment and Dilution in a Simulated Cumulus Congestus", Journal of the Atmospheric Sciences, American Meteorological Society, Vol 74, Num 2, pp 375-392, 2017, doi:10.1175/jas-d-16-0144.1


John J. Podesta and Vadim Roytershteyn: "The Most Intense Electrical Currents in the Solar Wind: Comparisons Between Single-Spacecraft Measurements and Plasma Turbulence Simulations", Journal of Geophysical Research: Space Physics, Wiley-Blackwell, Vol 122, Num 7, pp 6991--7004, 2017, doi:10.1002/2017ja024074


Ashraf Idkaidek, Vineet Agarwal, and Iwona Jasiuk: "Finite Element Simulation of Reference Point Indentation on Bone", Journal of the Mechanical Behavior of Biomedical Materials, Elsevier BV, Vol 65, pp 574-583, 2017, doi:10.1016/j.jmbbm.2016.08.031


Paul Michael Hime: "Genomic Perspectives on Amphibian Evolution across Multiple Phylogenetic Scales", University of Kentucky Libraries, UKnowledge, Vol Theses and Dissertations, Num 45, 2017, doi:10.13023/ETD.2017.284


Morteza Khabiri and Peter L. Freddolino: "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 20, pp 5151-5161, 2017, doi:10.1021/acs.jpcb.6b12450


E.A. Huerta, Prayush Kumar, Bhanu Agarwal, Daniel George, Hsi-Yu Schive, Harald P. Pfeiffer, Roland Haas, Wei Ren, Tony Chu, Michael Boyle, Daniel A. Hemberger, Lawrence E. Kidder, Mark A. Scheel, and Bela Szilagyi: "Complete Waveform Model for Compact Binaries on Eccentric Orbits", Physical Review D, American Physical Society, Vol 95, Num 2, pp 024038, 2017, doi:10.1103/physrevd.95.024038


Katharine J. Cahill, Scott Lathrop, and Steven Gordon: "Building a Community of Practice to Prepare the HPC Workforce", Elsevier BV, Procedia Computer Science (17th annual International Conference on Computational Science, ICCS 2017), Vol 108, pp 2131-2140, Zürich, Switzerland, 2017, doi:10.1016/j.procs.2017.05.059


Y. Omori, R. Chown, G. Simard, K. T. Story, K. Aylor, E. J. Baxter, B. A. Benson, L. E. Bleem, J. E. Carlstrom, C. L. Chang, H-M. Cho, T. M. Crawford, A. T. Crites, T. de Haan, M. A. Dobbs, W. B. Everett, E. M. George, N. W. Halverson, N. L. Harrington, G. P. Holder, Z. Hou, W. L. Holzapfel, J. D. Hrubes, L. Knox, A. T. Lee, E. M. Leitch, D. Luong-Van, A. Manzotti, D. P. Marrone, J. J. McMahon, S. S. Meyer, L. M. Mocanu, J. J. Mohr, T. Natoli, S. Padin, C. Pryke, C. L. Reichardt, J. E. Ruhl, J. T. Sayre, K. K. Schaffer, E. Shirokoff, Z. Staniszewski, A. A. Stark, K. Vanderlinde, J. D. Vieira, R. Williamson, O. Zahn: "A 2500 deg(2) CMB Lensing Map from Combined South Pole Telescope and Planck Data", Astrophysical Journal, The American Astronomical Society, Vol 849, Num 2, pp 124, 2017, doi:10.3847/1538-4357/aa8d1d


J. Komijani, A. Bazavov, C. Bernard, N. Brambilla, N. Brown, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, E. Gámiz, Steven Gottlieb, U.M. Heller, A.S. Kronfeld, J. Laiho, P.B. Mackenzie, C. Monahan, Heechang Na, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint, A. Vairo, R.S. Van de Water: "Decay constants fB and fBs and quark masses mb and mc from HISQ simulations", Proceedings of Science, Proceedings, 34th International Symposium on Lattice Field Theory (Lattice 2016), Vol 256, pp 294, Southampton, England, U.K., 2017, doi:10.22323/1.256.0294


Bret M. Boyd, Julie M. Allen, Nam-Phuong Nguyen, Andrew D. Sweet, Tandy Warnow, Michael D. Shapiro, Scott M. Villa, Sarah E. Bush, Dale H. Clayton, Kevin P. Johnson: "Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola)", Systematic Biology, Oxford University Press, Vol 66, Num 6, pp 896–911, 2017, doi:10.1093/sysbio/syx027


Julie M. Allen, Bret Boyd, Nam-Phuong Nguyen, Pranjal Vachaspati, Tandy Warnow, Daisie I. Huang, Patrick G. S. Grady, Kayce C. Bell, Quentin C. B. Cronk, Lawrence Mugisha, Barry R. Pittendrigh, M. Soledad Leonardi, David L. Reed, Kevin P. Johnson: "Phylogenomics from Whole Genome Sequences Using aTRAM", Systematic Biology, Oxford University Press, Vol 66, Num 5, pp 786–798, 2017, doi:10.1093/sysbio/syw105


Y. Feng and C. Modi: "A Fast Algorithm for Identifying Friends-of-Friends Halos", Astronomy and Computing, Elsevier BV, Vol 20, pp 44-51, 2017, doi:10.1016/j.ascom.2017.05.004


Di Matteo, Tiziana and Croft, Rupert A. C. and Feng, Yu and Waters, Dacen and Wilkins, Stephen: "The origin of the most massive black holes at high-z: BlueTides and the next quasar frontier", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 467, Num 4, pp 4243-4251, 2017, doi:10.1093/mnras/stx319


Yan Li, Miroslav Hodak, Wenchang Lu, and J. Bernholc: "Selective Sensing of Ethylene and Glucose Using Carbon-Nanotube-Based Sensors: An Ab Initio Investigation", Nanoscale, Royal Society of Chemistry, Vol 9, Num 4, pp 1687-1698, 2017, doi:10.1039/c6nr07371a


Chuanxu Ma, Zhongcan Xiao, Honghai Zhang, Liangbo Liang, Jingsong Huang, Wenchang Lu, Bobby G. Sumpter, Kunlun Hong, J. Bernholc, and An-Ping Li: "Controllable Conversion of Quasi-Freestanding Polymer Chains to Graphene Nanoribbons", Nature Communications, Springer Nature, Vol 8, pp 14815, 2017, doi:10.1038/ncomms14815


Yash Thakur, Bing Zhang, Rui Dong, Wenchang Lu, C. Iacob, J. Runt, J. Bernholc, and Q.M. Zhang: "Generating High Dielectric Constant Blends from Lower Dielectric Constant Dipolar Polymers Using Nanostructure Engineering", Nano Energy, Elsevier BV, Vol 32, pp 73--79, 2017, doi:10.1016/j.nanoen.2016.12.021


Natalia V. Dolgova, Corey Yu, John P. Cvitkovic, Miroslav Hodak, Kurt H. Nienaber, Kelly L. Summers, Julien J. H. Cotelesage, Jerzy Bernholc, George A. Kaminski, Ingrid J. Pickering, Graham N. George, and Oleg Y. Dmitriev: "Binding of Copper and Cisplatin to Atox1 Is Mediated by Glutathione Through the Formation of Metal-Sulfur Clusters", Biochemistry, American Chemical Society, Vol 56, Num 24, pp 3129-3141, 2017, doi:10.1021/acs.biochem.7b00293


Ozgur Tumuklu and Deborah A. Levin: "On the Temporal Evolution in Laminar Separated Boundary Layer Shock-Interaction Flows Using DSMC", American Institute of Aeronautics and Astronautics, 55th AIAA Aerospace Sciences Meeting, Grapevine, Texas, U.S.A., 2017, doi:10.2514/6.2017-1614


Saurabh Sawant, Ozgur Tumuklu, Revathi Jambunathan, and Deborah A. Levin: "Novel Use of AMR Unstructured Grids in DSMC Compressible Flow Simulations", American Institute of Aeronautics and Astronautics, 47th AIAA Thermophysics Conference, Denver, Colorado, U.S.A., 2017, doi:10.2514/6.2017-4028


P. J. Mendygral, N. Radcliffe, K. Kandalla, D. Porter, B. J. O’Neill, C. Nolting, P. Edmon, J. M. F. Donnert, and T. W. Jones: "WOMBAT: A Scalable and High-performance Astrophysical Magnetohydrodynamics Code", Astrophysical Journal Supplement Series, American Astronomical Society, Vol 228, Num 2, pp 23, 2017, doi:10.3847/1538-4365/aa5b9c


S. Jones, R. Andrassy, S. Sandalski, A. Davis, P. Woodward, and F. Herwig: "Idealized hydrodynamic simulations of turbulent oxygen-burning shell convection in 4 pi geometry", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 465, Num 3, pp 2991-3010, 2017, doi:10.1093/mnras/stw2783


Shamsi, Zahra and Moffett, Alexander S. and Shukla, Diwakar: "Enhanced unbiased sampling of protein dynamics using evolutionary coupling information", Scientific Reports, Springer Nature, Vol 7, Num 1, 2017, doi:10.1038/s41598-017-12874-7


Juan R. Perilla and Klaus Schulten: "Physical Properties of the HIV-1 Capsid from All-Atom Molecular Dynamics Simulations", Nature Communications, Springer Nature, Vol 8, pp 15959, 2017, doi:10.1038/ncomms15959


T. Primer, A. Bazavov, C. Bernard, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, E. Gamiz, S. Gottlieb, U.M. Heller, J. Komijani, A.S. Kronfeld, J. Laiho, P.B. Mackenzie, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint, R.S. Van de Water, R. Zhou and Fermilab Lattice and MILC Collaborations: "D meson semileptonic form factors with HISQ valence and sea quarks", Proceedings of Science, Proceedings, 34th International Symposium on Lattice Field Theory (Lattice 2016), Vol 256, pp 305, Southhampton, England, U.K., 2017, doi:10.22323/1.256.0305


E. Gámiz, A. Bazavov, C. Bernard, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, Steven Gottlieb, U.M. Heller, J. Komijani, A.S. Kronfeld, J. Laiho, P.B. Mackenzie, E.T. Neil, T. Primer, J.N. Simone, R. Sugar, D. Toussaint, R.S. Van de Water, Ran Zhou: "Kaon semileptonic decays with Nf=2+1+1 HISQ fermions and physical light-quark masses", Proceedings of Science, Proceedings, 34th International Symposium on Lattice Field Theory (Lattice 2016), Vol 256, pp 286, Southampton, England, U.K., 2017, doi:10.22323/1.256.0286


Tyler M. Earnest, Reika Watanabe, John E. Stone, Julia Mahamid, Wolfgang Baumeister, Elizabeth Villa, and Zaida Luthey-Schulten: "Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 15, pp 3871-3881, 2017, doi:10.1021/acs.jpcb.7b00672


Valerio Formicola, Saurabh Jha, Daniel Chen, Fei Deng, Amanda Bonnie, Mike Mason, Jim Brandt, Ann Gentile, Larry Kaplan, Jason Repik, Jeremy Enos, Mike Showerman, Annette Greiner, Zbigniew Kalbarczyk, Ravishankar K. Iyer, William Kramer: "Understanding Fault Scenarios and Impacts through Fault Injection Experiments in Cielo", presented at CUG 2017, Redmond, Washington, U.S.A., 2017


Mert Hidayetogglu, Carl Pearson, Levent Gurel, Wen-Mei Hwu, and Weng Cho Chew: "Scalable Parallel DBIM Solutions of Inverse-Scattering Problems", Institute of Electrical & Electronics Engineers, 2017 Computing and Electromagnetics International Workshop (CEM), pp 65-66, Barcelona, Spain, 2017, doi:10.1109/cem.2017.7991889


Mert Hidayetogglu, Carl Pearson, Weng Cho Chew, Levent Gurel, and Wen-Mei Hwu: "Large Inverse-Scattering Solutions with DBIM on GPU-Enabled Supercomputers", Institute of Electrical & Electronics Engineers, 2017 International Applied Computational Electromagnetics Society Symposium - Italy (ACES), pp 1-2, Florence, Italy, 2017, doi:10.23919/ropaces.2017.7916310


Saurabh Jha, Valerio Formicola, Catello Di Martino, Mark Dalton, William T. Kramer, Zbigniew Kalbarczyk, and Ravishankar K. Iyer: "Resiliency of HPC Interconnects: A Case Study of Interconnect Failures and Recovery in Blue Waters", IEEE Transactions on Dependable and Secure Computing, Institute of Electrical and Electronics Engineers, Vol 15, Num 6, pp 915-930, 2017, doi:10.1109/tdsc.2017.2737537


Saurabh Jha, Jim Brandt, Ann Gentile, Zbigniew Kalbarczyk, Greg Bauer, Jeremy Enos, Michael Showerman, Larry Kaplan, Brett Bode, Annette Greiner, Amanda Bonnie, Mike Mason, William Kramer, and Ravishankar Iyer: "Holistic Measurement Driven System Assessment", Institute of Electrical & Electronics Engineers, 2017 IEEE International Conference on Cluster Computing (CLUSTER), pp 797-800, Honolulu, Hawai'i, U.S.A., 2017, doi:10.1109/CLUSTER.2017.124


Brett Bode, Jim Glasgow, Michelle Butler, Sean Stevens, Nate Schumann, Frank Zago: "Implementing a Hierarchical Storage Management system in a large-scale Lustre and HPSS environment", presented at CUG 2017, Redmond, Washington, U.S.A., 2017


Greg Bauer, Victor Anisimov, Galen Arnold, Brett Bode, Robert Brunner, Tom Cortese, Roland Haas, Andriy Kot, William Kramer, JaeHyuk Kwack, Jing Li, Celso Mendes, Ryan Mokos, Craig Steffen: "Updating the SPP Benchmark Suite for Extreme-Scale Systems", presented at CUG 2017, Redmond, Washington, U.S.A., 2017


Colin Maclean: "Python Usage Metrics on Blue Waters", presented at CUG 2017, Redmond, Washington, U.S.A., 2017


Cong Xu, Shane Snyder, Vishwanath Venkatesan, Philip Carns, Omkar Kulkarni, Suren Byna, Robert Sisneros, Kalyana Chadalavada: "DXT: Darshan eXtended Tracing", presented at CUG 2017, Redmond, Washington, U.S.A., 2017


Mohammad Raji, Alok Hota, Robert Sisneros, Peter Messmer, and Jian Huang: "Photo-Guided Exploration of Volume Data Features", The Eurographics Association, Eurographics Symposium on Parallel Graphics and Visualization, pp 31-39, Barcelona, Spain, 2017, doi:10.2312/pgv.20171091


Sarma Rani: "Direct Numerical Simulations of The Relative Motion of High-Inertia Particles in Isotropic Turbulence", 2017 Blue Waters Annual Report, pp 152-153, 2017


Patrick Small, David Gill, Philip J. Maechling, Ricardo Taborda, Scott Callaghan, Thomas H. Jordan, Kim B. Olsen, Geoffrey P. Ely, and Christine Goulet: "The SCEC Unified Community Velocity Model Software Framework", Seismological Research Letters, GeoScienceWorld, Vol 88, Num 6, pp 1539-1552, 2017, doi:10.1785/0220170082


Lisa G. Lippert, Tali Dadosh, Jodi A. Hadden, Vishakha Karnawat, Benjamin T. Diroll, Christopher B. Murray, Erika L. F. Holzbaur, Klaus Schulten, Samara L. Reck-Peterson, and Yale E. Goldman: "Angular Measurements of the Dynein Ring Reveal a Stepping Mechanism Dependent on a Flexible Stalk", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 114, Num 23, pp E4564-E4573, 2017, doi:10.1073/pnas.1620149114


David Ackerman: "Exploring Confinement vs. Orientation Effects in Rigid and Semi-Flexible Polymers Using A Massiveley Parallel Framework", 2017 Blue Waters Annual Report, pp 102-103, 2017


Morgan Smith and Andrew Mercer: "Blue Waters Supercomputing Applications in Climate Modeling with the WRF Model", Journal of Computational Science Education, Shodor, Vol 8, Num 3, pp 36-43, 2017, doi:10.22369/issn.2153-4136/8/3/6


Juan R. Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L. Byeon, Angela M. Gronenborn, Tatyana Polenova, and Peijun Zhang: "CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 15, pp 3853-3863, 2017, doi:10.1021/acs.jpcb.6b13105


Jennifer Corcoran: "Image Processing to Build a Multi-Temporal Vegetation Elevation Model (MTVEM) of the Great Lakes Basin", 2017 Blue Waters Annual Report, pp 66-67, 2017


Wendy Cho: "Enabling Redistricting Reform: A Computational Study of Zoning Optimization", 2017 Blue Waters Annual Report, pp 254-255, 2017


Daniel Bodony: "Reducing Jet Aircraft Noise", 2017 Blue Waters Annual Report, pp 112-113, 2017


John E. Stone, Juan R. Perilla, C. Keith Cassidy, and Klaus Schulten: "GPU-Accelerated Molecular Dynamics Clustering Analysis with OpenACC", Elsevier, Parallel Programming with OpenACC, pp 215-240, 2017, doi:10.1016/b978-0-12-410397-9.00011-1


Frances J. D. Alvarez, Shaoda He, Juan R. Perilla, Sooin Jang, Klaus Schulten, Alan N. Engelman, Sjors H. W. Scheres, and Peijun Zhang: "CryoEM Structure of MxB Reveals a Novel Oligomerization Interface Critical for HIV Restriction", Science Advances, American Association for the Advancement of Science, Vol 3, Num 9, pp e1701264, 2017, doi:10.1126/sciadv.1701264


Iryna Butsky: "The Role of Cosmic Rays in Isolated Disk Galaxies", 2017 Blue Waters Annual Report, pp 262-263, 2017


Robert J. Trapp, Geoffrey R. Marion, and Stephen W. Nesbitt: "The Regulation of Tornado Intensity by Updraft Width", Journal of the Atmospheric Sciences, American Meteorological Society, Vol 74, Num 12, pp 4199-4211, 2017, doi:10.1175/jas-d-16-0331.1


Aleksei Aksimentiev: "Molecular Mechanisim of Nuclear Transport", 2017 Blue Waters Annual Report, pp 194-195, 2017


Minseung Kim, Ameen Eetemadi, and Ilias Tagkopoulos: "DeepPep: Deep Proteome Inference from Peptide Profiles", PLOS Computational Biology, Public Library of Science (PLoS), Vol 13, Num 9, pp e1005661, 2017, doi:10.1371/journal.pcbi.1005661


Alan Calder, Platon I. Karpov, Maria Barrios Sazo, Michael Zingale, and Weiqun Zhang: "Toward simulating Black Widow binaries with CASTRO", Journal of Computational Science Education, Shodor, Vol 8, Num 3, pp 25-29, 2017, doi:10.22369/issn.2153-4136/8/3/4


Wesley Yu and Hans Mark: "Parallelized Model of Low-Thrust Cargo Spacecraft Trajectories and Payload Capabilities to Mars", Journal of Computational Science Education, Shodor, Vol 8, Num 2, pp 46-53, 2017, doi:10.22369/issn.2153-4136/8/2/7


Linh Nguyen and Paul Hemler: "GPU Acceleration for SQL Queries on Large-Scale Distributed Systems", Journal of Computational Science Education, Shodor, Vol 8, Num 1, pp 20-26, 2017, doi:10.22369/issn.2153-4136/8/1/5


Eric Peterson, Max Kelly, and Dr. Victor Pinks II: "How to Build a Fast HPC n-Body Engine From Scratch", Journal of Computational Science Education, Shodor, Vol 8, Num 2, pp 37-45, 2017, doi:10.22369/issn.2153-4136/8/2/6


Junzhe Geng, Prasad Sarangapani, Erik Nelson, Ben Browne, Carl Wordelman, Tillmann Kubis, and Gerhard Klimeck: "NEMO5: Realistic and Efficient NEGF Simulations of GaN Light-Emitting Diodes", SPIE, Proceedings, Physics and Simulation of Optoelectronic Devices XXV (SPIE OPTO), Vol 10098, Num 13, San Francisco, California, U.S.A., 2017, doi:10.1117/12.2256236


Raphael D. Isokpehi, Kiara M. Wootson, Dominique R. Smith-McInnis, and Shaneka S. Simmons: "Interactive Analytics for Complex Cognitive Activities on Information from Annotations of Prokaryotic Genomes", Journal of Computational Science Education, Vol 8, Num 2, pp 29-36, 2017, doi:10.22369/issn.2153-4136/8/2/5


Vincenzo Carnevale: "Mechanism of Temperature Sensitivity in TRPV1 Channel", 2017 Blue Waters Annual Report, pp 202-203, 2017


Reed Hodges, Cleon Dean, and Maxim Durach: "Optical Neutrality: Invisibility Without Cloaking", Optics Letters, The Optical Society, Vol 42, Num 4, pp 691, 2017, doi:10.1364/ol.42.000691


Aleksei Aksimentiev: "DNA Origami Membrane Channels", 2017 Blue Waters Annual Report, pp 192-193, 2017


Dinshaw S. Balsara: "Simulating Two-Fluid MHD Turbulence in Star-Forming Molecular Clouds on The Blue Waters System", 2017 Blue Waters Annual Report, pp 18-19, 2017


Isaac Cann: "Cellusome Structure Determination by Atomistic Simulations Combined with Experimental Assays", 2017 Blue Waters Annual Report, pp 200-201, 2017


Maureen Brooks: "Modeling nonlinear physical-biological interactions: Eddies and Sargassum in the North Atlantic", 2017 Blue Waters Annual Report, pp 260-261, 2017


Joseph S. Haddad, Timothy W. O'Neil, Anthony Deeter, and Zhong-Hui Duan: "An Implementation of Parallel Bayesian Network Learning", Journal of Computational Science Education, Shodor, Vol 8, Num 2, pp 24-28, 2017, doi:10.22369/issn.2153-4136/8/2/4


Venkata Suhas Maringanti, Basileal Imana, and Peter Yoon: "GPU-Accelerated VLSI Routing Using Group Steiner Trees", Journal Of Computational Science Education, Shodor, Vol 8, Num 1, pp 16-19, 2017, doi:10.22369/issn.2153-4136/8/1/4


Ange-Therese Akono: "Multi-Scale and Multi-Physics Modeling of Geopolymer Cement Composites", 2017 Blue Waters Annual Report, pp 104-105, 2017


James Healy and Carlos O. Lousto: "Remnant of binary black-hole mergers: New simulations and peak luminosity studies", Physical Review D, American Physical Society, Vol 95, Num 2, pp 024037, 2017, doi:10.1103/PhysRevD.95.024037


Thomas Cheatham: "Exploring The Structure and Dynamics of Converged Ensembles of DNA and RNA through Molecular Dynamics Simulations", 2017 Blue Waters Annual Report, pp 204-205, 2017


James Healy, Carlos O Lousto, Yosef Zlochower, and Manuela Campanelli: "The RIT binary black hole simulations catalog", Classical and Quantum Gravity, IOP Publishing Ltd, Vol 34, Num 22, pp 224001, 2017, doi:10.1088/1361-6382/aa91b1


Anglés-Alcázar, Daniel; Faucher-Giguère, Claude-André; Quataert, Eliot; Hopkins, Philip F.; Feldmann, Robert; Torrey, Paul; Wetzel, Andrew; Kereš, Dušan: "Black Holes on FIRE: Stellar Feedback Limits Early Feeding of Galactic Nuclei", Monthly Notices of the Royal Astronomical Society: Letters, The Royal Astronomical Society, Vol 472, Num 1, pp L109-L114, 2017, doi:10.1093/mnrasl/slx161


David Ceperley: "Properties of Dense Hydrogen", 2017 Blue Waters Annual Report, pp 114-115, 2017


Jerzy Bernholc: "Petaflops simulation and design of nanoscale materials and devices", 2017 Blue Waters Annual Report, pp 110-111, 2017


Elizabeth Agee: "Resolving plant functional biodiversity to quantify forest drought resistance in the Amazon", 2017 Blue Waters Annual Report, pp 258-259, 2017


Asher Elmquist, Dylan Hatch, Radu Serban, and Dan Negrut: "An Overview of a Connected Autonomous Vehicle Emulator (CAVE)", The American Society of Mechanical Engineers, ASME 2017 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference (IDETC/CIE 2017), Vol 6: 13th International Conference on Multibody Systems, Nonlinear Dynamics, and Control, pp V006T10A036, Cleveland, Ohio, U.S.A., 2017, doi:10.1115/DETC2017-68322


Raul A. Briceño, Jozef J. Dudek, Robert G. Edwards, and David J. Wilson (for the Hadron Spectrum Collaboration): "Isoscalar pi pi Scattering and the sigma Meson Resonance from QCD", Physical Review Letters, American Physical Society, Vol 118, Num 2, pp 022002, 2017, doi:10.1103/physrevlett.118.022002


Huck Beng Chew: "Scalable Nanopatterning of Graphene by Hydrogen-Plasma Etching", 2017 Blue Waters Annual Report, pp 116-117, 2017


Chi-Hing Cheng: "Structural Basis for Extreme Cold Stability in the Eye Lenses of Teleost Fishes", 2017 Blue Waters Annual Report, pp 206-207, 2017


Jon Calhoun: "Analyzing The Propagation of Soft-Error Corruption in HPC Applications", 2017 Blue Waters Annual Report, pp 264-265, 2017


Marin Clark: "High-Resolution Digital Surface Models of The 2016 Mw 7.8 Kaikoura Earthquake, New Zealand", 2017 Blue Waters Annual Report, pp 64-65, 2017


Gustavo Caetano-Anolles: "How function shapes dynamics in protein evolution", 2017 Blue Waters Annual Report, pp 198-199, 2017


Jean Paul Allain: "Harnessing petascale computing to elucidate fundamental mechanisms driving nanopatterning of multicomponent surfaces by directed irradiation synthesis", 2017 Blue Waters Annual Report, pp 106-107, 2017


Narayana Aluru: "Study of DIBs with Functional Channels", 2017 Blue Waters Annual Report, pp 108-109, 2017


Maxim Durach, Reed M. Hodges, and Kelvin Rosado-Ayala: "Computational approaches to scattering by microspheres", Journal of Computational Science Education, Shodor, Vol 8, Num 3, pp 19-24, 2017, doi:10.22369/issn.2153-4136/8/3/3


Andrew Mercer and Taylor Prislovsky: "Using Blue Waters to Assess Non-Tornadic Outbreak Forecast Capability by Lead Time", Journal of Computational Science Education, Shodor, Vol 8, Num 3, pp 30-35, 2017, doi:10.22369/issn.2153-4136/8/3/5


Angela B. Shiflet, George W. Shiflet, Daniel S. Couch, Pietro Hiram Guzzi, and Mario Cannataro: "Educational Module on Genomic Sequence Alignment Using HPC", Journal of Computational Science Education, Shodor, Vol 8, Num 1, pp 7-11, 2017, doi:10.22369/issn.2153-4136/8/1/2


Nathan Sloat, Jui-Wen Liu, and Susan J. Schroeder: "Swellix: a computational tool to explore RNA conformational space", BMC Bioinformatics, Springer Nature, Vol 18, Num 1, pp 504, 2017, doi:10.1186/s12859-017-1910-7


David Toth and Olivia Alford: "Energy-Efficient Virtual Screening with ARM-CPU-Based Computers", Journal of Computational Science Education, Shodor, Vol 8, Num 2, pp 17-23, 2017, doi:10.22369/issn.2153-4136/8/2/3


Max Collins and Dr. Alan B. Craig: "VisMo: Augmented Reality Visualization of Scientific Data and Molecular Structures", Journal of Computational Science Education, Shodor, Vol 8, Num 1, pp 12-15, 2017, doi:10.22369/issn.2153-4136/8/1/3


Donna Cox: "CADENS NSF Project: Digital Literacy, Data Visualization, and The Cinematic Presentation of Science", 2017 Blue Waters Annual Report, pp 170-171, 2017


Davide Curreli: "hPIC: A Scalable Electrostatic Particle-in-Cell for Plasma–Material Interactions", 2017 Blue Waters Annual Report, pp 118-119, 2017


Larry Di Girolamo: "The Terra Data Fusion Project", 2017 Blue Waters Annual Report, pp 68-69, 2017


Tiziana Di Matteo: "Supermassive Black Holes at The Cosmic Frontier", 2017 Blue Waters Annual Report, pp 20-21, 2017


Ken Dill: "Predicting protein structures with physical petascale molecular simulations", 2017 Blue Waters Annual Report, pp 208-209, 2017


Jerry Draayer: "Innovative ab initio symmetry-adapted no-core shell model for advancing fundamental physics and astrophysics", 2017 Blue Waters Annual Report, pp 120-121, 2017


Said Elghobashi: "Dispersion of fully resolved liquid droplets in isotropic turbulent flow", 2017 Blue Waters Annual Report, pp 124-125, 2017


Justin Drake: "Toward Developing A Thermodynamic Model of Binding-Induced Conformational Transitions in Short, Disordered Protein Regions", 2017 Blue Waters Annual Report, pp 266-267, 2017


Ahmed Elbanna: "Multiscale Modeling of Biofilm Dynamics in Drinking Water Distribution Systems: Towards predictive modeling of pathogen outbreaks", 2017 Blue Waters Annual Report, pp 210-211, 2017


Lian Duan: "DNS of Pressure Fluctuations Induced by Supersonic Turbulent Boundary Layers", 2017 Blue Waters Annual Report, pp 122-123, 2017


Paul Fischer: "Numerical methods and software for computational fluid dynamics, NEK5000", 2017 Blue Waters Annual Report, pp 128-129, 2017


Peter Freddolino: "Comprehensive In Silico Mapping of DNA-Binding Protein Affinity Landscapes", 2017 Blue Waters Annual Report, pp 212-213, 2017


Marcelo Garcia: "Direct Numerical Simulation of Turbulence and Sediment Transport in Oscillatory Boundary Layer Flows", 2017 Blue Waters Annual Report, pp 130-131, 2017


Marcelo Garcia: "Large Eddy Simulation of Sediment Transport and Hydrodynamics at River Bifurcations: Using a highly scalable spectral element based CFD solver", 2017 Blue Waters Annual Report, pp 70-71, 2017


Mattia Gazzola: "Optimal bio-locomotion strategies in fluids", 2017 Blue Waters Annual Report, pp 134-135, 2017


Paolo Gardoni: "3D Probabilistic Physics-Based Seismic Hazard Maps for Regional Risk Analysis", 2017 Blue Waters Annual Report, pp 132-133, 2017


Bill Gropp: "Algorithms for extreme-scale systems", 2017 Blue Waters Annual Report, pp 172-173, 2017


Sharon Hammes-Schiffer: "Non-Born-Oppenheimer Effects between Electrons and Protons", 2017 Blue Waters Annual Report, pp 214-215, 2017


Levent Gurel: "Parallelization of the Multilevel Fast Multipole Algorithm (MLFMA) on Heterogeneous CPU-GPU Architectures", 2017 Blue Waters Annual Report, pp 174-175, 2017


Lars Hansen and Yongyang Cai: "Policy Responses to Climate Change in a Dynamic Stochastic Economy", 2017 Blue Waters Annual Report, pp 252-253, 2017


Paul Hime: "Genomic Perspectives on The Amphibian Tree of Life", 2017 Blue Waters Annual Report, pp 268-269, 2017


So Hirata: "Brueckner–Goldstone Quantum Monte Carlo", 2017 Blue Waters Annual Report, pp 216-217, 2017


Gilbert Holder: "Theoretical astrophysics and data analysis", 2017 Blue Waters Annual Report, pp 22-23, 2017


Michael Howard: "Multiscale simulations of complex fluid rheology", 2017 Blue Waters Annual Report, pp 270-271, 2017


Ian Howat: "The Reference Elevation Model of Antarctica", 2017 Blue Waters Annual Report, pp 72-73, 2017


Eliu Huerta Escudero: "Detection of Gravitational Wave Sources in Dense Stellar Environments", 2017 Blue Waters Annual Report, pp 24-25, 2017


Eliu Huerta Escudero: "Deep Neural Networks to Enable Real-Time Multimessenger Astrophysics", 2017 Blue Waters Annual Report, pp 26-27, 2017


Kathryn Huff: "Coupled Multi-Physics of Advanced Molten Salt Nuclear Reactors", 2017 Blue Waters Annual Report, pp 136-137, 2017


Ravishankar Iyer: "Predicting Performance Degradation and Failure of Applications Through System Activity Monitoring", 2017 Blue Waters Annual Report, pp 176-177, 2017


Sohrab Ismail-Beigi: "Understanding Hydrogen Storage in Metal Organic Frameworks Using Massively-Parallel Electronic Structure Calculations", 2017 Blue Waters Annual Report, pp 138-139, 2017


Prashant Jain: "Atomistic Modeling of Transformations in Nanocrystals", 2017 Blue Waters Annual Report, pp 140-141, 2017


Thomas Jones: "Toward Robust Magnetohydrodynamic Simulations of Galaxy Cluster Formation", 2017 Blue Waters Annual Report, pp 28-29, 2017


Alexandra Jones: "High Accuracy Radiative Transfer in Cloudy Atmospheres", 2017 Blue Waters Annual Report, pp 272-273, 2017


Peter Kasson: "How viral membrane organization controls influenza entry", 2017 Blue Waters Annual Report, pp 218-219, 2017


Andrew Kirby: "High Fidelity Blade-Resolved Wind Farm Simulations", 2017 Blue Waters Annual Report, pp 274-275, 2017


Sara Kokkila Schumacher: "Reducing The Computational Cost of Coupled Clustery Theory", 2017 Blue Waters Annual Report, pp 276-277, 2017


Sonia Lasher-Trapp: "Untangling Entrainment and Precipitation in Convective Clouds", 2017 Blue Waters Annual Report, pp 74-75, 2017


Eric Lentz: "Exploring The Nature of Exploding Massive Stars with High Resolution", 2017 Blue Waters Annual Report, pp 30-31, 2017


Deborah Levin: "Modeling Plasma Flows with Kinetic Approaches Using Hybrid CPU-GPU Computing", 2017 Blue Waters Annual Report, pp 32-33, 2017


Deborah Levin: "Kinetic Simulations of Unsteady Shock-Boundary Layer Interactions", 2017 Blue Waters Annual Report, pp 146-147, 2017


Lijun Liu: "Understanding The 4-D Evolution of The Solid Earth Using Geodynamic Models with Data Assimilation", 2017 Blue Waters Annual Report, pp 76-77, 2017


Yi-Hsin Liu: "Three-Dimensional Nature of Collisionless Magnetic Reconnection at Earth's Magnetopause", 2017 Blue Waters Annual Report, pp 34-35, 2017


Zaida Luthey-Schulten: "A Hybrid Stochastic-Deterministic Simulation Method Enables Fast Simulation of Cellular Processes in Eukaryotes", 2017 Blue Waters Annual Report, pp 220-221, 2017


Paul Mackenzie: "High Energy Physics on Blue Waters", 2017 Blue Waters Annual Report, pp 148-149, 2017


James Mazzuca: "Quantum Effects of Proton Transfer in Biological Systems", 2017 Blue Waters Annual Report, pp 226-227, 2017


Paul Morin: "Enhanced Digital Elevation Model for The Arctic", 2017 Blue Waters Annual Report, pp 80-81, 2017


Burkhard Militzer: "First-Principles Computer Simulations of Hydrocarbons under Fusion Conditions", 2017 Blue Waters Annual Report, pp 150-151, 2017


Warren Mori: "Transformative Petascale Particle-in-cell simulations", 2017 Blue Waters Annual Report, pp 36-37, 2017


Rakesh Nagi: "Parallel Algorithms for Solving Large Assignment Problems", 2017 Blue Waters Annual Report, pp 178-179, 2017


Luke Olson: "Localizing Communication in Sparse Matrix Operations", 2017 Blue Waters Annual Report, pp 180-181, 2017


Scott Noble: "Mini-Disk Dynamics about Supermassive Black Holes Binaries", 2017 Blue Waters Annual Report, pp 38-39, 2017


Kevin Olson: "A Critical Evaluation of The OP2/OPS Parallel Meshing and Code-Generation Software", 2017 Blue Waters Annual Report, pp 188, 2017


Michael Norman: "Realistic Simulations of the Intergalactic Medium: The Search for Missing Physics", 2017 Blue Waters Annual Report, pp 40-41, 2017


Brian O'Shea: "Simulating Galaxy Formation across Cosmic Time", 2017 Blue Waters Annual Report, pp 42-43, 2017


Leigh G. Orf: "Simulating The Most Devastating Tornadoes Embedded within Supercell Thunderstorms", 2017 Blue Waters Annual Report, pp 82-83, 2017


Christian Ott: "3D General-Relativistic Radiation-Hydrodynamic Simulations of Core-Collapse Supernovae", 2017 Blue Waters Annual Report, pp 44-45, 2017


Vijay Pande: "Machine Learning Reveals Ligand-Directed Conformational Change of μ Opioid Receptor", 2017 Blue Waters Annual Report, pp 230-231, 2017


Nikolai Pogorelov: "Modeling Physical Processes in the Solar Wind and Local Interstellar Medium with a Multi-Scale Fluid-Kinetic Simulation Suite", 2017 Blue Waters Annual Report, pp 46-47, 2017


Robert Rauber: "High-Resolution Earth-System Modeling Using Blue Waters's Capabilities", 2017 Blue Waters Annual Report, pp 84-85, 2017


Larissa Reames: "Simulated effects of urban environments on the dynamics of a supercell thunderstorm", 2017 Blue Waters Annual Report, pp 278-279, 2017


Sherwood Richers: "Monte Carlo Neutrino Closures in 3D GRMHD Simulations of Core-Collapse Supernovae and Neutron Star Mergers", 2017 Blue Waters Annual Report, pp 280-281, 2017


Caroline Riedl: "Mapping Proton Quark Structure Using Petabytes of COMPASS Data", 2017 Blue Waters Annual Report, pp 154-155, 2017


Benoit Roux: "Elucidating The Molecular Mechanism of C-Type Inactivation in Potassium Channels", 2017 Blue Waters Annual Report, pp 232-233, 2017


Vadim Roytershteyn: "Kinetic Simulations of Large-Scale Plasma Turbulence", 2017 Blue Waters Annual Report, pp 50-51, 2017


Hsi-Yu Schive: "GPU-accelerated Adaptive Mesh Refinement", 2017 Blue Waters Annual Report, pp 52-53, 2017


Stuart Shapiro: "Magnetorotational Collapse of Supermassive Stars: Black-Hole Formation, Graviational Waves, and Jets", 2017 Blue Waters Annual Report, pp 54-55, 2017


Andre Schleife: "Optical Determination of Crystal Phase in Semiconductor Nanocrystals", 2017 Blue Waters Annual Report, pp 156-157, 2017


Sean Seyler: "Understanding The Role of Hydrodynamic Fluctuations in Biomacromolecular Dynamics through The Development of Hybrid Atomistic-Continuum Simulation", 2017 Blue Waters Annual Report, pp 282-283, 2017


Ashok Srinivasan: "Simulation of Viral Infection Propagation Through Air Travel", 2017 Blue Waters Annual Report, pp 242-243, 2017


Marcos Sotomayor: "Stretching The Cadherin Molecular Velcro of Cell-Cell Junctions", 2017 Blue Waters Annual Report, pp 240-241, 2017


Ivan Soltesz: "Data-driven, biologically constrained computational model of the hippocampal network at full scale", 2017 Blue Waters Annual Report, pp 238-239, 2017


Edgar Solomonik: "Performance Evaluation of New Algebraic Algorithms and Libraries", 2017 Blue Waters Annual Report, pp 182-183, 2017


Jamesina Simpson: "Location-Specific Space-Weather Hazards to Electric-Power Grids Calculated on A Global Scale", 2017 Blue Waters Annual Report, pp 86-87, 2017


Ryan Sriver: "Impact of Ocean Coupling on Simulated Tropical-Cyclone in The High-Resolution Community Earth-System Mode", 2017 Blue Waters Annual Report, pp 88-89, 2017


Ronald Stenz: "The Impacts of Hydrometeor Centrifuging on Tornado Dynamics", 2017 Blue Waters Annual Report, pp 284-285, 2017


Brad Sutton: "High-Resolution Magnetic Resonance Imaging of Mechanical Properties of The Brain", 2017 Blue Waters Annual Report, pp 244-245, 2017


Ilias Tagkopoulos: "A Crystal Ball of Bacterial Behavior: From Data to Prediction Using Genome-Scale Models", 2017 Blue Waters Annual Report, pp 246-247, 2017


Ahmed Taha: "Advanced Digital Technology for Materials and Manufacturing", 2017 Blue Waters Annual Report, pp 158-159, 2017


Alexander Tchekhovskoy: "GPU-Accelerated Simulations: Black Holes, Spaghettified Stars, and Tilted Disks", 2017 Blue Waters Annual Report, pp 56-57, 2017


Erin Teich: "Glassy Dynamics and Identity Crises in Hard-Particle Systems", 2017 Blue Waters Annual Report, pp 286-287, 2017


Brian Thomas: "Transient Multiphase Flow Phenomena and Defect Formation in Steel Continuous Casting", 2017 Blue Waters Annual Report, pp 160-161, 2017


Rafael Tinoco Lopez: "High Resolution Numerical Simulation of Oscillatory Flow and Sediment Transport through Aquatic Vegetation", 2017 Blue Waters Annual Report, pp 162-163, 2017


Gabor Toth: "Advanced Space Weather Modeling", 2017 Blue Waters Annual Report, pp 58-59, 2017


Samuel Totorica: "Magnetic reconnection in laser-driven plasmas: from astrophysics to the laboratory in silico", 2017 Blue Waters Annual Report, pp 288-289, 2017


Robert Trapp: "Petascale modeling of convective storms under climate change and variability", 2017 Blue Waters Annual Report, pp 90-91, 2017


Albert J. Valocchi: "Pore-Scale Simulation of Multiphase Flow in Porous Media with Applications to Geological Sequestration of Carbon Dioxide", 2017 Blue Waters Annual Report, pp 94-95, 2017


Junshik Um: "Impacts of Orientation and Morphology of Small Atmospheric Ice Crystals on In Situ Aircraft Measurements: Scattering Calculations", 2017 Blue Waters Annual Report, pp 92-93, 2017


Lucas Wagner: "Quantum Monte Carlo simulations of magnetism and models in condensed matter", 2017 Blue Waters Annual Report, pp 164-165, 2017


Gregory Voth: "Large-Scale Coarse-Grained Molecular Simulations of The Viral Lifecylce of HIV-1", 2017 Blue Waters Annual Report, pp 248-249, 2017


Tandy Warnow: "Parallel Algorithms for Big-data Phylogenomics, Proteomics, and Metagenomics", 2017 Blue Waters Annual Report, pp 184-185, 2017


Matthew West: "3D particle-resolved aerosol model to quantify and reduce uncertainties in aerosol-atmosphere interactions", 2017 Blue Waters Annual Report, pp 96-97, 2017


Tao Xie: "Hardware Acceleration of Deep Learning", 2017 Blue Waters Annual Report, pp 186-187, 2017


Donald J. Wuebbles: "Particulate-Matter Prediction and Source Attribution for U.S. Air-Quality Management in a Changing World", 2017 Blue Waters Annual Report, pp 98-99, 2017


Rebecca D. McAuliffe, Christopher A. Miller, Xiao Zhang, Benjamin S. Hulbert, Ashfia Huq, Clarina dela Cruz, André Schleife, and Daniel P. Shoemaker: "Structural, Electronic, and Optical Properties of K2Sn3O7 with an Offset Hollandite Structure", Inorganic Chemistry, American Chemical Society, Vol 56, Num 5, pp 2914-2918, 2017, doi:10.1021/acs.inorgchem.6b03007


Lange, J., O'Shaughnessy, R., Boyle, M., Calderón Bustillo, J., Campanelli, M., Chu, T., Clark, J. A., Demos, N., Fong, H., Healy, J., Hemberger, D. A., Hinder, I., Jani, K., Khamesra, B., Kidder, L. E., Kumar, P., Laguna, P., Lousto, C. O., Lovelace, G., Ossokine, S., Pfeiffer, H., Scheel, M. A., Shoemaker, D. M., Szilagyi, B., Teukolsky, S. and Zlochower, Y.: "Parameter Estimation Method That Directly Compares Gravitational Wave Observations to Numerical Relativity", Physical Review D, American Physical Society, Vol 96, Num 10, pp 104041, 2017, doi:10.1103/physrevd.96.104041


Michael Nute, Chou Jed, Erin K. Molloy, and Tandy Warnow: "Data from: The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data", University of Illinois at Urbana-Champaign, Illinois Data Bank, 2017, doi:10.13012/B2IDB-7735354_V1


Myoung-Jong Noh,and Ian M. Howat: "The Surface Extraction from TIN Based Search-Space Minimization (SETSM) Algorithm", ISPRS Journal of Photogrammetry and Remote Sensing, Elsevier BV, Vol 129, pp 55-76, 2017, doi:10.1016/j.isprsjprs.2017.04.019


Christensen, Sarah, Molloy, Erin K., Vachaspati, Pranjal, and Warnow, Tandy: "Datasets from the study OCTAL: Optimal Completion of Gene Trees in Polynomial Time", University of Illinois at Urbana-Champaign, Illinois Data Bank, 2017, doi:10.13012/B2IDB-1616387_V1


Carlo Pierleoni, Markus Holzmann, and David M. Ceperley: "Local Structure in Dense Hydrogen at the Liquid-Liquid Phase Transition by Coupled Electron-Ion Monte Carlo", Contributions to Plasma Physics, Wiley-Blackwell, Vol 58, Num 2-3, pp 99-106, 2017, doi:10.1002/ctpp.201700184


Yuhang Jing, Hiroshige Matsumoto, and Narayana R. Aluru: "Mechanistic Insights Into Hydration of Solid Oxides", Chemistry of Materials, American Chemical Society, Vol 30, Num 1, pp 138-144, 2017, doi:10.1021/acs.chemmater.7b03476


Kirk S. S. Barrow, John H. Wise, Michael L. Norman, Brian W. O'Shea, and Hao Xu: "First light: exploring the spectra of high-redshift galaxies in the Renaissance Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 469, Num 4, pp 4863-4878, 2017, doi:10.1093/mnras/stx1181


Karl Decker, Martin Page, and Aleksei Aksimentiev: "Nanoscale Ion Pump Derived from a Biological Water Channel", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 33, pp 7899-7906, 2017, doi:10.1021/acs.jpcb.7b05568


Benjamin Cressiot, Sandra J. Greive, Wei Si, Tomas C. Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw T. Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A. Antson, and Meni Wanunu: "Porphyrin-Assisted Docking of a Thermophage Portal Protein Into Lipid Bilayers: Nanopore Engineering and Characterization", ACS Nano, American Chemical Society, Vol 11, Num 12, pp 11931-11945, 2017, doi:10.1021/acsnano.7b06980


Aaron J. Wolfe, Wei Si, Zhengqi Zhang, Adam R. Blanden, Yi-Ching Hsueh, Jack F. Gugel, Bach Pham, Min Chen, Stewart N. Loh, Sharon Rozovsky, Aleksei Aksimentiev, and Liviu Movileanu: "Quantification of Membrane Protein-Detergent Complex Interactions", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 44, pp 10228-10241, 2017, doi:10.1021/acs.jpcb.7b08045


Laura Restrepo-Pérez, Shalini John, Aleksei Aksimentiev, Chirlmin Joo, and Cees Dekker: "SDS-Assisted Protein Transport Through Solid-State Nanopores", Nanoscale, Royal Society of Chemistry, Vol 9, Num 32, pp 11685-11693, 2017, doi:10.1039/c7nr02450a


Kai Tian, Karl Decker, Aleksei Aksimentiev, and Li-Qun Gu: "Interference-Free Detection of Genetic Biomarkers Using Synthetic Dipole-Facilitated Nanopore Dielectrophoresis", ACS Nano, American Chemical Society (ACS), Vol 11, Num 2, pp 1204-1213, 2017, doi:10.1021/acsnano.6b07570


Mohammad Amin Alibakhshi, Justin R. Halman, James Wilson, Aleksei Aksimentiev, Kirill A. Afonin, and Meni Wanunu: "Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores", ACS Nano, American Chemical Society, Vol 11, Num 10, pp 9701-9710, 2017, doi:10.1021/acsnano.7b04923


Wei Si and Aleksei Aksimentiev: "Nanopore Sensing of Protein Folding", ACS Nano, American Chemical Society, Vol 11, Num 7, pp 7091-7100, 2017, doi:10.1021/acsnano.7b02718


Manish Shankla and Aleksei Aksimentiev: "Modulation of Molecular Flux Using a Graphene Nanopore Capacitor", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 15, pp 3724-3733, 2017, doi:10.1021/acs.jpcb.6b10574


Christopher Maffeo and Aleksei Aksimentiev: "Molecular mechanism of DNA association with single-stranded DNA binding protein", Nucleic Acids Research, Oxford University Press, Vol 45, Num 21, pp 12125-12139, 2017, doi:10.1093/nar/gkx917


Juan I. Blanco Capurro, Chad W. Hopkins, Gustavo Pierdominici Sottile, Mariano C. González Lebrero, Adrian E. Roitberg, and Marcelo A. Marti: "Theoretical Insights Into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 3, pp 471-478, 2017, doi:10.1021/acs.jpcb.6b10130


Christina Bergonzo and Thomas E. Cheatham: "Mg2+ Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction", Biophysical Journal, Elsevier BV, Vol 113, Num 2, pp 313-320, 2017, doi:10.1016/j.bpj.2017.06.008


Erik W. Lentz, Thomas R. Quinn, Leslie J. Rosenberg, and Michael J. Tremmel: "A New Signal Model for Axion Cavity Searches from N -body Simulations", Astrophysical Journal, The American Astronomical Society, Vol 845, Num 2, pp 121, 2017, doi:10.3847/1538-4357/aa80dd


D. Roten, K. B. Olsen, S. M. Day, and Y. Cui: "Quantification of Fault-Zone Plasticity Effects with Spontaneous Rupture Simulations", Pure and Applied Geophysics, Springer Nature, Vol 174, Num 9, pp 3369-3391, 2017, doi:10.1007/s00024-017-1466-5


M. Tremmel, M. Karcher, F. Governato, M. Volonteri, T. R. Quinn, A. Pontzen, L. Anderson, and J. Bellovary: "The Romulus cosmological simulations: a physical approach to the formation, dynamics and accretion models of SMBHs", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 470, Num 1, pp 1121-1139, 2017, doi:10.1093/mnras/stx1160


Jonathan Lai, Zhaleh Ghaemi, and Zaida Luthey-Schulten: "The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains", Biochemistry, American Chemical Society, Vol 56, Num 45, pp 5972-5979, 2017, doi:10.1021/acs.biochem.7b00591


David Bock: "Visualization of Tropical Cyclone-Ocean Interactions", ACM Press, PEARC '17: Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact, pp 79:1-79:3, New Orleans, Louisiana, U.S.A., 2017, doi:10.1145/3093338.3104149


Kaiyu Guan, Jin Wu, John S. Kimball, Martha C. Anderson, Steve Frolking, Bo Li, Christopher R. Hain, and David B. Lobell: "The Shared and Unique Values of Optical, Fluorescence, Thermal and Microwave Satellite Data for Estimating Large-Scale Crop Yields", Remote Sensing of Environment, Elsevier BV, Vol 199, pp 333-349, 2017, doi:10.1016/j.rse.2017.06.043


Jinho Kim, Dinshaw S. Balsara, Maxim Lyutikov, and Sergei S. Komissarov: "On the linear stability of magnetized jets without current sheets relativistic case", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 467, Num 4, pp 4647-4662, 2017, doi:10.1093/mnras/stx409


Dinshaw S. Balsara, and Roger Käppeli: "Von Neumann Stability Analysis of Globally Divergence-Free RKDG Schemes for the Induction Equation Using Multidimensional Riemann Solvers", Journal of Computational Physics, Elsevier BV, Vol 336, pp 104-127, 2017, doi:10.1016/j.jcp.2017.01.056


Jinho Kim, Sudip K. Garain, Dinshaw S. Balsara, and Sandip K. Chakrabarti: "General relativistic numerical simulation of sub-Keplerian transonic accretion flows on to black holes: Schwarzschild space–time", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 472, Num 1, pp 542-549, 2017, doi:10.1093/mnras/stx1986


Dinshaw S. Balsara, and Boniface Nkonga: "Multidimensional Riemann Problem with Self-Similar Internal Structure - Part III - a Multidimensional Analogue of the HLLI Riemann Solver for Conservative Hyperbolic Systems", Journal of Computational Physics, Elsevier BV, Vol 346, pp 25-48, 2017, doi:10.1016/j.jcp.2017.05.038


Dinshaw S. Balsara, Allen Taflove, Sudip Garain, and Gino Montecinos: "Computational Electrodynamics in Material Media with Constraint-Preservation, Multidimensional Riemann Solvers and Sub-Cell Resolution - Part I, Second-Order FVTD Schemes", Journal of Computational Physics, Elsevier BV, Vol 349, pp 604-635, 2017, doi:10.1016/j.jcp.2017.07.024


Benjamin R. Ryan, Charles F. Gammie, Sebastien Fromang, and Pierre Kestener: "Resolution Dependence of Magnetorotational Turbulence in the Isothermal Stratified Shearing Box", Astrophysical Journal, The American Astronomical Society, Vol 840, Num 1, pp 6, 2017, doi:10.3847/1538-4357/aa6a52


Lawrence E. Kidder, Scott E. Field, Francois Foucart, Erik Schnetter, Saul A. Teukolsky, Andy Bohn, Nils Deppe, Peter Diener, François Hébert, Jonas Lippuner, Jonah Miller, Christian D. Ott, Mark A. Scheel, and Trevor Vincent: "SpECTRE: A Task-Based Discontinuous Galerkin Code for Relativistic Astrophysics", Journal of Computational Physics, Elsevier BV, Vol 335, pp 84-114, 2017, doi:10.1016/j.jcp.2016.12.059


Emad Tajkhorshid and Klaus Schulten: "Studying Cellular Processes through the Computational Microscope", 2017 Blue Waters Annual Report, pp 234-235, 2017


Philip J. Maechling: "Physics-Based Modeling of High-Frequency Ground Motions and Probabilistic Seismic Hazard Analysis", 2017 Blue Waters Annual Report, pp 78-79, 2017


Eric Johnsen: "Numerical Simulations of Collapsing Cavitation Bubbles on Blue Waters", 2017 Blue Waters Annual Report, pp 142-143, 2017


Alexander S. Moffett, Kyle W. Bender, Steven C. Huber, and Diwakar Shukla: "Allosteric Control of a Plant Receptor Kinase Through S-Glutathionylation", Biophysical Journal, Elsevier BV, Vol 113, Num 11, pp 2354-2363, 2017, doi:10.1016/j.bpj.2017.08.059


Shriyaa Mittal and Diwakar Shukla: "Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 42, pp 9761-9770, 2017, doi:10.1021/acs.jpcb.7b04785


Jacob Heldenbrand, Yingxue Ren, Yan Asmann, and Liudmila S. Mainzer: "Step-by-Step Guide for Downloading Very Large Datasets to a Supercomputer Using the SRA Toolkit V1 (protocols.io.kb6csre)", ZappyLab, Inc., Protocols.io, 2017, doi:10.17504/protocols.io.kb6csre


Gregory Bauer: "Improving NWCHEM scalability using Dataspaces framework", 2017 Blue Waters Annual Report, pp 196-197, 2017


Mahmoud Moradi: "Thermodynamic Characterization of Conformational Landscape in Proton-Coupled Oligopeptide Transporters", 2017 Blue Waters Annual Report, pp 228-229, 2017


Paul R. Woodward: "3-D Simulations of i-Process Nucleosynthesis", 2017 Blue Waters Annual Report, pp 60-61, 2017


Sherwood Richers, Hiroki Nagakura, Christian Ott, Joshua Dolence, Kohsuke Sumiyoshi, and Shoichi Yamada: "A Detailed Comparison of Multi-Dimensional Boltzmann Neutrino Transport Methods in Core-Collapse Supernovae", Zenodo, Zenodo (website), 2017, doi:10.5281/zenodo.807765


Ashraf Idkaidek, Seid Koric, and Iwona Jasiuk: "Fracture Analysis of Multi-Osteon Cortical Bone Using XFEM", Computational Mechanics, Springer Nature, Vol 62, Num 2, pp 171-184, 2017, doi:10.1007/s00466-017-1491-3


N. V. Pogorelov, J. Heerikhuisen, V. Roytershteyn, L. F. Burlaga, D. A. Gurnett, and W. S. Kurth: "Three-dimensional Features of the Outer Heliosphere Due to Coupling between the Interstellar and Heliospheric Magnetic Field. V. The Bow Wave, Heliospheric Boundary Layer, Instabilities, and Magnetic Reconnection", Astrophysical Journal, The American Astronomical Society, Vol 845, Num 1, 2017, doi:10.3847/1538-4357/aa7d4f


K.D. Launey, A.C. Dreyfuss, G.H. Sargsyan, R.B. Baker, M. Miora, J.P. Draayer, and T. Dytrych: "Ab initio Picture of Nuclei: Shapes, Rotations, and Vibrations from Chiral Potentials", Heron Press Ltd., Bulgarian Journal of Physics: Shapes and Dynamics of Atomic Nuclei: Contemporary Aspects (SDANCA-17), Vol 44, Num 4, pp 345-356, Sofia, Bulgaria, 2017


A. C. Dreyfuss, J. P. Draayer, K. D. Launey, T. Dytrych, and R. B. Baker: "Simple Patterns in Nuclei", World Scientific, Fission and Properties of Neutron-Rich Nuclei: Proceedings of the 6th International Conference on Fission and Properties of Neutron-Rich Nuclei (ICFN6), pp 321-330, Sanibel Island, Florida, U.S.A., 2017, doi:10.1142/9789813229426_0058


Matthew L.S. Zappulla and Brian G. Thomas: "Thermal-Mechanical Model of Depression Formation in Steel Continuous Casting", Springer International Publishing, TMS 2017 146th Annual Meeting and Exhibition Supplemental Proceedings, pp 501-510, San Diego, California, U.S.A., 2017, doi:10.1007/978-3-319-51493-2_48


E.A. Huerta, Roland Haas, Edgar Fajardo, Daniel S. Katz, Stuart Anderson, Peter Couvares, Josh Willis, Timothy Bouvet, Jeremy Enos, William T.C. Kramer, Hon Wai Leong, and David Wheeler: "BOSS-LDG: A Novel Computational Framework That Brings Together Blue Waters, Open Science Grid, Shifter and the LIGO Data Grid to Accelerate Gravitational Wave Discovery", Institute of Electrical & Electronics Engineers, 2017 IEEE 13th International Conference on e-Science (e-Science), Auckland, New Zealand, 2017, doi:10.1109/escience.2017.47


X. L. Xu, F. Li, W. An, T. N. Dalichaouch, P. Yu, W. Lu, C. Joshi, and W. B. Mori: "High Quality Electron Bunch Generation Using a Longitudinal Density-Tailored Plasma-Based Accelerator in the Three-Dimensional Blowout Regime", Physical Review Accelerators and Beams, American Physical Society, Vol 20, Num 11, pp 111303, 2017, doi:10.1103/physrevaccelbeams.20.111303


Mingzhang Wang, Caitlin M. Quinn, Juan R. Perilla, Huilan Zhang, Randall Shirra, Guangjin Hou, In-Ja Byeon, Christopher L. Suiter, Sherimay Ablan, Emiko Urano, Theodore J. Nitz, Christopher Aiken, Eric O. Freed, Peijun Zhang, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova: "Quenching Protein Dynamics Interferes with HIV Capsid Maturation", Nature Communications, Springer Nature, Vol 8, Num 1, pp 1779, 2017, doi:10.1038/s41467-017-01856-y


Quan Zhou, Lijun Liu, and Jiashun Hu: "Western US Volcanism Due to Intruding Oceanic Mantle Driven by Ancient Farallon Slabs", Nature Geoscience, Springer Nature, Vol 11, Num 1, pp 70-76, 2017, doi:10.1038/s41561-017-0035-y


Quan Zhou and Lijun Liu: "A Hybrid Approach to Data Assimilation for Reconstructing the Evolution of Mantle Dynamics", Geochemistry, Geophysics, Geosystems, American Geophysical Union, Vol 18, Num 11, pp 3854-3868, 2017, doi:10.1002/2017gc007116


Lin Chen, Fabio A. Capitanio, Lijun Liu, and Taras V. Gerya: "Crustal Rheology Controls on the Tibetan Plateau Formation During India-Asia Convergence", Nature Communications, Springer Nature, Vol 8, pp 15992, 2017, doi:10.1038/ncomms15992


Yuxi Chen, Gabor Toth, Paul Cassak, Xianzhe Jia, Tamas I. Gombosi, James A. Slavin, Stefano Markidis, Ivy Bo Peng, Vania K. Jordanova, and Michael G. Henderson: "Global Three-Dimensional Simulation of Earth's Dayside Reconnection Using a Two-Way Coupled Magnetohydrodynamics with Embedded Particle-in-Cell Model: Initial Results", Journal of Geophysical Research: Space Physics, American Geophysical Union, Vol 122, Num 10, pp 10,318-10,335, 2017, doi:10.1002/2017ja024186


Gabor Toth, Yuxi Chen, Tamas I. Gombosi, Paul Cassak, Stefano Markidis, and Ivy Bo Peng: "Scaling the Ion Inertial Length and Its Implications for Modeling Reconnection in Global Simulations", Journal of Geophysical Research: Space Physics, American Geophysical Union, Vol 122, Num 10, pp 10,336-10,355, 2017, doi:10.1002/2017ja024189


Tao Jiang, Kuai Yu, H Criss Hartzell, and Emad Tajkhorshid: "Lipids and Ions Traverse the Membrane by the Same Physical Pathway in the nhTMEM16 Scramblase", eLife, eLife Sciences Organisation, Ltd., Vol 6, 2017, doi:10.7554/elife.28671


Junji Huang, Lian Duan, Jianxun Wang, Rui Sun, and Heng Xiao: "High-Mach-Number Turbulence Modeling Using Machine Learning and Direct Numerical Simulation Database", American Institute of Aeronautics and Astronautics, 55th AIAA Aerospace Sciences Meeting, Grapevine, Texas, U.S.A., 2017, doi:10.2514/6.2017-0315


Jing Li, Jared Ostmeyer, Eliot Boulanger, Huan Rui, Eduardo Perozo, and Benoît Roux: "Chemical Substitutions in the Selectivity Filter of Potassium Channels Do Not Rule Out Constricted-Like Conformations for C-Type Inactivation", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 114, Num 42, pp 11145-11150, 2017, doi:10.1073/pnas.1706983114


Vamseedhar Rayaprolu, Alan Moore, Joseph Che-Yen Wang, Boon Chong Goh, Juan R Perilla, Adam Zlotnick, and Suchetana Mukhopadhyay: "Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles", Journal of Physics: Condensed Matter, Vol 29, Num 48, pp 484003, 2017, doi:10.1088/1361-648X/aa90d0


Vincenzo Carnevale and Michael L Klein: "Small Molecule Modulation of Voltage Gated Sodium Channels", Current Opinion in Structural Biology, Elsevier BV, Vol 43, pp 156-162, 2017, doi:10.1016/j.sbi.2017.02.002


Daniele Granata, Luca Ponzoni, Cristian Micheletti, and Vincenzo Carnevale: "Patterns of Coevolving Amino Acids Unveil Structural and Dynamical Domains", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 114, Num 50, pp E10612-E10621, 2017, doi:10.1073/pnas.1712021114


Ximena Steinberg, Marina A. Kasimova, Deny Cabezas-Bratesco, Jason D. Galpin, Ernesto Ladron-de-Guevara, Federica Villa, Vincenzo Carnevale, Leon Islas, Christopher A. Ahern, and Sebastian E. Brauchi: "Conformational Dynamics in TRPV1 Channels Reported by an Encoded Coumarin Amino Acid", eLife, eLife Sciences Organisation, Ltd., Vol 6, 2017, doi:10.7554/elife.28626


Asghar M. Razavi, Lucie Delemotte, Joshua R. Berlin, Vincenzo Carnevale, and Vincent A. Voelz: "Molecular Simulations and Free-Energy Calculations Suggest Conformation-Dependent Anion Binding to a Cytoplasmic Site as a Mechanism for Na+/K+-ATPase Ion Selectivity", Journal of Biological Chemistry, American Society for Biochemistry & Molecular Biology, Vol 292, Num 30, pp 12412-12423, 2017, doi:10.1074/jbc.m117.779090


Chuanxu Ma, Liangbo Liang, Zhongcan Xiao, Alexander A. Puretzky, Kunlun Hong, Wenchang Lu, Vincent Meunier, J. Bernholc, and An-Ping Li: "Seamless Staircase Electrical Contact to Semiconducting Graphene Nanoribbons", Nano Letters, American Chemical Society, Vol 17, Num 10, pp 6241-6247, 2017, doi:10.1021/acs.nanolett.7b02938


L. Lamy, R. Prangé, K. C. Hansen, C. Tao, S. W. H. Cowley, T. S. Stallard, H. Melin, N. Achilleos, P. Guio, S. V. Badman, T. Kim, and N. Pogorelov: "The Aurorae of Uranus Past Equinox", Journal of Geophysical Research: Space Physics, American Geophysical Union, Vol 122, Num 4, pp 3997-4008, 2017, doi:10.1002/2017ja023918


Dinshaw S. Balsara: "Higher-Order Accurate Space-Time Schemes for Computational astrophysics, Part I: Finite Volume Methods", Living Reviews in Computational Astrophysics, Springer Nature, Vol 3, Num 1, 2017, doi:10.1007/s41115-017-0002-8


Kevin Hauser, Yiqing He, Miguel Garcia-Diaz, Carlos Simmerling, and Evangelos Coutsias: "Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis", Journal of Chemical Information and Modeling, American Chemical Society, Vol 57, Num 4, pp 864-874, 2017, doi:10.1021/acs.jcim.6b00721


Haoquan Li, Anton V. Endutkin, Christina Bergonzo, Lin Fu, Arthur Grollman, Dmitry O. Zharkov, and Carlos Simmerling: "DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase", Journal of the American Chemical Society, American Chemical Society, Vol 139, Num 7, pp 2682-2692, 2017, doi:10.1021/jacs.6b11433


Carlos O. Lousto, Yosef Zlochower, and Manuela Campanelli: "Modeling the Black Hole Merger of QSO 3C 186", Astrophysical Journal Letters, The American Astronomical Society, Vol 841, Num 2, pp L28, 2017, doi:10.3847/2041-8213/aa733c


Venkata Giridhar Poosarla, Tong Li, Boon Chong Goh, Klaus Schulten, Thomas K. Wood, and Costas D. Maranas: "Computational De Novo Design of Antibodies Binding to a Peptide with High Affinity", Biotechnology and Bioengineering, Wiley, Vol 114, Num 6, pp 1331-1342, 2017, doi:10.1002/bit.26244


Marc Wehmer, Till Rudack, Florian Beck, Antje Aufderheide, Günter Pfeifer, Jürgen M. Plitzko, Friedrich Förster, Klaus Schulten, Wolfgang Baumeister, and Eri Sakata: "Structural Insights Into the Functional Cycle of the ATPase Module of the 26S Proteasome", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 114, Num 6, pp 1305-1310, 2017, doi:10.1073/pnas.1621129114


Jeffrey Comer, Klaus Schulten, and Christophe Chipot: "Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles", Journal of Chemical Theory and Computation, American Chemical Society, Vol 13, Num 6, pp 2523-2532, 2017, doi:10.1021/acs.jctc.7b00264


Suvrajit Maji, Rezvan Shahoei, Klaus Schulten, and Joachim Frank: "Quantitative Characterization of Domain Motions in Molecular Machines", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 15, pp 3747-3756, 2017, doi:10.1021/acs.jpcb.6b10732


J. P. Naiman, Kalina Borkiewicz, and A. J. Christensen: "Houdini for Astrophysical Visualization", Publications of the Astronomical Society of the Pacific, The Astronomical Society of the Pacific, Vol 129, Num 975, pp 058008, 2017, doi:10.1088/1538-3873/aa51b3


Anderson, Lauren, Governato, F., Karcher, M., Quinn, T., and Wadsley, J.: "The little Galaxies that could (reionize the universe): predicting faint end slopes & escape fractions at z>4", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 468, Num 4, pp 4077-4092, 2017, doi:10.1093/mnras/stx709


Rodrigo Galindo-Murillo and Thomas E. Cheatham: "Computational DNA Binding Studies of (-)-Epigallocatechin-3-Gallate", Journal of Biomolecular Structure and Dynamics, Informa UK Limited, Vol 113, Num 49, pp 1-13, 2017, doi:10.1080/07391102.2017.1389306


Hyunjin Yang, Surya P. Vanka, and Brian G. Thomas: "Hybrid Eulerian-Eulerian Discrete Phase Model of Turbulent Bubbly Flow", The American Society of Mechanical Engineers, ASME 2017 International Mechanical Engineering Congress and Exposition (IMECE 2017), Vol 7: Fluids Engineering, Tampa, Florida, U.S.A., 2017, doi:10.1115/imece2017-70337


Scott Callaghan, Gideon Juve, Karan Vahi, Philip J. Maechling, Thomas H. Jordan, and Ewa Deelman: "rvGAHP: Push-based Job Submission Using Reverse SSH Connections", The Association for Computing Machinery, Proceedings of the 12th Workshop on Workflows in Support of Large-Scale Science (WORKS '17), pp 3:1-3:8, Denver, Colorado, U.S.A., 2017, doi:10.1145/3150994.3151003


Tobias Verdorfer, Rafael C. Bernardi, Aylin Meinhold, Wolfgang Ott, Zaida Luthey-Schulten, Michael A. Nash, and Hermann E. Gaub: "Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics", Journal of the American Chemical Society, The American Chemical Society, Vol 139, Num 49, pp 17841-17852, 2017, doi:10.1021/jacs.7b07574


Kuang-Chung Wang, Teodor K. Stanev, Daniel Valencia, James Charles, Alex Henning, Vinod K. Sangwan, Aritra Lahiri, Daniel Mejia, Prasad Sarangapani, Michael Povolotskyi, Aryan Afzalian, Jesse Maassen, Gerhard Klimeck, Mark C. Hersam, Lincoln J. Lauhon, Nathaniel P. Stern, and Tillmann Kubis: "Control of interlayer physics in 2H transition metal dichalcogenides", Journal of Applied Physics, AIP Publishing LLC, Vol 122, Num 22, pp 224302, 2017, doi:10.1063/1.5005958


David Radice, Adam Burrows, David Vartanyan, M. Aaron Skinner, and Joshua C. Dolence: "Electron-capture and Low-mass Iron-core-collapse Supernovae: New Neutrino-radiation-hydrodynamics Simulations", Astrophysical Journal, The American Astronomical Society, Vol 850, Num 1, 2017, doi:10.3847/1538-4357/aa92c5


Thomas Simonson, Gerhard Hummer, and Benoît Roux: "Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies", Journal of Physical Chemistry A, American Chemical Society, Vol 121, Num 7, pp 1525-1530, 2017, doi:10.1021/acs.jpca.6b12691


Haohao Fu, Wensheng Cai, Jérôme Hénin, Benoît Roux, and Christophe Chipot: "New Coarse Variables for the Accurate Determination of Standard Binding Free Energies", Journal of Chemical Theory and Computation, American Chemical Society, Vol 13, Num 11, pp 5173-5178, 2017, doi:10.1021/acs.jctc.7b00791


Edwin Mathews: "Numerical and Theoretical Analysis of Aero-Optics with Application to an Optical Turret", Hesburgh Libraries of Notre Dame., CurateND, Vol Doctoral dissertation, 2017


Ariana S. Minot: "Distributed Optimization Methods for Monitoring and Operating Electric Power Systems", Harvard Library Office for Scholarly Communication, Digital Access to Scholarship at Harvard, Vol Faculty of Arts and Sciences Theses and Dissertations, 2017


Justin Alexander Drake: "Biophysical mechanisms of intrinsic protein disorder: lessons from a protein backbone model", The University of Texas Medical Branch, UTMB Health SHARED, Vol Electronic Theses and Dissertations, 2017


Bilge Acun, Ronak Buch, Laxmikant V. Kale, and James C. Phillips: "NAMD: Scalable molecular dynamics based on the charm++ parallel runtime system", CRC Press, Exascale Scientific Applications: Scalability and Performance Portability, pp 119-143, 2017, doi:10.1201/b21930-5


Brian K. Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C. Phillips, Klaus Schulten, and Benoît Roux: "Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems", Journal of Chemical Theory and Computation, American Chemical Society, Vol 13, Num 12, pp 5933-5944, 2017, doi:10.1021/acs.jctc.7b00875


Antonia Statt, Michael P. Howard, and Athanassios Z. Panagiotopoulos: "Solvent quality influences surface structure of glassy polymer thin films after evaporation", Journal of Chemical Physics, AIP Publishing, Vol 147, Num 18, pp 184901, 2017, doi:10.1063/1.4996119


Arash Nikoubashman and Michael P. Howard: "Equilibrium Dynamics and Shear Rheology of Semiflexible Polymers in Solution", Macromolecules, American Chemical Society, Vol 50, Num 20, pp 8279-8289, 2017, doi:10.1021/acs.macromol.7b01876


Michael P. Howard, Arash Nikoubashman, and Athanassios Z. Panagiotopoulos: "Stratification in Drying Polymer–Polymer and Colloid–Polymer Mixtures", Langmuir, American Chemical Society, Vol 33, Num 42, pp 11390-11398, 2017, doi:10.1021/acs.langmuir.7b02074


Michael P. Howard, Arash Nikoubashman, and Athanassios Z. Panagiotopoulos: "Stratification Dynamics in Drying Colloidal Mixtures", Langmuir, American Chemical Society, Vol 33, Num 15, pp 3685-3693, 2017, doi:10.1021/acs.langmuir.7b00543


Wesley F. Reinhart, Andrew W. Long, Michael P. Howard, Andrew L. Ferguson, and Athanassios Z. Panagiotopoulos: "Machine learning for autonomous crystal structure identification", Soft Matter, The Royal Society of Chemistry, Vol 13, Num 27, pp 4733-4745, 2017, doi:10.1039/C7SM00957G


Michael P. Howard, Antonia Statt, and Athanassios Z. Panagiotopoulos: "Note: Smooth torsional potentials for degenerate dihedral angles", Journal of Chemical Physics, AIP Publishing, Vol 146, Num 22, pp 226101, 2017, doi:10.1063/1.4985251


Jon Cameron Calhoun: "From detection to optimization: impact of soft errors on high-performance computing applications", University of Illinois at Urbana-Champaign, Illinois Digital Environment for Access to Learning and Scholarship, Vol Doctoral dissertation, 2017


George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri: "Order or Shuffle: Empirically Evaluating Vertex Order Impact on Parallel Graph Computations", Institute of Electrical & Electronics Engineers, 2017 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp 588-597, Lake Buena Vista, Florida, U.S.A., 2017, doi:10.1109/IPDPSW.2017.164


George M. Slota, Sivasankaran Rajamanickam; Karen Devine; and Kamesh Madduri: "Partitioning Trillion-Edge Graphs in Minutes", Institute of Electrical & Electronics Engineers, 2017 IEEE International Parallel and Distributed Processing Symposium (IPDPS), pp 646-655, Orlando, Florida, U.S.A., 2017, doi:10.1109/IPDPS.2017.95


Amy Marshall-Colon, Stephen P. Long, Douglas K. Allen, Gabrielle Allen, Daniel A. Beard, Bedrich Benes, Susanne von Caemmerer, A. J. Christensen, Donna J. Cox, John C. Hart, Peter M. Hirst, Kavya Kannan, Daniel S. Katz, Jonathan P. Lynch, Andrew J. Millar, Balaji Panneerselvam, Nathan D. Price, Przemyslaw Prusinkiewicz, David Raila, Rachel G. Shekar, Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Matthew J. Turk, Eberhard O. Voit, Yu Wang Xinyou Yin, and Xin-Guang Zhu: "Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform", Frontiers in Plant Science, Frontiers, Vol 8, pp 786, 2017, doi:10.3389/fpls.2017.00786


Kalina Borkiewicz, A. J. Christensen, and John E. Stone: "Communicating Science through Visualization in an Age of Alternative Facts", Association for Computing Machinery, SIGGRAPH '17: ACM SIGGRAPH 2017 Courses, pp 8, Los Angeles, California, U.S.A., 2017, doi:10.1145/3084873.3084935


Kirit Makwana, Hui Li, Fan Guo, and Xiaocan Li: "Dissipation and particle energization in moderate to low beta turbulent plasma via {PIC} simulations", IOP Publishing Ltd., Journal of Physics: Conference Series (11th International Conference on Numerical Modeling of Space Plasma Flows, ASTRONUM 2016), Vol 837, pp 012004, Monterey, California, U.S.A., 2017, doi:10.1088/1742-6596/837/1/012004


Mijo Simunovic, Anđela Šarić, J. Michael Henderson, Ka Yee C. Lee, and Gregory A. Voth: "Long-Range Organization of Membrane-Curving Proteins", ACS Central Science, American Chemical Society, Vol 3, Num 12, pp 1246-1253, 2017, doi:10.1021/acscentsci.7b00392


Zachary Zobel, Jiali Wang, Donald J. Wuebbles, and V. Rao Kotamarthi: "High‐Resolution Dynamical Downscaling Ensemble Projections of Future Extreme Temperature Distributions for the United States", Earth's Future, American Geophysical Union, Vol 5, Num 12, pp 1234-1251, 2017, doi:10.1002/2017EF000642


Larissa Reames: "Simulated effects of urban environments on the dynamics of a supercell thunderstorm", The University of Oklahoma Libraries, Oklahoma State University Libraries, and the University of Central Oklahoma Max Chambers Library, SHAREOK Repository, Vol OU dissertations, 2017


Ming-Fu Lin, Max A. Verkamp, Joshua Leveillee, Elizabeth S. Ryland, Kristin Benke, Kaili Zhang, Clemens Weninger, Xiaozhe Shen, Renkai Li, David Fritz, Uwe Bergmann, Xijie Wang, André Schleife, and Josh Vura-Weis: "Carrier-Specific Femtosecond XUV Transient Absorption of PbI2 Reveals Ultrafast Nonradiative Recombination", Journal of Physical Chemistry C, American Chemical Society, Vol 121, Num 50, pp 27886-27893, 2017, doi:10.1021/acs.jpcc.7b11147


André Schleife, Xiao Zhang, Qi Li, Paul Erhart, and Daniel Åberg: "Excitons in scintillator materials: Optical properties and electron-energy loss spectra of NaI, LaBr3, BaI2, and SrI2", Journal of Materials Research, Cambridge University Press, Vol 32, Num 1, pp 56–63, 2017, doi:10.1557/jmr.2016.395


Laurie S. Huning, Steven A. Margulis, Bin Guan, Duane E. Waliser, and Paul J. Neiman: "Implications of Detection Methods on Characterizing Atmospheric River Contribution to Seasonal Snowfall Across Sierra Nevada, USA", Geophysical Research Letters, American Geophysical Union, Vol 44, Num 20, pp 10,445-10,453, 2017, doi:10.1002/2017GL075201


Laurie S. Huning and Steven A. Margulis: "Climatology of seasonal snowfall accumulation across the Sierra Nevada (USA): Accumulation rates, distributions, and variability", Water Resources Research, American Geophysical Union, Vol 53, Num 7, pp 6033-6049, 2017, doi:10.1002/2017WR020915


D. Buaria and P.K. Yeung: "A highly scalable particle tracking algorithm using partitioned global address space (PGAS) programming for extreme-scale turbulence simulations", Computer Physics Communications, Elsevier B.V., Vol 221, pp 246-258, 2017, doi:10.1016/j.cpc.2017.08.022


D. Roten, K. B. Olsen, and S. M. Day: "Off-fault deformations and shallow slip deficit from dynamic rupture simulations with fault zone plasticity", Geophysical Research Letters, American Geophysical Union, Vol 44, Num 15, pp 7733-7742, 2017, doi:10.1002/2017GL074323


Saurabh S. Sawant, Abhilash Harpale, Revathi Jambunathan, Huck Beng Chew, and Deborah A. Levin: "High fidelity and multi-scale thermal response modeling of an Avcoat-like TPS", American Institute of Aeronautics and Astronautics, 55th AIAA Aerospace Sciences Meeting, Grapevine, Texas, U.S.A., 2017, doi:10.2514/6.2017-0438


2016

Saurabh Jha, Valerio Formicola, Catello Di Martino, Zbigniew Kalbarczyk, William T. Kramer, Ravishankar K. Iyer: "Analysis of Gemini Interconnect Recovery Mechanisms: Methods and Observations", presented at CUG 2016, London, England, U.K., 2016


Phuong Cao, Eric C. Badger, Zbigniew T. Kalbarczyk, and Ravishankar K. Iyer: "A Framework for Generation, Replay, and Analysis of Real-World Attack Variants", Association for Computing Machinery, Proceedings of the Symposium and Bootcamp on the Science of Security (HotSos '16), pp 28-37, Pittsburgh, Pennsylvania, U.S.A., 2016, doi:10.1145/2898375.2898392


Subho S. Banerjee, Arjun P. Athreya, Liudmila S. Mainzer, C. Victor Jongeneel, Wen-Mei Hwu, Zbigniew T. Kalbarczyk, and Ravishankar K. Iyer: "Efficient and Scalable Workflows for Genomic Analyses", Association for Computing Machinery, Proceedings of the ACM International Workshop on Data-Intensive Distributed Computing (DIDC '16), pp 27-36, Kyoto, Japan, 2016, doi:10.1145/2912152.2912156


Ketan Date and Rakesh Nagi: "GPU-Accelerated Hungarian Algorithms for the Linear Assignment Problem", Parallel Computing, Elsevier BV, Vol 57, Num C, pp 52, 2016, doi:10.1016/j.parco.2016.05.012


David J. Luitz: "Long Tail Distributions Near the Many-Body Localization Transition", Physical Review B, American Physical Society, Vol 93, Num 13, pp 134201, 2016, doi:10.1103/physrevb.93.134201


Xiongjie Yu, David J. Luitz, and Bryan K. Clark: "Bimodal Entanglement Entropy Distribution in the Many-Body Localization Transition", Physical Review B, American Physical Society, Vol 94, Num 18, pp 184202, 2016, doi:10.1103/physrevb.94.184202


Peicheng Yu, Xinlu Xu, Asher Davidson, Adam Tableman, Thamine Dalichaouch, Fei Li, Michael D. Meyers, Weiming An, Frank S. Tsung, Viktor K. Decyk, Frederico Fiuza, Jorge Vieira, Ricardo A. Fonseca, Wei Lu, Luis O. Silva, and Warren B. Mori: "Enabling Lorentz Boosted Frame Particle-in-Cell Simulations of Laser Wakefield Acceleration in Quasi-3D Geometry", Journal of Computational Physics, Elsevier BV, Vol 316, pp 747-759, 2016, doi:10.1016/j.jcp.2016.04.014


C. E. Clayton, E. Adli, J. Allen, W. An, C. I. Clarke, S. Corde, J. Frederico, S. Gessner, S. Z. Green, M. J. Hogan, C. Joshi, M. Litos, W. Lu, K. A. Marsh, W. B. Mori, N. Vafaei-Najafabadi, X. Xu, and V. Yakimenko: "Self-Mapping the Longitudinal Field Structure of a Nonlinear Plasma Accelerator Cavity", Nature Communications, Springer Nature, Vol 7, Num 19, pp 12483, Savannah, Georgia, U.S.A., 2016, doi:10.1038/ncomms12483


Xu, X. L. and Pai, C.-H. and Zhang, C. J. and Li, F. and Wan, Y. and Wu, Y. P. and Hua, J. F. and Lu, W. and An, W. and Yu, P. and Joshi, C. and Mori, W. B.: "Nanoscale Electron Bunching in Laser-Triggered Ionization Injection in Plasma Accelerators", Physical Review Letters, American Physical Society, Vol 117, Num 3, pp 034801, 2016, doi:10.1103/physrevlett.117.034801


Joshua S. Méndez Harper and Josef Dufek: "The Effects of Granular Dynamics on the Triboelectric Charging of Volcanic ash: Experiments and Numerical Simulations", Electrostatics Society of America, Proceedings of the 2016 Electrostatics Joint Conference, West Lafayette, Indiana, U.S.A., 2016


Samuel R. Totorica, Tom Abel, and Frederico Fiuza: "Nonthermal Electron Energization from Magnetic Reconnection in Laser-Driven Plasmas", Physical Review Letters, American Physical Society, Vol 116, Num 9, pp 095003, 2016, doi:10.1103/physrevlett.116.095003


Colin M. Zarzycki, Kevin A. Reed, Julio T. Bacmeister, Anthony P. Craig, Susan C. Bates, and Nan A. Rosenbloom: "Impact of Surface Coupling Grids on Tropical Cyclone Extremes in High-Resolution Atmospheric Simulations", Geoscientific Model Development, Copernicus GmbH, Vol 9, Num 2, pp 779-788, 2016, doi:10.5194/gmd-9-779-2016


Jiashun Hu and Lijun Liu: "Abnormal Seismological and Magmatic Processes Controlled by the Tearing South American Flat Slabs", Earth and Planetary Science Letters, Elsevier BV, Vol 450, pp 40-51, 2016, doi:10.1016/j.epsl.2016.06.019


Jiashun Hu, Lijun Liu, Armando Hermosillo, and Quan Zhou: "Simulation of Late Cenozoic South American Flat-Slab Subduction Using Geodynamic Models with Data Assimilation", Earth and Planetary Science Letters, Elsevier BV, Vol 438, pp 1-13, 2016, doi:10.1016/j.epsl.2016.01.011


Tiffany Leonard and Lijun Liu: "The Role of a Mantle Plume in the Formation of Yellowstone Volcanism", Geophysical Research Letters, Wiley-Blackwell, Vol 43, Num 3, pp 1132-1139, 2016, doi:10.1002/2015gl067131


Pei-Hung Lin and Paul R. Woodward: "Transforming the Multifluid PPM Algorithm to Run on GPUs", Journal of Parallel and Distributed Computing, Elsevier BV, Vol 93-94, pp 56--65, 2016, doi:10.1016/j.jpdc.2016.04.005


Gregory M. Laskowski, James Kopriva, Vittorio Michelassi, Sriram Shankaran, Umesh Paliath, Rathakrishnan Bhaskaran, Qiqi Wang, Chaitanya Talnikar, Zhi J. Wang, and Feilin Jia: "Future Directions of High Fidelity CFD for Aerothermal Turbomachinery Analysis and Design", American Institute of Aeronautics and Astronautics, 46th AIAA Fluid Dynamics Conference, Washington, D.C., U.S.A., 2016, doi:10.2514/6.2016-3322


Jason Jaacks, Steven L. Finkelstein, and Kentaro Nagamine: "Connecting the Dots: Tracking Galaxy Evolution Using Constant Cumulative Number Density at 3 ≤ z ≤ 7", Astrophysical Journal, American Astronomical Society, Vol 817, Num 2, pp 174, 2016, doi:10.3847/0004-637x/817/2/174


D. Roten, Y. Cui, K. Olsen, S. Day, K. Withers, W. Savran, and P. Wang: "High-Frequency Nonlinear Earthquake Simulations on Petascale Heterogeneous Supercomputers", Institute of Electrical & Electronics Engineers Press, SC '16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, pp 82:1-82:12, Salt Lake City, Utah, U.S.A., 2016, doi:10.5555/3014904.3015015


Ricardo Taborda, Shima Azizzadeh-Roodpish, Naeem Khoshnevis, and Keli Cheng: "Evaluation of the Southern California Seismic Velocity Models Through Simulation of Recorded Events", Geophysical Journal International, Oxford University Press, Vol 205, Num 3, pp 1342-1364, 2016, doi:10.1093/gji/ggw085


W.H. Savran and K.B. Olsen: "Model for Small-Scale Crustal Heterogeneity in Los Angeles Basin Based on Inversion of Sonic Log Data", Geophysical Journal International, Oxford University Press, Vol 205, Num 2, pp 856-863, 2016, doi:10.1093/gji/ggw050


Yosef Zlochower, Hiroyuki Nakano, Bruno C. Mundim, Manuela Campanelli, Scott Noble, and Miguel Zilhão: "Inspiraling Black-Hole Binary Spacetimes: Challenges in Transitioning from Analytical to Numerical Techniques", Physical Review D, American Physical Society, Vol 93, Num 12, pp 124072, 2016, doi:10.1103/physrevd.93.124072


John M. A. Grime, James F. Dama, Barbie K. Ganser-Pornillos, Cora L. Woodward, Grant J. Jensen, Mark Yeager, and Gregory A. Voth: "Coarse-Grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly", Nature Communications, Springer Nature, Vol 7, pp 11568, 2016, doi:10.1038/ncomms11568


Christina Bergonzo, Kathleen B. Hall, and Thomas E. Cheatham: "Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics", Journal of Chemical Theory and Computation, American Chemical Society, Vol 12, Num 7, pp 3382-3389, 2016, doi:10.1021/acs.jctc.6b00173


James T. Waters, Xiang-Jun Lu, Rodrigo Galindo-Murillo, James C. Gumbart, Harold D. Kim, Thomas E. Cheatham, and Stephen C. Harvey: "Transitions of Double-Stranded DNA Between the A- and B-Forms", Journal of Physical Chemistry B, American Chemical Society, Vol 120, Num 33, pp 8449-8456, 2016, doi:10.1021/acs.jpcb.6b02155


Lucía Álvarez, Ariel Lewis-Ballester, Adrián Roitberg, Darío A. Estrin, Syun-Ru Yeh, Marcelo A. Marti, and Luciana Capece: "Structural Study of a Flexible Active Site Loop in Human Indoleamine 2, 3-Dioxygenase and Its Functional Implications", Biochemistry, American Chemical Society, Vol 55, Num 19, pp 2785-2793, 2016, doi:10.1021/acs.biochem.6b00077


Rodrigo Galindo-Murillo, Darrell R. Davis, and Thomas E. Cheatham: "Probing the Influence of Hypermodified Residues Within the tRNA3Lys Anticodon Stem Loop Interacting with the A-Loop Primer Sequence from HIV-1", Biochimica et Biophysica Acta (BBA) - General Subjects, Elsevier BV, Vol 1860, Num 3, pp 607-617, 2016, doi:10.1016/j.bbagen.2015.11.009


Rodrigo Galindo-Murillo, James C. Robertson, Marie Zgarbová, Jiří Šponer, Michal Otyepka, Petr Jurečka, and Thomas E. Cheatham III: "Assessing the Current State of Amber Force Field Modifications for DNA", Journal of Chemical Theory and Computation, American Chemical Society, Vol 12, Num 8, pp 4114-4127, 2016, doi:10.1021/acs.jctc.6b00186


S. Corde, E. Adli, J. M. Allen, W. An, C. I. Clarke, B. Clausse, C. E. Clayton, J. P. Delahaye, J. Frederico, S. Gessner, S. Z. Green, M. J. Hogan, C. Joshi, M. Litos, W. Lu, K. A. Marsh, W. B. Mori, N. Vafaei-Najafabadi, D. Walz, and V. Yakimenko: "High-Field Plasma Acceleration in a High-Ionization-Potential Gas", Nature Communications, Springer Nature, Vol 7, pp 11898, 2016, doi:10.1038/ncomms11898


Sheel C. Dodani, Gert Kiss, Jackson K. B. Cahn, Ye Su, Vijay S. Pande, and Frances H. Arnold: "Discovery of a Regioselectivity Switch in Nitrating P450s Guided by Molecular Dynamics Simulations and Markov Models", Nature Chemistry, Nature Publishing Group, Vol 8, Num 5, pp 419-425, 2016, doi:10.1038/nchem.2474


James Charles, Prasad Sarangapani, Roksana Golizadeh-Mojarad, Robert Andrawis, Daniel Lemus, Xinchen Guo, Daniel Mejia, James E. Fonseca, Michael Povolotskyi, Tillmann Kubis, and Gerhard Klimeck: "Incoherent Transport in NEMO5: Realistic and Efficient Scattering on Phonons", Journal of Computational Electronics, Springer Nature, Vol 15, Num 4, pp 1123-1129, 2016, doi:10.1007/s10825-016-0845-y


Yu Wang, Archana Tankasala, Lloyd C L Hollenberg, Gerhard Klimeck, Michelle Y Simmons, and Rajib Rahman: "Highly Tunable Exchange in Donor Qubits in Silicon", npj Quantum Information, Nature Publishing Group, Vol 2, pp 16008, 2016, doi:10.1038/npjqi.2016.8


A. Bazavov, C. Bernard, N. Brown, J. Komijani, C. DeTar, J. Foley, L. Levkova, Steven Gottlieb, U.M. Heller, J. Laiho, R.L. Sugar, D. Toussaint, and R.S. Van de Water: "Gradient Flow and Scale Setting on MILC HISQ Ensembles", Physical Review D, American Physical Society, Vol 93, Num 9, pp 094510, 2016, doi:10.1103/physrevd.93.094510


Daniel R. Bolton, Raúl A. Briceño, and David J. Wilson: "Connecting Physical Resonant Amplitudes and Lattice QCD", Physics Letters B, Elsevier BV, Vol 757, pp 50-56, 2016, doi:10.1016/j.physletb.2016.03.043


Kai Germaschewski, William Fox, Stephen Abbott, Narges Ahmadi, Kristofor Maynard, Liang Wang, Hartmut Ruhl, and Amitava Bhattacharjee: "The Plasma Simulation Code: A Modern Particle-in-Cell Code with Patch-Based Load-Balancing", Journal of Computational Physics, Elsevier BV, Vol 318, pp 305-326, 2016, doi:10.1016/j.jcp.2016.05.013


A. M. Jacobs, M. Zingale, A. Nonaka, A. S. Almgren, and J. B. Bell: "Low Mach Number Modeling of Convection in Helium Shells on Sub-Chandrasekhar White Dwarfs II: Bulk Properties of Simple Models", Astrophysical Journal, The American Astronomical Society, Vol 827, Num 1, pp 84, 2016, doi:10.3847/0004-637x/827/1/84


Max P. Katz, Michael Zingale, Alan C. Calder, F. Douglas Swesty, Ann S. Almgren, and Weiqun Zhang: "White Dwarf Mergers on Adaptive Meshes I. Methodology and Code Verification", Astrophysical Journal, American Astronomical Society, Vol 819, Num 2, pp 94, 2016, doi:10.3847/0004-637x/819/2/94


Hao Xu, John H. Wise, Michael L. Norman, Kyungjin Ahn, and Brian W. O'Shea: "Galaxy Properties and UV Escape Fractions During Epoch of Reionization: Results from the Renaissance Simulations", Astrophysical Journal, The American Astronomical Society, Vol 833, Num 1, pp 84, 2016, doi:10.3847/1538-4357/833/1/84


Chuang Liu and Juan R. Perilla and Jiying Ning and Manman Lu and Guangjin Hou and Ruben Ramalho and Benjamin A. Himes and Gongpu Zhao and Gregory J. Bedwell and In-Ja Byeon and Jinwoo Ahn and Angela M. Gronenborn and Peter E. Prevelige and Itay Rousso and Christopher Aiken and Tatyana Polenova and Klaus Schulten and Peijun Zhang: "Cyclophilin a Stabilizes the HIV-1 Capsid Through a Novel Non-Canonical Binding Site", Nature Communications, Nature Publishing Group, Vol 7, pp 10714, 2016, doi:10.1038/ncomms10714


John E. Stone and Melih Sener and Kirby L. Vandivort and Angela Barragan and Abhishek Singharoy and Ivan Teo and João V. Ribeiro and Barry Isralewitz and Bo Liu and Boon Chong Goh and James C. Phillips and Craig MacGregor-Chatwin and Matthew P. Johnson and Lena F. Kourkoutis and C. Neil Hunter and Klaus Schulten: "Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing", Parallel Computing, Elsevier BV, Vol 55, pp 17-27, 2016, doi:10.1016/j.parco.2015.10.015


John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten: "High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL", Institute of Electrical and Electronics Engineers, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp 1014-1023, Chicago, Illinois, U.S.A., 2016, doi:10.1109/ipdpsw.2016.127


John E. Stone, William R. Sherman, and Klaus Schulten: "Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering", Institute of Electrical & Electronics Engineers, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp 1048-1057, Chicago, Illinois, U.S.A., 2016, doi:10.1109/ipdpsw.2016.121


E. J. Zirnstein, J. Heerikhuisen, H. O. Funsten, G. Livadiotis, D. J. McComas, and N. V. Pogorelov: "Local Interstellar Magnetic Field Determined from the Interstellar Boundary Explorer Ribbon", Astrophysical Journal, American Astronomical Society, Vol 818, Num 1, pp L18, 2016, doi:10.3847/2041-8205/818/1/l18


N. V. Pogorelov: "The Heliotail: Theory and Modeling", IOP Publishing, Journal of Physics: Conference Series (10th International Conference on Numerical Modeling of Space Plasma Flows, ASTRONUM 2015), Vol 719, pp 012013, Avignon, France, 2016, doi:10.1088/1742-6596/719/1/012013


Nikolai Pogorelov: "Modeling Heliophysics and Astrophysics Phenomena with a Multi-Scale Fluid-Kinetic Simulation Suite: From The Solar Surface to The Local Interstellar Medium", 2016 Blue Waters Annual Report, pp 36-38, 2016


Kristina D. Launey, Tomas Dytrych, and Jerry P. Draayer: "Symmetry-Guided Large-Scale Shell-Model Theory", Progress in Particle and Nuclear Physics, Elsevier BV, Vol 89, pp 101-136, 2016, doi:10.1016/j.ppnp.2016.02.001


Yongyang Cai, Timothy M. Lenton, and Thomas S. Lontzek: "Risk of Multiple Interacting Tipping Points Should Encourage Rapid CO2 Emission Reduction", Nature Climate Change, Nature Publishing Group, Vol 6, Num 5, pp 520-525, 2016, doi:10.1038/nclimate2964


Anshul Gupta, Natalia Gimelshein, Seid Koric, and Steven Rennich: "Effective Minimally-Invasive GPU Acceleration of Distributed Sparse Matrix Factorization", Springer International Publishing, Lecture Notes in Computer Science: Euro-Par 2016 (Parallel Processing), pp 672-683, Grenoble, France, 2016, doi:10.1007/978-3-319-43659-3_49


J. Kwack, G. H Bauer, and S. Koric: "Performance Test of Parallel Linear Equation Solvers on Blue Waters-Cray XE6/XK7 system", presented at CUG 2016, London, England, U.K., 2016


R. I. Barabash, V. Agarwal, S. Koric, I. Jasiuk, and J. Z. Tischler: "Finite Element Simulation and X-Ray Microdiffraction Study of Strain Partitioning in a Layered Nanocomposite", Journal of Crystallography, Hindawi Publishing Corporation, Vol 2016, pp 1-11, 2016, doi:10.1155/2016/4351347


Seid Koric and Anshul Gupta: "Sparse Matrix Factorization in the Implicit Finite Element Method on Petascale Architecture", Computer Methods in Applied Mechanics and Engineering, Elsevier BV, Vol 302, pp 281-292, 2016, doi:10.1016/j.cma.2016.01.011


Vladimir Puzyrev, Seid Koric, and Scott Wilkin: "Evaluation of Parallel Direct Sparse Linear Solvers in Electromagnetic Geophysical Problems", Computers & Geosciences, Elsevier BV, Vol 89, pp 79-87, 2016, doi:10.1016/j.cageo.2016.01.009


Milton Ruiz, Ryan N. Lang, Vasileios Paschalidis, and Stuart L. Shapiro: "Binary Neutron Star Mergers: A Jet Engine for Short Gamma-Ray Bursts", Astrophysical Journal Letters, American Astronomical Society, Vol 824, Num 1, pp L6, 2016, doi:10.3847/2041-8205/824/1/l6


Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev: "De Novo Reconstruction of DNA Origami Structures Through Atomistic Molecular Dynamics Simulation", Nucleic Acids Research, Oxford University Press, Vol 44, Num 7, pp 3013-3019, 2016, doi:10.1093/nar/gkw155


Maxim Belkin and Aleksei Aksimentiev: "Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores", ACS Applied Materials & Interfaces, American Chemical Society, Vol 8, Num 20, pp 12599-12608, 2016, doi:10.1021/acsami.6b00463


S. Slone, J. Yoo, C.-Y. Li, and A. Aksimentiev: "Molecular Mechanics of DNA Bricks: In Situ Structure, Mechanical Properties and Ionic Conductivity", New Journal of Physics, IOP Publishing Ltd and Deutsche Physikalische Gesellschaft, Vol 18, Num 5, pp 055012, 2016, doi:10.1088/1367-2630/18/5/055012


JaeHyuk Kwack, Arif Masud, and K. R. Rajagopal: "Stabilized Mixed Three-Field Formulation for a Generalized Incompressible Oldroyd-B Model", International Journal for Numerical Methods in Fluids, Wiley-Blackwell, Vol 83, Num 9, pp 704--734, 2016, doi:10.1002/fld.4287


Tyler M. Earnest, John A. Cole, Joseph R. Peterson, Michael J. Hallock, Thomas E. Kuhlman, and Zaida Luthey-Schulten: "Ribosome Biogenesis in Replicating Cells: Integration of Experiment and Theory", Biopolymers, Wiley-Blackwell, Vol 105, Num 10, pp 735, 2016, doi:10.1002/bip.22892


Dacen Waters, Stephen M. Wilkins, Tiziana Di Matteo, Yu Feng, Rupert Croft, and Daisuke Nagai: "Monsters in the Dark: Predictions for Luminous Galaxies in the Early Universe from the BlueTides Simulation", Monthly Notices of the Royal Astronomical Society: Letters, Oxford University Press, Vol 461, Num 1, pp L51-L55, 2016, doi:10.1093/mnrasl/slw100


Dacen Waters, Tiziana Di Matteo, Yu Feng, Stephen M. Wilkins, and Rupert A.C. Croft: "Forecasts for the WFIRST High Latitude Survey using the BlueTides Simulation", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 463, Num 4, pp 3520-3530, 2016, doi:10.1093/mnras/stw2000


Stephen M. Wilkins, Yu Feng, Tiziana Di Matteo, Rupert Croft, Elizabeth R. Stanway, Andrew Bunker, Dacen Waters, and Christopher Lovell: "The Photometric Properties of Galaxies in the Early Universe", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 460, Num 3, pp 3170-3178, 2016, doi:10.1093/mnras/stw1154


Stephen M. Wilkins, Yu Feng, Tiziana Di Matteo, Rupert Croft, Elizabeth R. Stanway, Rychard J. Bouwens, and Peter Thomas: "The Lyman-Continuum Photon Production Efficiency in the High-Redshift Universe", Monthly Notices of the Royal Astronomical Society: Letters, Oxford University Press, Vol 458, Num 1, pp L6-L9, 2016, doi:10.1093/mnrasl/slw007


Leigh Orf, Robert Wilhelmson, and Louis Wicker: "Visualization of a Simulated Long-Track EF5 Tornado Embedded Within a Supercell Thunderstorm", Parallel Computing, Elsevier BV, Vol 55, pp 28-34, 2016, doi:10.1016/j.parco.2015.10.014


Leigh Orf, Robert Wilhelmson, Bruce Lee, Cathy Finley, and Adam Houston: "Evolution of a Long-Track Violent Tornado Within a Simulated Supercell", Bulletin of the American Meteorological Society, American Meteorological Society, Vol 98, Num 1, pp 45, 2016, doi:10.1175/bams-d-15-00073.1


Kai Jin, Surya P. Vanka, Brian G. Thomas, and Xiaoming Ruan: "Large Eddy Simulations of the Effects of Double-Ruler Electromagnetic Braking and Nozzle Submergence Depth on Molten Steel Flow in a Commercial Continuous Casting Mold", Wiley-Blackwell, CFD Modeling and Simulation in Materials Processing 2016, pp 159-166, 2016, doi:10.1002/9781119274681.ch20


Seong-Mook Cho, Brian G. Thomas, and Seon-Hyo Kim: "Transient Two-Phase Flow in Slide-Gate Nozzle and Mold of Continuous Steel Slab Casting with and Without Double-Ruler Electro-Magnetic Braking", Metallurgical and Materials Transactions B, Springer Nature, Vol 47, Num 5, pp 3080--3098, 2016, doi:10.1007/s11663-016-0752-4


Alexandra L. Jones: "Development of an Accurate 3D Monte Carlo Broadband Atmospheric Radiative Transfer Model", University of Illinois at Urbana-Champaign, Illinois Digital Environment for Access to Learning and Scholarship, Vol Doctoral dissertation, 2016


Michael A. Salim, Soohaeng Yoo Willow, and So Hirata: "Ice Ih Anomalies: Thermal Contraction, Anomalous Volume Isotope Effect, and Pressure-Induced Amorphization", Journal of Chemical Physics, AIP Publishing, Vol 144, Num 20, pp 204503, 2016, doi:10.1063/1.4951687


S. Hirata, K. Gilliard, X. He, M. Keçeli, J. Li, M. A. Salim, O. Sode, and K. Yagi: "Ab Initio Ice, Dry Ice, and Liquid Water", Wiley, Chichester, Fragmentation: Toward Accurate Calculations on Complex Molecular Systems, pp 245-295, 2016, doi:10.1002/9781119129271.ch9


Soohaeng Yoo Willow, Xiao Cheng Zeng, Sotiris S. Xantheas, Kwang S. Kim, and So Hirata: "Why Is MP2-Water "Cooler" and "Denser" Than DFT-Water?", Journal of Physical Chemistry Letters, American Chemical Society, Vol 7, Num 4, pp 680-684, 2016, doi:10.1021/acs.jpclett.5b02430


Puja Goyal, Christine A. Schwerdtfeger, Alexander V. Soudackov, and Sharon Hammes-Schiffer: "Proton Quantization and Vibrational Relaxation in Nonadiabatic Dynamics of Photoinduced Proton-Coupled Electron Transfer in a Solvated Phenol-Amine Complex", Journal of Physical Chemistry B, American Chemical Society, Vol 120, Num 9, pp 2407-2417, 2016, doi:10.1021/acs.jpcb.5b12015


Tanner Culpitt, Kurt R. Brorsen, Michael V. Pak, and Sharon Hammes-Schiffer: "Multicomponent Density Functional Theory Embedding Formulation", Journal of Chemical Physics, AIP Publishing, Vol 145, Num 4, pp 044106, 2016, doi:10.1063/1.4958952


Carlo Pierleoni, Miguel A. Morales, Giovanni Rillo, Markus Holzmann, and David M. Ceperley: "Liquid-Liquid Phase Transition in Hydrogen by Coupled Electron-Ion Monte Carlo Simulations", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 113, Num 18, pp 4953-4957, 2016, doi:10.1073/pnas.1603853113


Yashar D. Hezaveh and Neal Dalal and Daniel P. Marrone and Yao-Yuan Mao and Warren Morningstar and Di Wen and Roger D. Blandford and John E. Carlstrom and Christopher D. Fassnacht and Gilbert P. Holder and Athol Kemball and Philip J. Marshall and Norman Murray and Laurence Perreault Levasseur and Joaquin D. Vieira and Risa H. Wechsler: "Detection of Lensing Substructure Using Alma Observations of the Dusty Galaxy SDP.81", Astrophysical Journal, American Astronomical Society, Vol 823, Num 1, pp 37, 2016, doi:10.3847/0004-637x/823/1/37


Abhilash Harpale, Marco Panesi, and Huck Beng Chew: "Plasma-Graphene Interaction and Its Effects on Nanoscale Patterning", Physical Review B, American Physical Society, Vol 93, Num 3, pp 035416, 2016, doi:10.1103/physrevb.93.035416


Haoran Wang and Huck Beng Chew: "Molecular Dynamics Simulations of Plasticity and Cracking in Lithiated Silicon Electrodes", Extreme Mechanics Letters, Elsevier BV, Vol 9, Num Part 3, pp 503-513, 2016, doi:10.1016/j.eml.2016.02.020


A. Sharma, P. Conry, H. J. S. Fernando, Alan F. Hamlet, J. J. Hellmann, and F. Chen: "Green and Cool Roofs to Mitigate Urban Heat Island Effects in the Chicago Metropolitan Area: Evaluation with a Regional Climate Model", Environmental Research Letters, IOP Publishing, Vol 11, Num 6, pp 064004, 2016, doi:10.1088/1748-9326/11/6/064004


Ashish Sharma, Harindra J.S. Fernando, Alan F. Hamlet, Jessica J. Hellmann, Michael Barlage, and Fei Chen: "Urban Meteorological Modeling Using WRF: A Sensitivity Study", International Journal of Climatology, John Wiley & Sons, Ltd, Vol 37, Num 4, pp 1885-1900, 2016, doi:10.1002/joc.4819


Dinshaw S. Balsara, Takanobu Amano, Sudip Garain, and Jinho Kim: "A High-Order Relativistic Two-Fluid Electrodynamic Scheme with Consistent Reconstruction of Electromagnetic Fields and a Multidimensional Riemann Solver for Electromagnetism", Journal of Computational Physics, Elsevier BV, Vol 318, pp 169-200, 2016, doi:10.1016/j.jcp.2016.05.006


Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper: "LES of an Aero-Optical Turret Flow at High Reynolds Number", American Institute of Aeronautics and Astronautics, 54th AIAA Aerospace Sciences Meeting, San Diego, California, U.S.A., 2016, doi:10.2514/6.2016-1461


Ariana Minot, Yue M. Lu, and Na Li: "A Parallel Primal-Dual Interior-Point Method for DC Optimal Power Flow", Institute of Electrical & Electronics Engineers, 2016 Power Systems Computation Conference (PSCC), pp 1-7, Genoa, Italy, 2016, doi:10.1109/pscc.2016.7540826


David Radice, Christian D. Ott, Ernazar Abdikamalov, Sean M. Couch, Roland Haas, and Erik Schnetter: "Neutrino-Driven Convection in Core-Collapse Supernovae: High-Resolution Simulations", Astrophysical Journal, American Astronomical Society, Vol 820, Num 1, pp 76, 2016, doi:10.3847/0004-637x/820/1/76


David Radice, Filippo Galeazzi, Jonas Lippuner, Luke F. Roberts, Christian D. Ott, and Luciano Rezzolla: "Dynamical Mass Ejection from Binary Neutron Star Mergers", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 460, Num 3, pp 3255-3271, 2016, doi:10.1093/mnras/stw1227


David Radice, Sebastiano Bernuzzi, and Christian D. Ott: "One-Armed Spiral Instability in Neutron Star Mergers and Its Detectability in Gravitational Waves", Physical Review D, American Physical Society (APS), Vol 94, Num 6, pp 064011, 2016, doi:10.1103/physrevd.94.064011


Luke F. Roberts, Christian D. Ott, Roland Haas, Evan P. O'Connor, Peter Diener, and Erik Schnetter: "General Relativistic Three-Dimensional Multi-Group Neutrino Radiation-Hydrodynamics Simulations of Core-Collapse Supernovae", Astrophysical Journal, The American Astronomical Society, Vol 831, Num 1, pp 98, 2016, doi:10.3847/0004-637X/831/1/98


Sebastiano Bernuzzi, David Radice, Christian D. Ott, Luke F. Roberts, Philipp Mösta, and Filippo Galeazzi: "How Loud Are Neutron Star Mergers?", Physical Review D, American Physical Society, Vol 94, Num 2, pp 024023, 2016, doi:10.1103/physrevd.94.024023


Joshua Wallace, Adam Burrows, and Joshua C. Dolence: "Detecting the Supernova Breakout Burst in Terrestrial Neutrino Detectors", Astrophysical Journal, American Astronomical Society, Vol 817, Num 2, pp 182, 2016, doi:10.3847/0004-637x/817/2/182


Alireza Samimi and Jamesina Simpson: "Parallelization of 3-D Global FDTD Earth-Ionosphere Waveguide Models at Resolutions on the Order of ~1 Km and Higher", IEEE Antennas and Wireless Propagation Letters, Institute of Electrical & Electronics Engineers, pp 1959-1962, 2016, doi:10.1109/lawp.2016.2545526


Schweitzer, Andreas and Aufderheide, Antje and Rudack, Till and Beck, Florian and Pfeifer, Günter and Plitzko, Jürgen M. and Sakata, Eri and Schulten, Klaus and Förster, Friedrich and Baumeister, Wolfgang: "Structure of the human 26S proteasome at a resolution of 3.9 angstrom", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 113, Num 28, pp 7816-7821, 2016, doi:10.1073/pnas.1608050113


Yi Zhang, Lela Vuković, Till Rudack, Wei Han, and Klaus Schulten: "Recognition of Poly-Ubiquitins by the Proteasome Through Protein Refolding Guided by Electrostatic and Hydrophobic Interactions", Journal of Physical Chemistry B, American Chemical Society, pp 8137-8146, 2016, doi:10.1021/acs.jpcb.6b01327


Junshik Um: "Applicability of Geometric Optics Method for Calculations of Single Scattering Properties of Atmospheric Ice Crystals", 2015 Blue Waters Annual Report, pp 56-57, 2016


Robert J. Trapp and Kimberly A. Hoogewind: "The Realization of Extreme Tornadic Storm Events Under Future Anthropogenic Climate Change", Journal of Climate, American Meteorological Society, Vol 29, Num 14, pp 5251-5265, 2016, doi:10.1175/jcli-d-15-0623.1


Hui Li, Ryan L. Sriver, and Marlos Goes: "Modeled Sensitivity of the Northwestern Pacific Upper-Ocean Response to Tropical Cyclones in a Fully Coupled Climate Model with Varying Ocean Grid Resolution", Journal of Geophysical Research: Oceans, Wiley-Blackwell, Vol 121, Num 1, pp 586-601, 2016, doi:10.1002/2015jc011226


Robert Sisneros and David Pugmire: "Tuned to Terrible: A Study of Parallel Particle Advection State of the Practice", Institute of Electrical & Electronics Engineers, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp 1058-1067, Chicago, Illinois, U.S.A., 2016, doi:10.1109/ipdpsw.2016.173


Iwona Jasiuk: "Multiscale Modeling Of Bone Fracture and Strength", 2016 Blue Waters Annual Report, pp 122-124, 2016


Iwona Jasiuk: "Multiscale Modeling Of Bone Fracture and Strength", 2015 Blue Waters Annual Report, pp 146-147, 2016


Vincent Le Chenadec: "First Principle and Modeling of Turbulent Two-Phase Flows", 2016 Blue Waters Annual Report, pp 154-155, 2016


Diwakar Shukla, Ariana Peck, and Vijay S. Pande: "Conformational Heterogeneity of the Calmodulin Binding Interface", Nature Communications, Nature Publishing Group, Vol 7, pp 10910, 2016, doi:10.1038/ncomms10910


Bo Sun: "Modeling Heat and Mass Transfer in Reacting Gas-solid Flow Using Particle-resolved Direct Numerical Simulation", ProQuest LLC, ProQuest Dissertations and Theses, pp 357, 2016


Nam-phuong Nguyen, Michael Nute, Siavash Mirarab, and Tandy Warnow: "HIPPI: Highly Accurate Protein Family Classification with Ensembles of HMMs", BMC Genomics, Springer Nature, Vol 17, Num S10, pp 765, 2016, doi:10.1186/s12864-016-3097-0


Nam-Phuong Nguyen, Tandy Warnow, Mihai Pop, and Bryan White: "A Perspective on 16S rRNA Operational Taxonomic Unit Clustering Using Sequence Similarity", npj Biofilms and Microbiomes, Nature Publishing Group, Vol 2, pp 16004, 2016, doi:10.1038/npjbiofilms.2016.4


Wendy K. Tam Cho and Yan Y. Liu: "A Parallel Evolutionary Algorithm for Subset Selection in Causal Inference Models", ACM Press, XSEDE16: Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, pp 7:1-7:8, Miami, Florida, U.S.A., 2016, doi:10.1145/2949550.2949568


Kerstin Göpfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev, and Ulrich F. Keyser: "Ion Channels Made from a Single Membrane-Spanning DNA Duplex", Nano Letters, American Chemical Society, Vol 16, Num 7, pp 4665-4669, 2016, doi:10.1021/acs.nanolett.6b02039


K. Jin, P. Kumar, S. P. Vanka, and B. G. Thomas: "Rise of an Argon Bubble in Liquid Steel in the Presence of a Transverse Magnetic Field", Physics of Fluids, AIP Publishing, Vol 28, Num 9, pp 093301, 2016, doi:10.1063/1.4961561


Kai Jin, Surya P. Vanka, and Brian G. Thomas: "Large Eddy Simulations of the Effects of EMBr and SEN Submergence Depth on Turbulent Flow in the Mold Region of a Steel Caster", Metallurgical and Materials Transactions B, Springer Nature, Vol 48, Num 1, pp 162-178, 2016, doi:10.1007/s11663-016-0801-z


Brian M. Sandroff, Curtis L. Johnson, and Robert W. Motl: "Exercise Training Effects on Memory and Hippocampal Viscoelasticity in Multiple Sclerosis: A Novel Application of Magnetic Resonance Elastography", Neuroradiology, Springer Nature, Vol 59, Num 1, pp 61-67, 2016, doi:10.1007/s00234-016-1767-x


Wendy K. Tam Cho and Yan Y. Liu: "Toward a Talismanic Redistricting Tool: A Computational Method for Identifying Extreme Redistricting Plans", Election Law Journal: Rules, Politics, and Policy, Mary Ann Liebert Inc, Vol 15, Num 4, pp 351-366, 2016, doi:10.1089/elj.2016.0384


Marianne J Bezaire, Ivan Raikov, Kelly Burk, Dhrumil Vyas, and Ivan Soltesz: "Interneuronal Mechanisms of Hippocampal Theta Oscillations in a Full-Scale Model of the Rodent CA1 Circuit", eLife, eLife Sciences Organisation, Ltd., Vol 5, 2016, doi:10.7554/elife.18566


Kerstin Göpfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser: "Large-Conductance Transmembrane Porin Made from DNA Origami", ACS Nano, American Chemical Society, Vol 10, Num 9, pp 8207-8214, 2016, doi:10.1021/acsnano.6b03759


Kalyan Immadisetty, Jeevapani Hettige, and Mahmoud Moradi: "What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT", Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 15, pp 3644-3656, 2016, doi:10.1021/acs.jpcb.6b09733


Cole M. Johnson, Alexander E. Doran, Jinmei Zhang, Edward F. Valeev, and So Hirata: "Monte Carlo Explicitly Correlated Second-Order Many-Body Perturbation Theory", Journal of Chemical Physics, AIP Publishing, Vol 145, Num 15, pp 154115, 2016, doi:10.1063/1.4964854


Alexander E. Doran and So Hirata: "Monte Carlo MP2 on Many Graphical Processing Units", Journal of Chemical Theory and Computation, American Chemical Society, Vol 12, Num 10, pp 4821-4832, 2016, doi:10.1021/acs.jctc.6b00588


Yan Y. Liu, Wendy K. Tam Cho, and Shaowen Wang: "PEAR: A Massively Parallel Evolutionary Computation Approach for Political Redistricting Optimization and Analysis", Swarm and Evolutionary Computation, Elsevier BV, Vol 30, pp 78-92, 2016, doi:10.1016/j.swevo.2016.04.004


A. Perez, J. A. Morrone, E. Brini, J. L. MacCallum, and K. A. Dill: "Blind Protein Structure Prediction Using Accelerated Free-Energy Simulations", Science Advances, American Association for the Advancement of Science, Vol 2, Num 11, pp e1601274-e1601274, 2016, doi:10.1126/sciadv.1601274


T. Dytrych, P. Maris, K. D. Launey, J. P. Draayer, J. P. Vary, D. Langr, E. Saule, M. A. Caprio, U. Catalyurek, and M. Sosonkina: "Efficacy of the SU(3) Scheme for Ab Initio Large-Scale Calculations Beyond the Lightest Nuclei", Computer Physics Communications, Elsevier BV, Vol 207, pp 202-210, 2016, doi:10.1016/j.cpc.2016.06.006


Hui Li and Ryan L. Sriver: "Effects of Ocean Grid Resolution on Tropical Cyclone-Induced Upper Ocean Responses Using a Global Ocean General Circulation Model", Journal of Geophysical Research: Oceans, Wiley-Blackwell, Vol 121, Num 11, pp 8305-8319, 2016, doi:10.1002/2016jc011951


Som Dutta, Paul Fischer, and Marcelo Garcia: "Large Eddy Simulation (LES) of Flow and Bedload Transport at an Idealized 90-Degree Diversion: Insight Into Bulle-Effect", CRC Press, River Flow 2016, pp 101-109, 2016, doi:10.1201/9781315644479-20


Lijun Liu and Derrick Hasterok: "High-Resolution Lithosphere Viscosity and Dynamics Revealed by Magnetotelluric Imaging", Science, American Association for the Advancement of Science, Vol 353, Num 6307, pp 1515-1519, 2016, doi:10.1126/science.aaf6542


David J. Luitz and Yevgeny Bar Lev: "Anomalous Thermalization in Ergodic Systems", Physical Review Letters, American Physical Society (APS), Vol 117, Num 17, pp 170404, 2016, doi:10.1103/physrevlett.117.170404


Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha: "Direct Evidence for Sequence-Dependent Attraction Between Double-Stranded DNA Controlled by Methylation", Nature Communications, Springer Nature, Vol 7, pp 11045, 2016, doi:10.1038/ncomms11045


Thuy T. M. Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei Aksimentiev, and Taekjip Ha: "Effects of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability", Nature Communications, Springer Nature, Vol 7, pp 10813, 2016, doi:10.1038/ncomms10813


Jejoong Yoo and Aleksei Aksimentiev: "The structure and intermolecular forces of DNA condensates", Nucleic Acids Research, Oxford University Press, Vol 44, Num 5, pp 2036, 2016, doi:10.1093/nar/gkw081


Jejoong Yoo and Aleksei Aksimentiev: "Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields", Journal of Chemical Theory and Computation, American Chemical Society, Vol 12, Num 1, pp 430-443, 2016, doi:10.1021/acs.jctc.5b00967


Jejoong Yoo, James Wilson, and Aleksei Aksimentiev: "Improved Model of Hydrated Calcium Ion for Molecular Dynamics Simulations Using Classical Biomolecular Force Fields", Biopolymers, Wiley-Blackwell, Vol 105, Num 10, pp 752-763, 2016, doi:10.1002/bip.22868


Spencer Carson, James Wilson, Aleksei Aksimentiev, Peter R. Weigele, and Meni Wanunu: "Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA", Nucleic Acids Research, Oxford University Press, Vol 44, Num 5, pp 2085, 2016, doi:10.1093/nar/gkv1199


Sergii Pud, Shu-Han Chao, Maxim Belkin, Daniel Verschueren, Teun Huijben, Casper van Engelenburg, Cees Dekker, and Aleksei Aksimentiev: "Mechanical Trapping of DNA in a Double-Nanopore System", Nano Letters, American Chemical Society, Vol 16, Num 12, pp 8021-8028, 2016, doi:10.1021/acs.nanolett.6b04642


Krishna Kumar, Hitesh J. Changlani, Bryan K. Clark, and Eduardo Fradkin: "Numerical evidence for a chiral spin liquid in the XXZ antiferromagnetic Heisenberg model on the kagome lattice at m=2/3 magnetization", Physical Review B, American Physical Society (APS), Vol 94, Num 13, pp 134410, 2016, doi:10.1103/physrevb.94.134410


Amanda Bienz, Robert D. Falgout, William Gropp, Luke N. Olson, and Jacob B. Schroder: "Reducing Parallel Communication in Algebraic Multigrid Through Sparsification", SIAM Journal on Scientific Computing, Society for Industrial & Applied Mathematics, Vol 38, Num 5, pp S332-S357, 2016, doi:10.1137/15m1026341


William Gropp, Luke N. Olson, and Philipp Samfass: "Modeling MPI Communication Performance on SMP Nodes: Is it Time to Retire the Ping Pong Test?", ACM Press, Proceedings of the 23rd European MPI Users' Group Meeting (EuroMPI 2016), pp 41-50, Edinburgh, Scotland, U.K., 2016, doi:10.1145/2966884.2966919


Paul R. Eller and William Gropp: "Scalable Non-Blocking Preconditioned Conjugate Gradient Methods", Institute of Electrical & Electronics Engineers, SC '16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, pp 204-215, 2016, doi:10.1109/sc.2016.17


Guangyu Zhao, Larry Di Girolamo, David J. Diner, Carol J. Bruegge, Kevin J. Mueller, and Dong L. Wu: "Regional Changes in Earth's Color and Texture as Observed from Space Over a 15-Year Period", IEEE Transactions on Geoscience and Remote Sensing, Institute of Electrical and Electronics Engineers, Vol 54, Num 7, pp 4240-4249, 2016, doi:10.1109/tgrs.2016.2538723


Jacob Heerikhuisen, Konstantin V. Gamayunov, Eric J. Zirnstein, and Nikolai V. Pogorelov: "Neutral Atom Properties in the Direction of the IBEX Ribbon", Astrophysical Journal, The American Astronomical Society, Vol 831, Num 2, pp 137, 2016, doi:10.3847/0004-637X/831/2/137


T. K. Kim, N. V. Pogorelov, G. P. Zank, H. A. Elliott, and D. J. McComas: "Modeling the Solar Wind at the Ulysses, Voyager, and New Horizons Spacecraft", Astrophysical Journal, The American Astronomical Society, Vol 832, Num 1, pp 72, 2016, doi:10.3847/0004-637X/832/1/72


N. V. Pogorelov, M. C. Bedford, I. A. Kryukov, and G. P. Zank: "Pickup Ion Effect of the Solar Wind Interaction with the Local Interstellar Medium", IOP Publishing Ltd, Journal of Physics: Conference Series (15th Annual International Astrophysics Conference: "The Science of Ed Stone: Celebrating his 80th Birthday"), Vol 767, Num 1, pp 012020, Cape Coral, Florida, U.S.A., 2016, doi:10.1088/1742-6596/767/1/012020


Viktoriya Morozova, Anthony L. Piro, Mathieu Renzo, and Christian D. Ott: "Numerical Modeling of the Early Light Curves of Type IIP Supernovae", Astrophysical Journal, The American Astronomical Society, Vol 829, Num 2, pp 109, 2016, doi:10.3847/0004-637X/829/2/109


Christian D. Ott: "Massive Computation for Understanding Core-Collapse Supernova Explosions", Computing in Science & Engineering, Institute of Electrical and Electronics Engineers, Vol 18, Num 5, pp 78-92, 2016, doi:10.1109/mcse.2016.81


Shuai Zhang, Kevin P. Driver, François Soubiran, and Burkhard Militzer: "Path Integral Monte Carlo Simulations of Warm Dense Sodium", High Energy Density Physics, Elsevier BV, Vol 21, pp 16-19, 2016, doi:10.1016/j.hedp.2016.09.004


S. X. Hu, B. Militzer, L. A. Collins, K. P. Driver, and J. D. Kress: "First-Principles Prediction of the Softening of the Silicon Shock Hugoniot Curve", Physical Review B, American Physical Society, Vol 94, Num 9, pp 094109, 2016, doi:10.1103/physrevb.94.094109


Ashraf Idkaidek and Iwona Jasiuk: "Cortical Bone Fracture Analysis Using XFEM - Case Study", International Journal for Numerical Methods in Biomedical Engineering, Wiley-Blackwell, Vol 33, Num 4, pp e2809, 2016, doi:10.1002/cnm.2809


Scott Lathrop: "A Call to Action to Prepare the High-Performance Computing Workforce", Computing in Science & Engineering, Institute of Electrical and Electronics Engineers, Vol 18, Num 6, pp 80-83, 2016, doi:10.1109/mcse.2016.101


Arif Masud: "Patient-Specifie HPC Models and Simulation-Based Imaging for Cardiovascular Surgical Planning", 2017 Blue Waters Annual Report, pp 224-225, 2016


Matthieu Dorier, Gabriel Antoniu, Franck Cappello, Marc Snir, Robert Sisneros, Orcun Yildiz, Shadi Ibrahim, Tom Peterka, and Leigh Orf: "Damaris: Addressing Performance Variability in Data Management for Post-Petascale Simulations", ACM Transactions on Parallel Computing, Association for Computing Machinery, Vol 3, Num 3, pp 15:1-15:43, 2016, doi:10.1145/2987371


Matthieu Dorier, Robert Sisneros, Leonardo Bautista Gomez, Tom Peterka, Leigh Orf, Lokman Rahmani, Gabriel Antoniu, and Luc Bouge: "Adaptive Performance-Constrained in Situ Visualization of Atmospheric Simulations", Institute of Electrical & Electronics Engineers, 2016 IEEE International Conference on Cluster Computing (CLUSTER), pp 269-278, Taipei, Taiwan, 2016, doi:10.1109/cluster.2016.25


Julio T. Bacmeister, Kevin A. Reed, Cecile Hannay, Peter Lawrence, Susan Bates, John E. Truesdale, Nan Rosenbloom, and Michael Levy: "Projected Changes in Tropical Cyclone Activity Under Future Warming Scenarios Using a High-Resolution Climate Model", Climatic Change, Springer Nature, Vol 146, Num 3-4, pp 547–560, 2016, doi:10.1007/s10584-016-1750-x


Nancy Makri: "Blip-Summed Quantum-Classical Path Integral with Cumulative Quantum Memory", Faraday Discussions, Royal Society of Chemistry, Vol 195, pp 81-92, 2016, doi:10.1039/c6fd00142d


Michael Nute and Tandy Warnow: "Scaling Statistical Multiple Sequence Alignment to Large Datasets", BMC Genomics, Springer Nature, Vol 17, Num S10, pp 764, 2016, doi:10.1186/s12864-016-3101-8


John D. Lueck, Adam L. Mackey, Daniel T. Infield, Jason D. Galpin, Jing Li, Benoît Roux, and Christopher A. Ahern: "Atomic Mutagenesis in Ion Channels with Engineered Stoichiometry", eLife, eLife Sciences Organisation, Ltd., Vol 5, 2016, doi:10.7554/elife.18976


Sarma Rani: "DNS and Stochastic Study of The Relative Motion of High Inertia Particles in Isotropic Turbulence", 2016 Blue Waters Annual Report, pp 131-133, 2016


Seong Mook Cho, Brian G. Thomas, Hyoung Jun Lee, and Seon Hyo Kim: "Effect of nozzle port angle on mold surface flow in steel slab casting", Association for Iron and Steel Technology, Proceedings of the Iron and Steel Technology Conference (AISTech 2016), Vol 3, pp 2651-2662, Pittsburgh, Pennsylvania, U.S.A., 2016


João V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C. Phillips, Peter L. Freddolino and Klaus Schulten: "QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts", Scientific Reports, Springer Nature, Vol 6, Num 1, pp 26536, 2016, doi:10.1038/srep26536


Robert Sisneros, Mohammad Raji, Mark W. Van Moer, and David Bock: "Chasing Rainbows: A Color-Theoretic Framework for Improving and Preserving Bad Colormaps", Springer International Publishing, Advances in Visual Computing (International Symposium on Visual Computing 2016), pp 391-402, Las Vegas Nevada, U.S.A., 2016, doi:10.1007/978-3-319-50835-1_36


Ashok Srinivasan, C. D. Sudheer, and Sirish Namilae: "Optimizing Massively Parallel Simulations of Infection Spread Through Air-Travel for Policy Analysis", Institute of Electrical & Electronics Engineers, 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), pp 136-145, Cartagena, Colombia, 2016, doi:10.1109/ccgrid.2016.23


Rafael O. Tinoco and Giovanni Coco: "A Laboratory Study on Sediment Resuspension Within Arrays of Rigid Cylinders", Advances in Water Resources, Elsevier BV, Vol 92, pp 1-9, 2016, doi:10.1016/j.advwatres.2016.04.003


R. Sisneros: "A Classification of Parallel I/O Toward Demystifying HPC I/O Best Practices", presented at CUG 2016, London, England, U.K., 2016


C. Xu, S. Byna, V. Venkatesan, R. Sisneros, O. Kulkarni, M. Chaarawi, K. Chadalavada: "LIOProf: Exposing Lustre File System Behavior for I/O Middleware", presented at CUG 2016, London, England, U.K., 2016


Nawrin Sultana, Alexander Calvert, Jeffrey L. Overbey, and Galen Arnold: "From OpenACC to OpenMP 4: Toward Automatic Translation", ACM Press, XSEDE '16: Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, pp 44:1-44:8, Miami, Florida, U.S.A., 2016, doi:10.1145/2949550.2949654


P. Forai, G. Peretti-Pezzi, B. Bode, K. Hoste: "Making Scientific Software Installation Reproducible on Cray Systems Using EasyBuild", presented at CUG 2016, London, England, U.K., 2016


Patricia M. Gregg and J. Cory Pettijohn: "A Multi-Data Stream Assimilation Framework for the Assessment of Volcanic Unrest", Journal of Volcanology and Geothermal Research, Elsevier BV, Vol 309, pp 63-77, 2016, doi:10.1016/j.jvolgeores.2015.11.008


David Ackerman: "Confinement and Orientation Effects in Semi-flexible Polymer Structures", 2016 Blue Waters Annual Report, pp 140-141, 2016


Huilan Zhang, Guangjin Hou, Manman Lu, Jinwoo Ahn, In-Ja L. Byeon, Christopher J. Langmead, Juan R. Perilla, Ivan Hung, Peter L. Gor'kov, Zhehong Gan, William W. Brey, David A. Case, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova: "HIV-1 Capsid Function Is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD", Journal of the American Chemical Society, American Chemical Society, Vol 138, Num 42, pp 14066-14075, 2016, doi:10.1021/jacs.6b08744


Thieker, David F. and Hadden, Jodi A. and Schulten, Klaus and Woods, Robert J.: "3D implementation of the symbol nomenclature for graphical representation of glycans", Glycobiology, Oxford University Press, Vol 26, Num 8, pp 786-787, 2016, doi:10.1093/glycob/cww076


Gustavo Caetano-Anolles: "Evolutionary dynamics of the protein structure-function relation and the origin of the genetic code", 2016 Blue Waters Annual Report, pp 196-198, 2016


Stephen W. Bruenn, Eric J. Lentz, W. Raphael Hix, Anthony Mezzacappa, J. Austin Harris, O. E. Bronson Messer, Eirik Endeve, John M. Blondin, Merek Austin Chertkow, Eric J. Lingerfelt, Pedro Marronetti, and Konstantin N. Yakunin: "The Development of Explosions in Axisymmetric Ab Initio Core-collapse Supernova Simulations of 12-25 M-circle dot Stars", Astrophysical Journal, The American Astronomical Society, Vol 818, Num 2, pp 123, 2016, doi:10.3847/0004-637X/818/2/123


Maureen Brooks: "Modeling nonlinear physical-biological interactions: Sargassum in the North Atlantic", 2016 Blue Waters Annual Report, pp 260-261, 2016


Minseung Kim, Navneet Rai, Violeta Zorraquino, and Ilias Tagkopoulos: "Multi-Omics Integration Accurately Predicts Cellular State in Unexplored Conditions for Escherichia Coli", Nature Communications, Springer Nature, Vol 7, pp 13090, 2016, doi:10.1038/ncomms13090


Yanbin Wu, Lucas K. Wagner, and Narayana R. Aluru: "Hexagonal Boron Nitride and Water Interaction Parameters", Journal of Chemical Physics, AIP Publishing, Vol 144, Num 16, pp 164118, 2016, doi:10.1063/1.4947094


Aleksei Aksimentiev: "Molecular Dynamics of Self-Assembled DNA Systems", 2016 Blue Waters Annual Report, pp 187-189, 2016


Hesameddin Ilatikhameneh, Tarek A. Ameen, Gerhard Klimeck, and Rajib Rahman: "Universal Behavior of Atomistic Strain in Self-Assembled Quantum Dots", IEEE Journal of Quantum Electronics, Institute of Electrical and Electronics Engineers, Vol 52, Num 7, pp 1-8, 2016, doi:10.1109/jqe.2016.2573959


Jon Calhoun: "Improving Checkpoint Restart with Lossy Compression", 2016 Blue Waters Annual Report, pp 264-265, 2016


Dylan Hatch: "Networking Architecture for the Distributed Simulation of Manned and Autonomous Vehicles", University of Wisconsin-Madison, Simulation-Based Engineering Lab (SBEL) Technical Reports, Num TR-2016-06, 2016


Jean Paul Allain: "Harnessing petascale computing to elucidate fundamental mechanisms driving nanopatterning of multicomponent surfaces by directed irradiation synthesis", 2016 Blue Waters Annual Report, pp 96-98, 2016


Thomas Cheatham: "Understanding Biomolecular Structure and Dynamics by Overcoming Barriers to Conformational Sampling", 2016 Blue Waters Annual Report, pp 203-205, 2016


Harshil M. Kamdar, Matthew J. Turk, and Robert J. Brunner: "Machine learning and cosmological simulations – II. Hydrodynamical simulations", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 457, Num 2, pp 1162-1179, 2016, doi:10.1093/mnras/stv2981


Harshil M. Kamdar, Matthew J. Turk, and Robert J. Brunner: "Machine learning and cosmological simulations – I. Semi-analytical models", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 455, Num 1, pp 642-658, 2016, doi:10.1093/mnras/stv2310


David Ceperley: "The Liquid-Liquid Transition in Dense Hydrogen", 2016 Blue Waters Annual Report, pp 104-105, 2016


Don Armstrong: "Making ancestral trees using Bayesian inference to identify disease-causing genetic variants", 2016 Blue Waters Annual Report, pp 194-195, 2016


Huck Beng Chew: "Nanoscale Mechanics of Deformation in High-Capacity Lithium-Ion Batteries", 2016 Blue Waters Annual Report, pp 115-117, 2016


Narayana Aluru: "Large-Scale Simulations of DNA Nanostructures for Drug Delivery and Applications of Novel Synthetic Membranes for Proteins/DNA Integration", 2016 Blue Waters Annual Report, pp 182-183, 2016


Isaac Cann: "Cellusome Structure Determination Employing Atomistic Simulations Combined to Experimental Assays", 2016 Blue Waters Annual Report, pp 200-202, 2016


Daniel Bodony: "Reducing jet aircraft noise by harnessing the hetergeneous XK nodes", 2016 Blue Waters Annual Report, pp 106-107, 2016


Thomas Allen: "Rigorous Quantum-Classical Simulation of Electron Transfer in A Bacterial Photosynthetic Reaction Center", 2016 Blue Waters Annual Report, pp 280-281, 2016


Rommie Amaro: "Virtual Flu, A Different Kind of Computer Virus", 2016 Blue Waters Annual Report, pp 184-186, 2016


David Toth and Ruth Catlett: "Revising and Expanding a Blue Waters Curriculum Module as a Parallel Computing Learning Experience", Journal of Computational Science Education, Shodor Education Foundation Inc., Vol 7, Num 1, pp 31-39, 2016, doi:10.22369/issn.2153-4136/7/1/4


Matthew LePain and Maxim Durach: "Abatement of Computational Issues Associated with Dark Modes in Optical Metamaterials", Journal of Computational Science Education, Shodor Education Foundation Inc., Vol 7, Num 1, pp 39-45, 2016, doi:10.22369/issn.2153-4136/7/1/5


Jiandong Feng, Michael Graf, Ke Liu, Dmitry Ovchinnikov, Dumitru Dumcenco, Mohammad Heiranian, Vishal Nandigana, Narayana R. Aluru, Andras Kis, and Aleksandra Radenovic: "Single-Layer MoS2 Nanopores as Nanopower Generators", Nature, Springer Nature, Vol 536, Num 7615, pp 197--200, 2016, doi:10.1038/nature18593


Wendy Cho: "A Computational Model for Causal Inference via Subset Selection", 2016 Blue Waters Annual Report, pp 254-255, 2016


Bryan Clark: "Simulating Strongly Correlated Systems: From Frustrated Magnets to Many-Body Localization", 2016 Blue Waters Annual Report, pp 98-100, 2016


Christopher Chipot: "Improving The Accuracy of Drug-Permeability Calculations", 2016 Blue Waters Annual Report, pp 198-199, 2016


B. P. Abbott et al. (LIGO Scientific Collaboration and Virgo Collaboration): "Properties of the Binary Black Hole Merger GW150914", Physical Review Letters, American Physical Society, Vol 116, Num 24, pp 241102, 2016, doi:10.1103/PhysRevLett.116.241102


Aleksei Aksimentiev: "Molecular Mechanism of Sequence Dependent DNA Looping", 2016 Blue Waters Annual Report, pp 190-192, 2016


Donna Cox: "Visualization for Public Outreach", 2016 Blue Waters Annual Report, pp 20-21, 2016


Davide Curreli: "Towards Large-Scale Kinetic Simulations of The Plasma-Material Interface", 2016 Blue Waters Annual Report, pp 108-109, 2016


Jia Deng: "Large-Scale Learning for Video Understanding", 2016 Blue Waters Annual Report, pp 161-162, 2016


Ken Dill: "Predicting protein structures with physical molecular simulations", 2016 Blue Waters Annual Report, pp 206-207, 2016


Tiziana Di Matteo: "The Most Massive Galaxies and Black Holes at The Cosmic Dawn of The Universe", 2016 Blue Waters Annual Report, pp 47-50, 2016


Said Elghobashi: "Direct Numerical Simulation of Fully Resolved Droplets in A Turbulent Flow", 2016 Blue Waters Annual Report, pp 152-153, 2016


Jerry Draayer: "Collaborative Research: Innovative ab initio symmetry-adapted no-core shell model for advancing fundamental physics and astrophysics", 2016 Blue Waters Annual Report, pp 112-115, 2016


Justin Drake: "Solvation Thermodynamics of The Protein Backbone: Implications for Collapse and Aggregation", 2016 Blue Waters Annual Report, pp 266-267, 2016


Elif Ertekin: "QMCDB: A Living Database to Accelerate Worldwide Development & Usage of Quantum Monte Carlo Methods", 2016 Blue Waters Annual Report, pp 110-112, 2016


Charles Gammie: "High-Resolution Simulations of Magnetohydrodynamic Turbulence in Accretion Disks", 2016 Blue Waters Annual Report, pp 22-23, 2016


Peter Freddolino: "Comprehensive In Silico Mapping of DNA-Binding Protein Affinity Landscapes", 2016 Blue Waters Annual Report, pp 208-209, 2016


Marcelo Garcia: "Large Eddy Simulation of Sediment Transport and Hydrodynamics at River Bifurcations", 2016 Blue Waters Annual Report, pp 84-86, 2016


John Gerlt: "Sequence Similarity Networks for the Protein "Universe"", 2016 Blue Waters Annual Report, pp 193-194, 2016


Sharon Glotzer: "Large-scale, long-time molecular dynamics simulation of crystal growth", 2016 Blue Waters Annual Report, pp 120-121, 2016


Patricia Gregg: "Building a data assimilation framework for forecasting volcanic activity during periods of unrest", 2016 Blue Waters Annual Report, pp 78-79, 2016


Claudio Grosman: "Elucidating the molecular details underlying charge-selectivity in pentameric Ligand-Gated Ion Channels", 2016 Blue Waters Annual Report, pp 210-211, 2016


Sharon Hammes-Schiffer: "Non-Born-Oppenheimer Effects between Electrons and Protons", 2016 Blue Waters Annual Report, pp 212-213, 2016


Kaiyu Guan: "Forecasting global crop productivity using novel satellite data and process-based models", 2016 Blue Waters Annual Report, pp 92-93, 2016


Levent Gurel: "Parallelization of the Multilevel Fast Multipole Algorithm (MLFMA) on Heterogeneous CPU-GPU Architectures", 2017 Blue Waters Annual Report, pp 174-175, 2016


Ravishankar Iyer: "Efficient, Scalable, and Fault Tolerant Genomics Pipeline", 2016 Blue Waters Annual Report, pp 158-160, 2016


Alexandra Jones: "High Accuracy Radiative Transfer in Cloudy Atmospheres", 2016 Blue Waters Annual Report, pp 278-279, 2016


Thomas Jordan: "Physics-Based Strong Ground Motion Simulations", 2016 Blue Waters Annual Report, pp 70-73, 2016


Sara Kokkila Schumacher: "Reducing The Computational Cost of Coupled Clustery Theory", 2016 Blue Waters Annual Report, pp 274-275, 2016


Michael Klein: "Unveiling allosteric pathways in ion channels", 2016 Blue Waters Annual Report, pp 219-220, 2016


Sonia Lasher-Trapp: "High-Resolution Simulations of Cumulus Entrainment", 2016 Blue Waters Annual Report, pp 91-93, 2016


Praveen Kumar: "Extreme-scale modeling - Understanding ecohydrologic dynamics under climate change", 2016 Blue Waters Annual Report, pp 64-65, 2016


Eric Lentz: "Core-Collapse Supernovae Through Cosmic Time", 2016 Blue Waters Annual Report, pp 80-81, 2016


Deborah Levin: "Kinetic Modeling and Simulation of Hypersonic, Shock-Boundary Layer Interactions using Petascale Computing", 2016 Blue Waters Annual Report, pp 150-151, 2016


David Luitz: "Numerical study of the many body localization transition", 2016 Blue Waters Annual Report, pp 129-131, 2016


Liudmila Mainzer: "Instrumenting Human Variant Calling Workflow at Scale", 2016 Blue Waters Annual Report, pp 225-227, 2016


Liudmila Mainzer: "Custom Genotyping Chip for African Populations", 2016 Blue Waters Annual Report, pp 224-225, 2016


Zaida Luthey-Schulten: "Ribosome Biogenesis in Replicating Cells", 2016 Blue Waters Annual Report, pp 221-223, 2016


Nancy Makri: "Quantum-Classical Path Integral Simulation of Charge Transfer Reactions", 2016 Blue Waters Annual Report, pp 228-229, 2016


Kiritkumar Makwana: "Simulating Plasma Turbulence from Driving Scales to Dissipative Scales", 2016 Blue Waters Annual Report, pp 52-53, 2016


Arif Masud: "Variational Multiscale Method for Blood-Flow Simulation in Patient-Specific Arterial Geometries", 2016 Blue Waters Annual Report, pp 234-237, 2016


Paul Morin: "Enhanced Digital Elevation Model for The Arctic", 2016 Blue Waters Annual Report, pp 66-67, 2016


Joshua Mendez: "The Triboelectric Charging of Volcanic Materials", 2016 Blue Waters Annual Report, pp 268-269, 2016


Warren Mori: "Transformative Petascale Particle-in-Cell Simulations of High Energy Density Plasmas", 2016 Blue Waters Annual Report, Num 145-147, 2016


Ariana Minot: "Distributed Algorithms for Power System Monitoring and Control", 2016 Blue Waters Annual Report, pp 270-271, 2016


Luke Olson: "The Next Generation of Large-Scale Sparse-Matrix Computations", 2016 Blue Waters Annual Report, pp 166-168, 2016


Rakesh Nagi: "Parallel Algorithms for Solving Large Assignment Problems", 2016 Blue Waters Annual Report, pp 164-166, 2016


Scott Noble: "Predicting The Transient Signals from Galactic Centers", 2016 Blue Waters Annual Report, pp 28-29, 2016


Brian O'Shea: "Connecting Galaxies in The Early Universe to The Milky Way", 2016 Blue Waters Annual Report, pp 30-31, 2016


Michael Norman: "Realistic Simulations of the Intergalactic Medium: The Search for Missing Physics", 2016 Blue Waters Annual Report, pp 26-27, 2016


Christian Ott: "Magnetars, Black-Hole Collisions for LIGO, and A Next-Generation Numerical Relativity Code", 2016 Blue Waters Annual Report, pp 32-35, 2016


Vijay Pande: "Allosteric Selectivity and Drug Binding Pathway of µ-Opioid Receptors", 2016 Blue Waters Annual Report, pp 230-231, 2016


Donald Petravick: "Deployment of The Dark Energy Survey Workflows", 2016 Blue Waters Annual Report, pp 39-41, 2016


Thomas Quinn: "Evolution of the Small Galaxy Population From High Redshift to the Present", 2016 Blue Waters Annual Report, pp 43-44, 2016


Robert Rauber: "High-Resolution Earth-System Modeling for International Climate Assessement", 2016 Blue Waters Annual Report, pp 87-89, 2016


Larissa Reames: "Sensitivity of Simulated Urban-Atmosphere Interactions in Oklahoma City to Urban Parameterization", 2016 Blue Waters Annual Report, pp 284-285, 2016


William Sanders: "Evaluating Data-Driven Detectors of Electricity Theft in Smart Grids", 2016 Blue Waters Annual Report, pp 168-169, 2016


Andre Schleife: "Lattice Screening and Optical Properties of Novel Perovskite Photovoltaic Materials", 2016 Blue Waters Annual Report, pp 136-138, 2016


Jose Schutt-Aine: "High-Speed Link Simulation Using X Parameters, Volterra Series and the Latency Insertion Method (LIM)", 2016 Blue Waters Annual Report, pp 176-178, 2016


André Schleife: "Non-Adiabatic Ultrafast Electron-Ion Dynamics Near Aluminum Surfaces", 2016 Blue Waters Annual Report, pp 148-149, 2016


Klaus Schulten: "The Recycling Machinery of The Cell", 2016 Blue Waters Annual Report, pp 249-251, 2016


Stuart Shapiro: "Binary Neutron Stars Mergers: A Jet Engine for Short Gamma-Ray Bursts", 2016 Blue Waters Annual Report, pp 45-47, 2016


Diwakar Shukla: "Computational investigation of drought-resistance in plants", 2016 Blue Waters Annual Report, pp 232-233, 2016


George Slota: "Processing Trillion Edge Graphs in Distributed Memory", 2016 Blue Waters Annual Report, pp 282-283, 2016


Jamesina Simpson: "Location-Specific Space-Weather Hazards to Electric-Power Grids Calculated on A Global Scale", 2016 Blue Waters Annual Report, pp 68-70, 2016


Robert Sisneros: "Impact Driven Research: Evaluating and Improving The De Facto Standard for Parallel Advection", 2016 Blue Waters Annual Report, pp 170-171, 2016


Shankar Subramaniam: "Particle-Resolved Direct Numerical Simulations of Fluid-Solid Heat Transfer", 2016 Blue Waters Annual Report, pp 138-140, 2016


Ryan Sriver: "Analyzing Tropical Cyclone-Climate Interactions Using The Community Earth-System Model (CESM)", 2016 Blue Waters Annual Report, pp 74-75, 2016


Robert F. Stein: "Ab Initio Models of Solar Activity", 2016 Blue Waters Annual Report, pp 41-42, 2016


Brad Sutton: "Improving the resolution of brain blood flow imaging with advanced MRI acquisitions and computation", 2016 Blue Waters Annual Report, pp 237-239, 2016


Robert Sugar: "Lattice QCD on Blue Waters", 2016 Blue Waters Annual Report, pp 117-119, 2016


Ahmed Taha: "Software Extreme Benchmarking", 2016 Blue Waters Annual Report, pp 172-173, 2016


Ilias Tagkopoulos: "Big Data on Small Organisms: Genome-Scale Modeling and Phenotypic Prediction of Escherichia Coli", 2016 Blue Waters Annual Report, pp 244-245, 2016


Brian Thomas: "Transient Two-Phase Flow and Electromagnetic Field Effect in Steel Continuous Casting", 2016 Blue Waters Annual Report, pp 101-103, 2016


Samuel Totorica: "Particle Acceleration in Laser-Driven Magnetic Reconection", 2016 Blue Waters Annual Report, pp 272-273, 2016


Robert Trapp: "Petascale modeling of convective storms under climate change and variability", 2016 Blue Waters Annual Report, pp 62-63, 2016


Junshik Um: "Dependence of The Directional Intensity and Polarization of Light Scattered by Small Ice Crystals on Their Shape and Size: Applications for Airborne Cloud Probes", 2016 Blue Waters Annual Report, pp 76-78, 2016


Gregory Voth: "Ultra-Coarse-Grained (UCG) Simulations of Viral Phenomena", 2016 Blue Waters Annual Report, pp 240-241, 2016


Tandy Warnow: "Advancing genome-scale phylogenomic analysis", 2016 Blue Waters Annual Report, pp 242-243, 2016


Robert Wilhelmson: "Simulating The Most Violent Thunderstorms", 2016 Blue Waters Annual Report, pp 80-81, 2016


Matthew West: "3D particle-resolved aerosol model to quantify and reduce uncertainties in aerosol-atmosphere interactions", 2016 Blue Waters Annual Report, pp 82-83, 2016


Varvara Zemskova: "Energetic Dynamics of A Rotating Horizontal Convection Model of The Southern Ocean with Surface Buoyancy and Wind Forcing", 2016 Blue Waters Annual Report, pp 276-277, 2016


Tao Xie: "Hardware Acceleration of Deep Learning", 2016 Blue Waters Annual Report, pp 178-179, 2016


Hao Xu, Kyungjin Ahn, Michael L. Norman, John H. Wise, and Brian W. O’Shea: "X-Ray Background at High Redshifts from Pop III Remnants: Results from Pop III Star Formation Rates in the Renaissance Simulations", Astrophysical Journal Letters, The American Astronomical Society, Vol 832, Num 1, pp L5, 2016, doi:10.3847/2041-8205/832/1/L5


Thana Sutthibutpong, Agnes Noy, and Sarah Harris: "Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis", Springer New York, Methods in Molecular Biology, Vol 1431, pp 195-219, 2016, doi:10.1007/978-1-4939-3631-1_15


Xi Luo, Marius S. Potgieter, Ming Zhang, Nikolai V. Pogorelov, Xueshang Feng, and R. du Toit Strauss: "A Numerical Simulation of Cosmic Ray Modulation Near the Heliopause. II. Some Physical Insights", Astrophysical Journal, The American Astronomical Society, Vol 826, Num 2, pp 182, 2016, doi:10.3847/0004-637X/826/2/182


Ming Zhang and Nikolai Pogorelov: "The Heliosphere as Seen in TeV Cosmic Rays", IOP Publishing Ltd, Journal of Physics: Conference Series (15th Annual International Astrophysics Conference: "The Science of Ed Stone: Celebrating his 80th Birthday"), Vol 767, Num 1, pp 012027, Cape Coral, Florida, U.S.A., 2016, doi:10.1088/1742-6596/767/1/012027


Claudia L. Ramírez, Ariel Petruk, Mauro Bringas, Dario A. Estrin, Adrian E. Roitberg, Marcelo A. Marti, and Luciana Capece: "Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions", Journal of Chemical Theory and Computation, American Chemical Society, Vol 12, Num 7, pp 3390-3397, 2016, doi:10.1021/acs.jctc.6b00278


Raúl Esteban Ithuralde, Adrián Enrique Roitberg, and Adrián Gustavo Turjanski: "Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations", Journal of the American Chemical Society, American Chemical Society, Vol 138, Num 28, pp 8742-8751, 2016, doi:10.1021/jacs.6b02016


Zahra Heidari, Daniel R. Roe, Rodrigo Galindo-Murillo, Jahan B. Ghasemi, and Thomas E. Cheatham: "Using Wavelet Analysis to Assist in Identification of Significant Events in Molecular Dynamics Simulations", Journal of Chemical Information and Modeling, American Chemical Society, Vol 56, Num 7, pp 1282-1291, 2016, doi:10.1021/acs.jcim.5b00727


Jinho Kim, Dinshaw S. Balsara, Maxim Lyutikov, and Serguei S. Komissarov: "On the linear stability of sheared and magnetized jets without current sheets - non-relativistic case", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 461, Num 1, pp 728-741, 2016, doi:10.1093/mnras/stw1051


Ali Ashraf, Yanbin Wu, Michael Cai Wang, Keong Yong, Tao Sun, Yuhang Jing, Richard T. Haasch, Narayana R. Aluru, and SungWoo Nam: "Doping-Induced Tunable Wettability and Adhesion of Graphene", Nano Letters, American Chemical Society, Vol 16, Num 7, pp 4708-4712, 2016, doi:10.1021/acs.nanolett.6b02228


Amir Barati Farimani, Mohammad Heiranian, and Narayana R. Aluru: "Nano-Electro-Mechanical Pump: Giant Pumping of Water in Carbon Nanotubes", Scientific Reports, Springer Nature, Vol 6, Num 1, 2016, doi:10.1038/srep26211


Amir Barati Farimani and Narayana R. Aluru: "Existence of Multiple Phases of Water at Nanotube Interfaces", Journal of Physical Chemistry C, American Chemical Society, Vol 120, Num 41, pp 23763-23771, 2016, doi:10.1021/acs.jpcc.6b06156


B. P. Abbott et al. (LIGO Scientific Collaboration and Virgo Collaboration): "Directly Comparing GW150914 with Numerical Solutions of Einstein's Equations for Binary Black Hole Coalescence", Physical Review D, American Physical Society, Vol 94, Num 6, pp 064035, 2016, doi:10.1103/physrevd.94.064035


Gregory M. Laskowski: "Compressible Large Eddy Simulation of a Film Cooled Stage One Nozzle at Different Freestream Turbulence Levels", 2016 Blue Waters Annual Report, pp 127-129, 2016


Paul R. Woodward: "3-D Simulations of i-Process Nucleosynthesis in the Early Universe", 2016 Blue Waters Annual Report, pp 54-57, 2016


Mariano Vázquez, Guillaume Houzeaux, Seid Koric, Antoni Artigues, Jazmin Aguado-Sierra, Ruth Arís, Daniel Mira, Hadrien Calmet, Fernando Cucchietti, Herbert Owen, Ahmed Taha, Evan Dering Burness, José María Cela, and Mateo Valero: "Alya: Multiphysics Engineering Simulation Toward Exascale", Journal of Computational Science, Elsevier BV, Vol 14, pp 15-27, 2016, doi:10.1016/j.jocs.2015.12.007


Markus Holzmann, Raymond C. Clay, Miguel A. Morales, Norm M. Tubman, David M. Ceperley, and Carlo Pierleoni: "Theory of Finite Size Effects for Electronic Quantum Monte Carlo Calculations of Liquids and Solids", Physical Review B, American Physical Society, Vol 94, Num 3, pp 035126, 2016, doi:10.1103/physrevb.94.035126


Mao Sheng Liu, Tiziana Di Matteo, and Yu Feng: "The effects of AGN feedback and SPH formulation on black hole growth in galaxies", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 458, Num 2, pp 1402-1416, 2016, doi:10.1093/mnras/stw342


Hauser, Kevin and Essuman, Bernard and He, Yiqing and Coutsias, Evangelos and Garcia-Diaz, Miguel, and Simmerling, Carlos: "A human transcription factor in search mode", Nucleic Acids Research, Oxford University Press, Vol 44, Num 1, pp 63-74, 2016, doi:10.1093/nar/gkv1091


Geoffrey Lovelace, Carlos O. Lousto, James Healy, Mark A. Scheel, Alyssa Garcia, Richard O’Shaughnessy, Michael Boyle, Manuela Campanelli, Daniel A. Hemberger, Lawrence E. Kidder, Harald P. Pfeiffer, Béla Szilágyi, Saul A. Teukolsky, and Yosef Zlochower: "Modeling the source of GW150914 with targeted numerical-relativity simulations", Classical and Quantum Gravity, IOP Publishing Ltd, Vol 33, Num 24, pp 244002, 2016, doi:10.1088/0264-9381/33/24/244002


Daniel Langr, Pavel Tvrdik, and Ivan Simecek: "AQsort: Scalable Multi-Array In-Place Sorting with OpenMP", Scalable Computing: Practice and Experience (Special Issue on New Approaches for Infrastructure Services), West University of Timisoara, Romania, Vol 17, Num 4, pp 369-391, 2016, doi:10.12694/scpe.v17i4.1207


Yin Wang, Feng Pan, Kristina D. Launey, Yan-An Luo, and J. P. Draayer: "Angular Momentum Projection for a Nilsson Mean-Field Plus Pairing Model", Nuclear Physics A, Elsevier BV, Vol 950, pp 1-28, 2016, doi:10.1016/j.nuclphysa.2016.03.012


Feng Pan, Shuli Yuan, Kristina D. Launey, and Jerry P. Draayer: "A new procedure for constructing basis vectors of SU(3) superset of SO(3)", Nuclear Physics A, Elsevier BV, Vol 952, pp 70-99, 2016, doi:10.1016/j.nuclphysa.2016.04.024


John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten: "Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms", Springer International Publishing, Lecture Notes in Computer Science: International Conference on High Performance Computing (ISC High Performance 2016), pp 188-206, Frankfurt, Germany, 2016, doi:10.1007/978-3-319-46079-6_14


Katrina J. Heyrana, Boon Chong Goh, Juan R. Perilla, Tam-Linh N. Nguyen, Matthew R. England, Maria C. Bewley, Klaus Schulten, and Rebecca C. Craven: "Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly", Journal of Virology, American Society for Microbiology, Vol 90, Num 12, pp 5700-5714, 2016, doi:10.1128/jvi.00378-16


Juan R. Perilla, Jodi A. Hadden, Boon Chong Goh, Christopher G. Mayne, and Klaus Schulten: "All-Atom Molecular Dynamics of Virus Capsids as Drug Targets", Journal of Physical Chemistry Letters, American Chemical Society, Vol 7, Num 10, pp 1836-1844, 2016, doi:10.1021/acs.jpclett.6b00517


J. Deeng, K.Y. Chan, E.O. van der Sluis, O. Berninghausen, W. Han, J. Gumbart, K. Schulten, B. Beatrix, and R. Beckmann: "Dynamic Behavior of Trigger Factor on the Ribosome", Journal of Molecular Biology, Elsevier BV, Vol 428, Num 18, pp 3588-3602, 2016, doi:10.1016/j.jmb.2016.06.007


G. S. Stinson, A. A. Dutton, L. Wang, A. V. Macciò, J. Herpich, J. D. Bradford, T. R. Quinn, J. Wadsley, and B. Keller: "NIHAO III: the constant disc gas mass conspiracy", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 454, Num 1, pp 1105-1116, 2016, doi:10.1093/mnras/stv1985


Erik W. Lentz, Thomas R. Quinn, and Leslie J. Rosenberg: "The Effects of Angular Momentum on Halo Profiles", Astrophysical Journal, The American Astronomical Society, Vol 822, Num 2, pp 89, 2016, doi:10.3847/0004-637X/822/2/89


Charlotte R. Christensen, Romeel Davé, Fabio Governato, Andrew Pontzen, Alyson Brooks, Ferah Munshi, Thomas Quinn, and James Wadsley: "In-N-Out: The Gas Cycle from Dwarfs to Spiral Galaxies", Astrophysical Journal, The American Astronomical Society, Vol 824, Num 1, pp 57, 2016, doi:10.3847/0004-637X/824/1/57


Jared M. Gabor, Pedro R. Capelo, Marta Volonteri, Frédéric Bournaud, Jillian Bellovary, Fabio Governato, and Thomas Quinn: "Comparison of black hole growth in galaxy mergers with gasoline and ramses", Astronomy & Astrophysics, EDP Sciences, Vol 592, Num A62, 2016, doi:10.1051/0004-6361/201527143


D. Buaria, P. K. Yeung, and B. L. Sawford: "A Lagrangian Study of Turbulent Mixing: Forward and Backward Dispersion of Molecular Trajectories in Isotropic Turbulence", Journal of Fluid Mechanics, Cambridge University Press, Vol 799, pp 352-382, 2016, doi:10.1017/jfm.2016.359


Rui Dong, V. Ranjan, Marco Buongiorno Nardelli, and J. Bernholc: "First-Principles Simulations of PVDF Copolymers with High Dielectric Energy Density: PVDF-HFP and PVDF-BTFE", Physical Review B, American Physical Society, Vol 94, Num 1, pp 014210, 2016, doi:10.1103/physrevb.94.014210


Yan Li, Miroslav Hodak, Wenchang Lu, and J. Bernholc: "Mechanisms of NH3 and NO2 Detection in Carbon-Nanotube-Based Sensors: An Ab Initio Investigation", Carbon, Elsevier BV, Vol 101, pp 177-183, 2016, doi:10.1016/j.carbon.2016.01.092


Pengyu Long, Evan Wilson, Jun Z. Huang, Gerhard Klimeck, Mark J. W. Rodwell, and Michael Povolotskyi: "Design and Simulation of GaSb/InAs 2D Transmission-Enhanced Tunneling FETs", IEEE Electron Device Letters, Institute of Electrical and Electronics Engineers, Vol 37, Num 1, pp 107-110, 2016, doi:10.1109/led.2015.2497666


Yu He, Yaohua Tan, Zhengping Jiang, Michael Povolotskyi, Gerhard Klimeck, and Tillmann Kubis: "Surface Passivation in Empirical Tight Binding", IEEE Transactions on Electron Devices, Institute of Electrical and Electronics Engineers, Vol 63, Num 3, pp 954-958, 2016, doi:10.1109/ted.2016.2519042


K. Miao, S. Sadasivam, J. Charles, G. Klimeck, T. S. Fisher, and T. Kubis: "Büttiker Probes for Dissipative Phonon Quantum Transport in Semiconductor Nanostructures", Applied Physics Letters, AIP Publishing, Vol 108, Num 11, pp 113107, 2016, doi:10.1063/1.4944329


Tillmann Kubis, Yu He, Robert Andrawis, and Gerhard Klimeck: "General Retarded Contact Self-energies in and beyond the Non-equilibrium Green's Functions Method", IOP Publishing Ltd, Journal of Physics: Conference Series (Progress in Non-equilibrium Green's Functions, PNGF VI), Vol 696, Num 1, pp 012019, Lund, Sweden, 2016, doi:10.1088/1742-6596/696/1/012019


Pengyu Long, Jun Z. Huang, Michael Povolotskyi, Gerhard Klimeck, and Mark J. W. Rodwell: "High-Current Tunneling FETs With (1(1)over-bar0) Orientation and a Channel Heterojunction", IEEE Electron Device Letters, Institute of Electrical and Electronics Engineers, Vol 37, Num 3, pp 345-348, 2016, doi:10.1109/led.2016.2523269


Yaohua Tan, Michael Povolotskyi, Tillmann Kubis, Timothy B. Boykin, and Gerhard Klimeck: "Transferable Tight-Binding Model for Strained Group IV and III-v Materials and Heterostructures", Physical Review B, American Physical Society, Vol 94, Num 4, pp 045311, 2016, doi:10.1103/physrevb.94.045311


Curtis L. Johnson, Hillary Schwarb, Matthew D.J. McGarry, Aaron T. Anderson, Graham R. Huesmann, Bradley P. Sutton, and Neal J. Cohen: "Viscoelasticity of Subcortical Gray Matter Structures", Human Brain Mapping, Wiley, Vol 37, Num 12, pp 4221-4233, 2016, doi:10.1002/hbm.23314


Catello Di Martino, Zbigniew Kalbarczyk, and Ravishankar Iyer: "Measuring the Resiliency of Extreme-Scale Computing Environments", Springer International Publishing, Springer Series in Reliability Engineering, pp 609-655, 2016, doi:10.1007/978-3-319-30599-8_24


Shiyu Chang, Guo-Jun Qi, Yingzhen Yang, Charu C. Aggarwal, Jiayu Zhou, Meng Wang, and Thomas S. Huang: "Large-scale supervised similarity learning in networks", Knowledge and Information Systems, Springer Nature Switzerland AG, Vol 48, Num 3, pp 707-740, 2016, doi:10.1007/s10115-015-0894-8


Yingzhen Yang, Jiashi Feng, Nebojsa Jojic, Jianchao Yang, and Thomas S. Huang: "l(0)-Sparse Subspace Clustering", Springer Nature Switzerland AG, Lecture Notes in Computer Science: Computer Vision - European Conference on Computer Vision (ECCV) 2016, pp 731-747, Amsterdam, The Netherlands, 2016, doi:10.1007/978-3-319-46475-6_45


B. P. Abbott et al. (LIGO Scientific Collaboration and Virgo Collaboration): "GW151226: Observation of Gravitational Waves from a 22-Solar-Mass Binary Black Hole Coalescence", Physical Review Letters, American Physical Society, Vol 116, Num 24, pp 241103, 2016, doi:10.1103/PhysRevLett.116.241103


Sunhwan Jo, Donghyuk Suh, Ziwei He, Christophe Chipot, and Benoît Roux: "Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations", Journal of Physical Chemistry B, American Chemical Society, Vol 120, Num 33, pp 8733-8742, 2016, doi:10.1021/acs.jpcb.6b05125


Kenza Sigrid Arraki: "Evolution of dwarf galaxy properties in local group environments", Department of Energy, Office of Scientific and Technical Information, Vol Thesis/Dissertation, 2016, doi:10.2172/1491856


Sara I. L. Kokkila Schumacher: "Graphics processing unit accelerated tensor hypercontraction for high performance computing [electronic resource] : a reduction in computational cost of Ab initio methods", Stanford University Libraries, SearchWorks, Vol Doctoral dissertation, 2016


Thomas Carlton Allen: "Atomistic quantum dynamics: implementation and applications of the quantum-classical path integral method", University of Illinois at Urbana-Champaign, Illinois Digital Environment for Access to Learning and Scholarship, Vol Doctoral dissertation, 2016


Justin A. Drake, Robert C. Harris, and B. Montgomery Pettitt: "Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility", Biophysical Journal, Elsevier, Vol 111, Num 4, pp 756-767, 2016, doi:10.1016/j.bpj.2016.07.013


George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri: "A Case Study of Complex Graph Analysis in Distributed Memory: Implementation and Optimization", Institute of Electrical & Electronics Engineers, 2016 IEEE International Parallel and Distributed Processing Symposium (IPDPS), pp 293-302, Chicago, Illinois, U.S.A., 2016, doi:10.1109/IPDPS.2016.93


George M. Slota, Kamesh Madduri, and Sivasankaran Rajamanickam: "Complex Network Partitioning Using Label Propagation", SIAM Journal on Scientific Computing, Society for Industrial & Applied Mathematics, Vol 38, Num 5, pp S620-S645, 2016, doi:10.1137/15M1026183


Hillary Schwarb, Curtis L. Johnson, Matthew D. J. McGarry, and Neal J. Cohen: "Medial temporal lobe viscoelasticity and relational memory performance", NeuroImage, Elsevier Inc., Vol 132, pp 534-541, 2016, doi:10.1016/j.neuroimage.2016.02.059


M. Wan, W. H. Matthaeus, V. Roytershteyn, T. N. Parashar, P. Wu, and H. Karimabadi: "Intermittency, coherent structures and dissipation in plasma turbulence", Physics of Plasmas, AIP Publishing LLC., Vol 23, Num 4, pp 042307, 2016, doi:10.1063/1.4945631


Nathaniel W. Chaney, Eric F. Wood, Alexander B. McBratney, Jonathan W. Hempel, Travis W. Nauman, Colby W. Brungard, and Nathan P. Odgers: "POLARIS: A 30-meter probabilistic soil series map of the contiguous United States", Geoderma, Elsevier B.V., Vol 274, pp 54-67, 2016, doi:10.1016/j.geoderma.2016.03.025


Nathaniel W. Chaney, Peter Metcalfe, and Eric F. Wood: "HydroBlocks: a field-scale resolving land surface model for application over continental extents", Hydrological Processes, Vol 30, Num 20, pp 3543-3559, 2016, doi:10.1002/hyp.10891


E. Janssen, R. L. Sriver, D. J. Wuebbles, and K. E. Kunkel: "Seasonal and regional variations in extreme precipitation event frequency using CMIP5", Geophysical Research Letters, American Geophysical Union, Vol 43, Num 10, pp 5385-5393, 2016, doi:10.1002/2016GL069151


James Wilson, Leila Sloman, Zhiren He, and Aleksei Aksimentiev: "Graphene Nanopores for Protein Sequencing", Advanced Functional Materials, John Wiley & Sons, Inc., Vol 26, Num 27, pp 4830-4838, 2016, doi:10.1002/adfm.201601272


Jejoong Yoo and Aleksei Aksimentiev: "Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations", Journal of Physical Chemistry Letters, American Chemical Society, Vol 7, Num 19, pp 3812-3818, 2016, doi:10.1021/acs.jpclett.6b01747


Sung Jun Lim, Liang Ma, André Schleife, and Andrew M. Smith: "Quantum dot surface engineering: Toward inert fluorophores with compact size and bright, stable emission", Coordination Chemistry Reviews, Elsevier B.V., Vol 320-321, pp 216-237, 2016, doi:10.1016/j.ccr.2016.03.012


Christophe Chipot and Jeffrey Comer: "Subdiffusion in Membrane Permeation of Small Molecules", Scientific Reports, Springer Nature Limited, Vol 6, Num 1, pp 35913, 2016, doi:10.1038/srep35913


Doriam Restrepo, Jacobo Bielak, Ricardo Serrano, Juan Gómez, and Juan Jaramillo: "Effects of realistic topography on the ground motion of the Colombian Andes - A case study at the Aburra Valley, Antioquia", Geophysical Journal International, The Royal Astronomical Society, Vol 204, Num 3, pp 1801-1816, 2016, doi:10.1093/gji/ggv556


2015

Catello Di Martino, Saurabh Jha, William Kramer, Zbigniew Kalbarczyk, and Ravishankar K. Iyer: "LogDiver: A Tool for Measuring Resilience of Extreme-Scale Systems and Applications", Association for Computing Machinery, Proceedings of the 5th Workshop on Fault Tolerance for HPC at eXtreme Scale (FTXS '15), pp 11-18, Portland, Oregon, U.S.A., 2015, doi:10.1145/2751504.2751511


Peter L. Walters and Nancy Makri: "Quantum-Classical Path Integral Simulation of Ferrocene-Ferrocenium Charge Transfer in Liquid Hexane", Journal of Physical Chemistry Letters, American Chemical Society, Vol 6, Num 24, pp 4959-4965, 2015, doi:10.1021/acs.jpclett.5b02265


B. B. Pollock, F. S. Tsung, F. Albert, J. L. Shaw, C. E. Clayton, A. Davidson, N. Lemos, K. A. Marsh, A. Pak, J. E. Ralph, W. B. Mori, and C. Joshi: "Formation of Ultrarelativistic Electron Rings from a Laser-Wakefield Accelerator", Physical Review Letters, American Physical Society, Vol 115, Num 5, pp 055004, 2015, doi:10.1103/physrevlett.115.055004


S. Corde, E. Adli, J. M. Allen, W. An, C. I. Clarke, C. E. Clayton, J. P. Delahaye, J. Frederico, S. Gessner, S. Z. Green, M. J. Hogan, C. Joshi, N. Lipkowitz, M. Litos, W. Lu, K. A. Marsh, W. B. Mori, M. Schmeltz, N. Vafaei-Najafabadi, D. Walz, V. Yakime: "Multi-Gigaelectronvolt Acceleration of Positrons in a Self-Loaded Plasma Wakefield", Nature, Nature Publishing Group, Vol 524, Num 7566, pp 442-445, 2015, doi:10.1038/nature14890


Xu, X. L. and Hua, J. F. and Wu, Y. P. and Zhang, C. J. and Li, F. and Wan, Y. and Pai, C.-H. and Lu, W. and An, W. and Yu, P. and Hogan, M. J. and Joshi, C. and Mori, W. B.: "Physics of Phase Space Matching for Staging Plasma and Traditional Accelerator Components Using Longitudinally Tailored Plasma Profiles", Physical Review Letters, American Physical Society, Vol 116, Num 12, pp 124801, Richmond, VA, 2015, doi:10.1103/PhysRevLett.116.124801


Joshua A. Schiller, Lucas K. Wagner, and Elif Ertekin: "Phase Stability and Properties of Manganese Oxide Polymorphs: Assessment and Insights from Diffusion Monte Carlo", Physical Review B, American Physical Society, Vol 92, Num 23, pp 235209, 2015, doi:10.1103/physrevb.92.235209


Rodrigo Galindo-Murillo, Daniel R. Roe, and Thomas E. Cheatham: "Convergence and Reproducibility in Molecular Dynamics Simulations of the DNA Duplex d(GCACGAACGAACGAACGC)", Biochimica et Biophysica Acta (BBA) - General Subjects, Elsevier BV, Vol 1850, Num 5, pp 1041-1058, 2015, doi:10.1016/j.bbagen.2014.09.007


Lijun Liu: "The Ups and Downs of North America: Evaluating the Role of Mantle Dynamic Topography Since the Mesozoic", Reviews of Geophysics, Wiley-Blackwell, Vol 53, Num 3, pp 1022-1049, 2015, doi:10.1002/2015rg000489


Lijun Liu and Quan Zhou: "Deep Recycling of Oceanic Asthenosphere Material During Subduction", Geophysical Research Letters, Wiley-Blackwell, Vol 42, Num 7, pp 2204-2211, 2015, doi:10.1002/2015gl063633


Ted Wetherbee, Elizabeth Jones, Michael Knox, Stou Sandalski, and Paul Woodward: "In-Core Volume Rendering for Cartesian Grid Fluid Dynamics Simulations", Association for Computing Machinery, XSEDE '15: Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure, Num 35, pp 35:1-35:8, St. Louis, Missouri, U.S.A., 2015, doi:10.1145/2792745.2792780


Ena Choi, Jeremiah P. Ostriker, Thorsten Naab, Ludwig Oser, and Benjamin P. Moster: "The Impact of Mechanical AGN Feedback on the Formation of Massive Early-Type Galaxies", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 449, Num 4, pp 4105-4116, 2015, doi:10.1093/mnras/stv575


Robert Thompson, Romeel Davé, and Kentaro Nagamine: "The rise and fall of a challenger: the Bullet Cluster in Lambda cold dark matter simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 452, Num 3, pp 3030-3037, 2015, doi:10.1093/mnras/stv1433


Kartik P. Iyer, Katepalli R. Sreenivasan, and P. K. Yeung: "Refined Similarity Hypothesis Using Three-Dimensional Local Averages", Physical Review E, American Physical Society, Vol 92, Num 6, pp 063024, 2015, doi:10.1103/physreve.92.063024


Pui-kuen Yeung: "Complexities of High Reynolds-Number Turbulence", 2015 Blue Waters Annual Report, pp 110-111, 2015


P. K. Yeung, X. M. Zhai, and Katepalli R. Sreenivasan: "Extreme Events in Computational Turbulence", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 112, Num 41, pp 12633--12638, 2015, doi:10.1073/pnas.1517368112


Huihuo Zheng and Lucas K. Wagner: "Computation of the Correlated Metal-Insulator Transition in Vanadium Dioxide from First Principles", Physical Review Letters, American Physical Society, Vol 114, Num 17, 2015, doi:10.1103/physrevlett.114.176401


Yigit Isbiliroglu, Ricardo Taborda, and Jacobo Bielak: "Coupled Soil-Structure Interaction Effects of Building Clusters During Earthquakes", Earthquake Spectra, Earthquake Engineering Research Institute, Vol 31, Num 1, pp 463-500, 2015, doi:10.1193/102412eqs315m


Erik Schnetter, Marek Blazewicz, Steven R. Brandt, David M. Koppelman, and Frank Löffler: "Chemora: A PDE-Solving Framework for Modern High-Performance Computing Architectures", Computing in Science & Engineering, Institute of Electrical and Electronics Engineers, Vol 17, Num 2, pp 53-64, 2015, doi:10.1109/mcse.2015.2


Ernazar Abdikamalov, Christian D. Ott, David Radice, Luke F. Roberts, Roland Haas, Christian Reisswig, Philipp Mösta, Hannah Klion, and Erik Schnetter: "Neutrino-Driven Turbulent Convection and Standing Accretion Shock Instability in Three-Dimensional Core-Collapse Supernovae", Astrophysical Journal, The American Astronomical Society, Vol 808, Num 1, pp 70, 2015, doi:10.1088/0004-637x/808/1/70


Hotaka Shiokawa, Julian H. Krolik, Roseanne M. Cheng, Tsvi Piran, and Scott C. Noble: "General Relativistic Hydrodynamic Simulation of Accretion Flow from a Stellar Tidal Disruption", Astrophysical Journal, The American Astronomical Society, Vol 804, Num 2, pp 85, 2015, doi:10.1088/0004-637x/804/2/85


Chad W. Hopkins, Scott Le Grand, Ross C. Walker, and Adrian E. Roitberg: "Long-Time-Step Molecular Dynamics Through Hydrogen Mass Repartitioning", Journal of Chemical Theory and Computation, American Chemical Society, Vol 11, Num 4, pp 1864-1874, 2015, doi:10.1021/ct5010406


Cheng-Tsung Lai, Huei-Jiun Li, Weixuan Yu, Sonam Shah, Gopal R. Bommineni, Victoria Perrone, Miguel Garcia-Diaz, Peter J. Tonge, and Carlos Simmerling: "Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium Tuberculosis InhA", Biochemistry, American Chemical Society, Vol 54, Num 30, pp 4683-4691, 2015, doi:10.1021/acs.biochem.5b00284


Christina Bergonzo, and Thomas E. Cheatham: "Improved Force Field Parameters Lead to a Better Description of RNA Structure", Journal of Chemical Theory and Computation, American Chemical Society, Vol 11, Num 9, pp 3969-3972, 2015, doi:10.1021/acs.jctc.5b00444


Christina Bergonzo, Kathleen B. Hall, and Thomas E. Cheatham: "Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg 2+ Bound Structure in the Presence of Monovalent Ions", Journal of Physical Chemistry B, American Chemical Society, Vol 119, Num 38, pp 12355-12364, 2015, doi:10.1021/acs.jpcb.5b05190


Christina Bergonzo, Niel M. Henriksen, Daniel R. Roe, and Thomas E. Cheatham: "Highly Sampled Tetranucleotide and Tetraloop Motifs Enable Evaluation of Common RNA Force Fields", RNA, Cold Spring Harbor Laboratory Press, Vol 21, Num 9, pp 1578-1590, 2015, doi:10.126/rna.051102.115


George M. Giambaşu, Darrin M. York, and David A. Case: "Structural Fidelity and NMR Relaxation Analysis in a Prototype RNA Hairpin", RNA, Cold Spring Harbor Laboratory Press, Vol 21, Num 5, pp 963-974, 2015, doi:10.1261/rna.047357.114


Hai Nguyen, Alberto Pérez, Sherry Bermeo, and Carlos Simmerling: "Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins", Journal of Chemical Theory and Computation, American Chemical Society, Vol 11, Num 8, pp 3714-3728, 2015, doi:10.1021/acs.jctc.5b00271


James A. Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E. Hauser, and Carlos Simmerling: "ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB", Journal of Chemical Theory and Computation, American Chemical Society, Vol 11, Num 8, pp 3696-3713, 2015, doi:10.1021/acs.jctc.5b00255


James C. Robertson, and Thomas E Cheatham: "DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations", Journal of Physical Chemistry B, American Chemical Society, Vol 119, Num 44, pp 14111-14119, 2015, doi:10.1021/acs.jpcb.5b08486


R. Galindo-Murillo, J. C. Garcia-Ramos, L. Ruiz-Azuara, T. E. Cheatham, and F. Cortes-Guzman: "Intercalation Processes of Copper Complexes in DNA", Nucleic Acids Research, Oxford University Press, Vol 43, Num 11, pp 5364-5376, 2015, doi:10.1093/nar/gkv467


Thakshila Dissanayake, Jason M. Swails, Michael E. Harris, Adrian E. Roitberg, and Darrin M. York: "Interpretation of pH-Activity Profiles for Acid-Base Catalysis from Molecular Simulations", Biochemistry, American Chemical Society, Vol 54, Num 6, pp 1307-1313, 2015, doi:10.1021/bi5012833


Thomas E. Cheatham and Daniel R. Roe: "The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis", Computing in Science & Engineering, Institute of Electrical & Electronics Engineers, Vol 17, Num 2, pp 30-39, 2015, doi:10.1109/mcse.2015.7


Gerhard Klimeck: "Leading Future Electronics into The Nano Regime Using Quantum Atomistic Simulations in NEMO5", 2017 Blue Waters Annual Report, pp 144-145, 2015


Gerhard Klimeck: "Nanoscale Electronic Devices with NEMO5", 2016 Blue Waters Annual Report, pp 124-126, 2015


Bozidar Novakovic and Gerhard Klimeck: "Atomistic Quantum Transport Approach to Time-Resolved Device Simulations", Institute of Electrical & Electronics Engineers, 2015 International Conference on Simulation of Semiconductor Processes and Devices (SISPAD), pp 8-11, Washington, D.C., U.S.A., 2015, doi:10.1109/sispad.2015.7292245


Fan W. Chen, Luis A. Jauregui, Yaohua Tan, Michael Manfra, Gerhard Klimeck, Yong P. Chen, and Tillmann Kubis: "In-Surface Confinement of Topological Insulator Nanowire Surface States", Applied Physics Letters, AIP Publishing, Vol 107, Num 12, pp 121605, 2015, doi:10.1063/1.4931975


Gerhard Klimeck: "Atomistic Modeling of Future Nanoscale Electronic Devices with NEMO5", 2015 Blue Waters Annual Report, pp 92-93, 2015


Mehdi Salmani-Jelodar, Saumitra R. Mehrotra, Hesameddin Ilatikhameneh, and Gerhard Klimeck: "Design Guidelines for Sub-12 Nm Nanowire MOSFETs", IEEE Transactions on Nanotechnology, Institute of Electrical & Electronics Engineers, Vol 14, Num 2, pp 210-213, 2015, doi:10.1109/tnano.2015.2395441


Parijat Sengupta, Tillmann Kubis, Yaohua Tan, and Gerhard Klimeck: "Proximity Induced Ferromagnetism, Superconductivity, and Finite-Size Effects on the Surface States of Topological Insulator Nanostructures", Journal of Applied Physics, AIP Publishing, Vol 117, Num 4, pp 044304, 2015, doi:10.1063/1.4906842


Ravi Pramod Vedula, Saumitra Mehrotra, Tillmann Kubis, Michael Povolotskyi, Gerhard Klimeck, and Alejandro Strachan: "Optimal Ge/SiGe Nanofin Geometries for Hole Mobility Enhancement: Technology Limit from Atomic Simulations", Journal of Applied Physics, AIP Publishing, Vol 117, Num 17, pp 174312, 2015, doi:10.1063/1.4919091


Yaohua P. Tan, Michael Povolotskyi, Tillmann Kubis, Timothy B. Boykin, and Gerhard Klimeck: "Tight-Binding Analysis of Si and GaAs Ultrathin Bodies with Subatomic Wave-Function Resolution", Physical Review B, American Physical Society, Vol 92, Num 8, pp 085301, 2015, doi:10.1103/physrevb.92.085301


A. Bazavov, C. Bernard, C. Bouchard, N. Brown, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, E. Gámiz, Steven Gottlieb, U.M. Heller, J. Komijani, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, C. Monahan, T. Primer, Heechang Na, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint, R.S. Van de Water, and R. Zhou: "Decay Constants fB and fBs from HISQ Simulations", Proceedings of Science, Proceedings, 33rd International Symposium on Lattice Field Theory (Lattice 2015), Vol 251, pp 331, Kobe, Japan, 2015, doi:10.22323/1.251.0331


David J. Wilson, Jozef J. Dudek, Robert G. Edwards, and Christopher E. Thomas: "Resonances in coupled pi K,eta K scattering from lattice QCD", Physical Review D, American Physical Society, Vol 91, Num 5, pp 054008, 2015, doi:10.1103/physrevd.91.054008


David J. Wilson, Raúl A. Briceño, Jozef J. Dudek, Robert G. Edwards, and Christopher E. Thomas: "Coupled pi pi, K(K)over-bar scattering in P-wave and the rho resonance from lattice QCD", Physical Review D, American Physical Society, Vol 92, Num 9, pp 094502, 2015, doi:10.1103/physrevd.92.094502


Raúl A. Briceño, Jozef J. Dudek, Robert G. Edwards, Christian J. Shultz, Christopher E. Thomas, and David J. Wilson: "The resonant π+γ → π+π⁰ amplitude from Quantum Chromodynamics", Physical Review Letters, American Physical Society, Vol 115, Num 24, pp 242001, 2015, doi:10.1103/physrevlett.115.242001


Thomas Primer, Claude Bernard, Carleton DeTar, Aida El-Khadra, Elvira Gamiz, Javad Komijani, Andreas Kronfeld, James Simone, Doug Toussaint, and Ruth S. Van de Water (Fermilab Lattice and MILC Collaborations): "D-meson Semileptonic Form Factors at Zero Momentum Transfer in (2+1+1)-Flavor Lattice QCD", Proceedings of Science, Proceedings, 33rd International Symposium on Lattice Field Theory (Lattice 2015), Vol 251, pp 338, Kobe, Japan, 2015, doi:10.22323/1.251.0338


Donald J. Wuebbles: "Using Petascale Computing Capabilities to Address Climate Change Uncertainties", 2015 Blue Waters Annual Report, pp 61-63, 2015


K. A. Reed, J. T. Bacmeister, N. A. Rosenbloom, M. F. Wehner, S. C. Bates, P. H. Lauritzen, J. E. Truesdale, and C. Hannay: "Impact of the Dynamical Core on the Direct Simulation of Tropical Cyclones in a High-Resolution Global Model", Geophysical Research Letters, Wiley-Blackwell, Vol 42, Num 9, pp 3603-3608, 2015, doi:10.1002/2015gl063974


Fan Guo, Yi-Hsin Liu, William Daughton, and Hui Li: "Particle Acceleration and Plasma Dynamics During Magnetic Reconnection in the Magnetically-Dominated Regime", Astrophysical Journal, The American Astronomical Society, Vol 806, Num 2, pp 167, 2015, doi:10.1088/0004-637x/806/2/167


K. D. Makwana, V. Zhdankin, H. Li, W. Daughton, and F. Cattaneo: "Energy Dynamics and Current Sheet Structure in Fluid and Kinetic Simulations of Decaying Magnetohydrodynamic Turbulence", Physics of Plasmas, AIP Publishing, Vol 22, Num 4, pp 042902, 2015, doi:10.1063/1.4916492


M. Wan, W. H. Matthaeus, V. Roytershteyn, H. Karimabadi, T. Parashar, P. Wu, and M. Shay: "Intermittent Dissipation and Heating in 3D Kinetic Plasma Turbulence", Physical Review Letters, American Physical Society, Vol 114, Num 17, pp 175002, 2015, doi:10.1103/physrevlett.114.175002


V. Roytershteyn, H. Karimabadi, and A. Roberts: "Generation of Magnetic Holes in Fully Kinetic Simulations of Collisionless Turbulence", Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, The Royal Society, Vol 373, Num 2041, pp 20140151-20140151, 2015, doi:10.1098/rsta.2014.0151


M. Zingale, C. M. Malone, A. Nonaka, A. S. Almgren, and J. B. Bell: "Comparisons of Two- and Three-Dimensional Convection in Type I X-Ray Bursts", Astrophysical Journal, The American Astronomical Society, Vol 807, Num 1, pp 60, 2015, doi:10.1088/0004-637x/807/1/60


Brian W. O'Shea, John H. Wise, Hao Xu, and Michael L. Norman: "Probing the Ultraviolet Luminosity Function of the Earliest Galaxies with the Renaissance Simulations", Astrophysical Journal Letters, The American Astronomical Society, Vol 807, Num 1, pp L12, 2015, doi:10.1088/2041-8205/807/1/l12


Britton D. Smith, John H. Wise, Brian W. O'Shea, Michael L. Norman, and Sadegh Khochfar: "The First Population II Stars Formed in Externally Enriched Mini-Haloes", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 452, Num 3, pp 2822-2836, 2015, doi:10.1093/mnras/stv1509


Kyungjin Ahn, Hao Xu, Michael L. Norman, Marcelo A. Alvarez, and John H. Wise: "Spatially Extended 21 Cm Signal from Strongly Clustered UV and X-Ray Sources in the Early Universe", Astrophysical Journal, The American Astronomical Society, Vol 802, Num 1, pp 8, 2015, doi:10.1088/0004-637x/802/1/8


Michael L. Norman, Daniel R. Reynolds, Geoffrey C. So, Robert P. Harkness, and John H. Wise: "Fully Coupled Simulation of Cosmic Reionization. I. Numerical Methods and Tests", Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 216, Num 1, pp 16, 2015, doi:10.1088/0067-0049/216/1/16


Boon Chong Goh, Juan R. Perilla, Matthew R. England, Katrina J. Heyrana, Rebecca C. Craven, and Klaus Schulten: "Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis", Structure, Elsevier BV, Vol 23, Num 8, pp 1414-1425, 2015, doi:10.1016/j.str.2015.05.017


C. Keith Cassidy, Benjamin A. Himes, Frances J. Alvarez, Jun Ma, Gongpu Zhao, Juan R. Perilla, Klaus Schulten, and Peijun Zhang: "CryoEM and Computer Simulations Reveal a Novel Kinase Conformational Switch in Bacterial Chemotaxis Signaling", eLife, eLife Sciences Organisation, Ltd., Vol 4, 2015, doi:10.7554/elife.08419


David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten: "Multilevel Summation Method for Electrostatic Force Evaluation", Journal of Chemical Theory and Computation, American Chemical Society, Vol 11, Num 2, pp 766-779, 2015, doi:10.1021/ct5009075


Juan R. Perilla, Boon Chong Goh, C. Keith Cassidy, Bo Liu, Rafael C. Bernardi, Till Rudack, Hang Yu, Zhe Wu, and Klaus Schulten: "Molecular Dynamics Simulations of Large Macromolecular Complexes", Current Opinion in Structural Biology, Elsevier BV, Vol 31, pp 64-74, 2015, doi:10.1016/j.sbi.2015.03.007


Klaus Schulten: "The Computational Microscope", 2016 Blue Waters Annual Report, pp 246-248, 2015


Rafael C. Bernardi, Marcelo C.R. Melo, and Klaus Schulten: "Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems", Biochimica et Biophysica Acta (BBA) - General Subjects, Elsevier BV, Vol 1850, Num 5, pp 872-877, 2015, doi:10.1016/j.bbagen.2014.10.019


Wen Ma and Klaus Schulten: "Mechanism of Substrate Translocation by a Ring-Shaped ATPase Motor at Millisecond Resolution", Journal of the American Chemical Society, American Chemical Society, Vol 137, Num 8, pp 3031-3040, 2015, doi:10.1021/ja512605w


F. Governato, D. Weisz, A. Pontzen, S. Loebman, D. Reed, A. M. Brooks, P. Behroozi, C. Christensen, P. Madau, L. Mayer, S. Shen, M. Walker, T. Quinn, B. W. Keller, and J. Wadsley: "Faint Dwarfs as a Test of DM Models: WDM Versus CDM", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 448, Num 1, pp 792-803, 2015, doi:10.1093/mnras/stu2720


Harshitha Menon, Lukasz Wesolowski, Gengbin Zheng, Pritish Jetley, Laxmikant Kale, Thomas Quinn, and Fabio Governato: "Adaptive Techniques for Clustered N-Body Cosmological Simulations", Computational Astrophysics and Cosmology, Springer Science + Business Media, Vol 2, Num 1, 2015, doi:10.1186/s40668-015-0007-9


M. Tremmel, F. Governato, M. Volonteri, and T. R. Quinn: "Off the Beaten Path: A New Approach to Realistically Model the Orbital Decay of Supermassive Black Holes in Galaxy Formation Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 451, Num 2, pp 1868-1874, 2015, doi:10.1093/mnras/stv1060


J. Heerikhuisen, Eric Zirnstein, and Nikolai Pogorelov: "kappa-distributed protons in the solar wind and their charge-exchange coupling to energetic hydrogen", Journal of Geophysical Research: Space Physics, Wiley-Blackwell, Vol 120, Num 3, pp 1516-1525, 2015, doi:10.1002/2014ja020636


Ming Zhang, Xi Luo, and Nikolai Pogorelov: "Where Is the Cosmic-Ray Modulation Boundary of the Heliosphere?", Physics of Plasmas, AIP Publishing, Vol 22, Num 9, pp 091501, 2015, doi:10.1063/1.4928945


N. V. Pogorelov, and S. N. Borovikov: "Mixing of the Interstellar and Solar Plasmas at the Heliospheric Interface", Astronomical Society of the Pacific, ASP Conference Series: 9th Annual International Conference on Numerical Modeling of Space Plasma Flows (ASTRONUM 2014), Vol 498, pp 160, Long Beach, California, U.S.A., 2015


N. V. Pogorelov, S. N. Borovikov, J. Heerikhuisen, and M. Zhang: "The Heliotail", Astrophysical Journal Letters, The American Astronomical Society, Vol 812, Num 1, pp L6, 2015, doi:10.1088/2041-8205/812/1/l6


P. Manoharan, T. Kim, N. V, Pogorelov, C. N. Arge, and P. K. Manoharan: "Modeling Solar Wind with Boundary Conditions from Interplanetary Scintillations", IOP Publishing, Journal of Physics: Conference Series (14th Annual International Astrophysics Conference 2015: Linear and Nonlinear Particle Energization throughout the Heliosphere and Beyond), Vol 642, pp 012016, Tampa, Florida, U.S.A., 2015, doi:10.1088/1742-6596/642/1/012016


R. L. Fermo, N. V. Pogorelov, and L. F. Burlaga: "Transient Shocks Beyond the Heliopause", IOP Publishing, Journal of Physics: Conference Series (14th Annual International Astrophysics Conference 2015: Linear and Nonlinear Particle Energization throughout the Heliosphere and Beyond), Vol 642, pp 012008, Tampa, Florida, U.S.A., 2015, doi:10.1088/1742-6596/642/1/012008


Xi Luo, Ming Zhang, Marius Potgieter, Xueshang Feng, and N. V. Pogorelov: "A Numerical Simulation of Cosmic-Ray Modulation Near the Heliopause", Astrophysical Journal, The American Astronomical Society, Vol 808, Num 1, pp 82, 2015, doi:10.1088/0004-637x/808/1/82


Rui Dong, V. Ranjan, Marco Buongiorno Nardelli, and J. Bernholc: "Atomistic Simulations of Aromatic Polyurea and Polyamide for Capacitive Energy Storage", Physical Review B, American Physical Society, Vol 92, Num 2, pp 024203, 2015, doi:10.1103/physrevb.92.024203


Yan Li, Miroslav Hodak, and J. Bernholc: "Enzymatic Mechanism of Copper-Containing Nitrite Reductase", Biochemistry, American Chemical Society, Vol 54, Num 5, pp 1233-1242, 2015, doi:10.1021/bi5007767


Yash Thakur, Rui Dong, Minren Lin, Shan Wu, Zhaoxi Cheng, Ying Hou, J. Bernholc, and Q.M. Zhang: "Optimizing Nanostructure to Achieve High Dielectric Response with Low Loss in Strongly Dipolar Polymers", Nano Energy, Elsevier BV, Vol 16, pp 227-234, 2015, doi:10.1016/j.nanoen.2015.06.021


N. W. Chaney, J. D. Herman, P. M. Reed, and E. F. Wood: "Flood and Drought Hydrologic Monitoring: The Role of Model Parameter Uncertainty", Hydrology and Earth System Sciences, Copernicus GmbH, Vol 19, Num 7, pp 3239-3251, 2015, doi:10.5194/hess-19-3239-2015


Nathaniel W. Chaney, Joshua K. Roundy, Julio E. Herrera-Estrada, and Eric F. Wood: "High-Resolution Modeling of the Spatial Heterogeneity of Soil Moisture: Applications in Network Design", Water Resources Research, Wiley-Blackwell, Vol 51, Num 1, pp 619-638, 2015, doi:10.1002/2013wr014964


Patrick M. Reed, Nathaniel W. Chaney, Jonathan D. Herman, Matthew P. Ferringer, and Eric F. Wood: "Internationally Coordinated Multi-Mission Planning Is Now Critical to Sustain the Space-Based Rainfall Observations Needed for Managing Floods Globally", Environmental Research Letters, IOP Publishing, Vol 10, Num 2, pp 024010, 2015, doi:10.1088/1748-9326/10/2/024010


Jerry Draayer: "Next-Generation Ab Initio Symmetry-Adapted No-Core Shell Model and Its Impact on Nucleosynthesis", 2015 Blue Waters Annual Report, pp 80-82, 2015


J. P. Draayer, T. Dytrych, K. D. Launey, A. C. Dreyfuss, and D. Langr: "Dominant Modes in Light Nuclei - Ab Initio View of Emergent Symmetries", IOP Publishing, Journal of Physics: Conference Series (XXXVII Symposium on Nuclear Physics, 2014), Vol 578, pp 012010, Cocoyoc, Mexico, 2015, doi:10.1088/1742-6596/578/1/012010


J. P. Draayer, T. Dytrych, K. D. Launey, A. C. Dreyfuss, and D. Langr: "HPC-Enabled Nuclear Structure Studies - Description and Applications of the Symmetry-Adapted No-Core Shell Model", IOP Publishing, Journal of Physics: Conference Series (11th International Spring Seminar on Nuclear Physics 2014: Shell Model and Nuclear Structure, achievements of the past two decades), Vol 580, pp 012044, Ischia, Italy, 2015, doi:10.1088/1742-6596/580/1/012044


K. D. Launey, A. C. Dreyfuss, R. B. Baker, J. P. Draayer, and T. Dytrych: "Emergent Symmetries in Atomic Nuclei from First Principles", IOP Publishing, Journal of Physics: Conference Series (XXXth International Colloquium on Group Theoretical Methods in Physics, Group30), Vol 597, pp 012054, Ghent, Belgium, 2015, doi:10.1088/1742-6596/597/1/012054


K. D. Launey, J. P. Draayer, T. Dytrych, G.-H. Sun, and S.-H. Dong: "Approximate Symmetries in Atomic Nuclei from a Large-Scale Shell-Model Perspective", International Journal of Modern Physics E, World Scientific Pub Co Pte Lt, Vol 24, Num 05, pp 1530005, 2015, doi:10.1142/s0218301315300052


T. Dytrych, K. D. Launey, J. P. Draayer, P. Maris, J. P. Vary, D. Langr, and T. Oberhuber: "Emergence of Simple Patterns in Complex Atomic Nuclei from First Principles", IOP Publishing, Journal of Physics: Conference Series (XXXVIII Symposium on Nuclear Physics, Cocoyoc 2015), Vol 639, pp 012008, Cocoyoc, Mexico, 2015, doi:10.1088/1742-6596/639/1/012008


T. Dytrych, A. C. Hayes, K. D. Launey, J. P. Draayer, P. Maris, J. P. Vary, D. Langr, and T. Oberhuber: "Electron-Scattering Form Factors for Li-6 in the Ab Initio Symmetry-Guided Framework", Physical Review C, American Physical Society, Vol 91, Num 2, pp 024326, 2015, doi:10.1103/physrevc.91.024326


Thomas S. Lontzek, Yongyang Cai, Kenneth L. Judd, and Timothy M. Lenton: "Stochastic Integrated Assessment of Climate Tipping Points Indicates the Need for Strict Climate Policy", Nature Climate Change, Nature Publishing Group, Vol 5, Num 5, pp 441-444, 2015, doi:10.1038/nclimate2570


Lars Hansen: "Policy Responses to Climate Change in a Dynamic Stochastic Economy", 2016 Blue Waters Annual Report, pp 256-257, 2015


Yongyang Cai, Kenneth L. Judd, Timothy M. Lenton, Thomas S. Lontzek, and Daiju Narita: "Environmental Tipping Points Significantly Affect the Cost-Benefit Assessment of Climate Policies", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 112, Num 15, pp 4606-4611, 2015, doi:10.1073/pnas.1503890112


Merle Giles, Seid Koric, and Evan Burness: "U. S. Industrial Supercomputing at NCSA", Chapman and Hall/CRC Press, Industrial Applications of High-Performance Computing, pp 179-194, 2015


Sohan Kale, Ankit Saharan, Seid Koric, and Martin Ostoja-Starzewski: "Scaling and Bounds in Thermal Conductivity of Planar Gaussian Correlated Microstructures", Journal of Applied Physics, AIP Publishing, Vol 117, Num 10, pp 104301, 2015, doi:10.1063/1.4914128


Sohan Kale, Seid Koric, and Martin Ostoja-Starzewski: "Stochastic Continuum Damage Mechanics Using Spring Lattice Models", Applied Mechanics and Materials, Trans Tech Publications, Vol 784, pp 350-357, 2015, doi:10.4028/www.scientific.net/amm.784.350


Vladimir Puzyrev and Seid Koric: "3D Multi-Source CSEM Simulations: Feasibility and Comparison of Parallel Direct Solvers", Society of Exploration Geophysicists, SEG Technical Program Expanded Abstracts 2015 (2015 SEG International Exposition and 85th Annual Meeting), pp 833-838, New Orleans, Louisiana, U.S.A., 2015, doi:10.1190/segam2015-5864005.1


Vasileios Paschalidis, Milton Ruiz, and Stuart L. Shapiro: "Relativistic Simulations of Black Hole-Neutron Star Coalescence: The Jet Emerges", Astrophysical Journal Letters, The American Astronomical Society, Vol 806, Num 1, pp L14, 2015, doi:10.1088/2041-8205/806/1/l14


Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev: "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field", ACS Nano, American Chemical Society, Vol 9, Num 2, pp 1420-1433, 2015, doi:10.1021/nn505825z


Jejoong Yoo and Aleksei Aksimentiev: "Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating", Journal of Physical Chemistry Letters, American Chemical Society, Vol 6, Num 23, pp 4680-4687, 2015, doi:10.1021/acs.jpclett.5b01964


Maxim Belkin, Shu-Han Chao, Magnus P. Jonsson, Cees Dekker, and Aleksei Aksimentiev: "Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA", ACS Nano, American Chemical Society, Vol 9, Num 11, pp 10598-10611, 2015, doi:10.1021/acsnano.5b04173


Yue-xiao Shen, Wen Si, Mustafa Erbakan, Karl Decker, Rita De Zorzi, Patrick O. Saboe, You Jung Kang, Sheereen Majd, Peter J. Butler, Thomas Walz, Aleksei Aksimentiev, Jun-li Hou, and Manish Kumar: "Highly Permeable Artificial Water Channels That Can Self-Assemble Into Two-Dimensional Arrays", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 112, Num 32, pp 9810--9815, 2015, doi:10.1073/pnas.1508575112


Lusheng Liang, Larry Di Girolamo, and Wenbo Sun: "Bias in MODIS Cloud Drop Effective Radius for Oceanic Water Clouds as Deduced from Optical Thickness Variability Across Scattering Angles", Journal of Geophysical Research: Atmospheres, Wiley-Blackwell, Vol 120, Num 15, pp 7661--7681, 2015, doi:10.1002/2015jd023256


JaeHyuk Kwack, Soonpil Kang, Geetha Bhat, and Arif Masud: "Time-Dependent Outflow Boundary Conditions for Blood Flow in the Arterial System", Springer International Publishing, Advances in Computational Fluid-Structure Interaction and Flow Simulation: New Methods and Challenging Computations, pp 359-377, 2015, doi:10.1007/978-3-319-40827-9_28


Jared C. Weddell, JaeHyuk Kwack, P. I. Imoukhuede, and Arif Masud: "Hemodynamic Analysis in an Idealized Artery Tree: Differences in Wall Shear Stress Between Newtonian and Non-Newtonian Blood Models", PLOS ONE, Public Library of Science (PLoS), Vol 10, Num 4, pp e0124575, 2015, doi:10.1371/journal.pone.0124575


Tyler M. Earnest, Jonathan Lai, Ke Chen, Michael J. Hallock, James R. Williamson, and Zaida Luthey-Schulten: "Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly", Biophysical Journal, Elsevier BV, Vol 109, Num 6, pp 1117-1135, 2015, doi:10.1016/j.bpj.2015.07.030


Yan Y. Liu, Wendy K. Tam Cho, and Shaowen Wang: "A Scalable Computational Approach to Political Redistricting Optimization", ACM Press, XSEDE '15: Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure, pp 6:1, St Louis, Missouri, U.S.A., 2015, doi:10.1145/2792745.2792751


Yan Y. Liu and Shaowen Wang: "A Scalable Parallel Genetic Algorithm for the Generalized Assignment Problem", Parallel Computing, Elsevier BV, Vol 46, pp 98-119, 2015, doi:10.1016/j.parco.2014.04.008


Rupert Croft, Tiziana Di Matteo, Nishikanta Khandai, and Yu Feng: "Petascale Cosmology: Simulations of Structure Formation", Computing in Science & Engineering, Institute of Electrical & Electronics Engineers, Vol 17, Num 2, pp 40-46, 2015, doi:10.1109/mcse.2015.5


Wilkins, Stephen M., Feng, Yu, Di Matteo, Tiziana, Croft, Rupert, Lovell, Christopher C., and Waters, Dacen: "The properties of the first galaxies in the BlueTides simulation", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 469, Num 3, pp 2517-2530, 2015, doi:10.1093/mnras/stx841


Yu Feng, Mark Straka, Tiziana Di Matteo, and Rupert Croft: "Sorting at Scale on BlueWaters in a Cosmological Simulation", presented at CUG 2015, Chicago, Illinois, U.S.A., 2015


Yu Feng, Tiziana Di Matteo, Rupert Croft, Ananth Tenneti, Simeon Bird, Nicholas Battaglia, and Stephen Wilkins: "The Formation of Milky Way-Mass Disk Galaxies in the First 500 Million Years of a Cold Dark Matter Universe", Astrophysical Journal Letters, The American Astronomical Society, Vol 808, Num 1, pp L17, 2015, doi:10.1088/2041-8205/808/1/l17


Yu Feng, Tiziana Di Matteo, Rupert A. Croft, Simeon Bird, Nicholas Battaglia, and Stephen Wilkins: "The BlueTides Simulation: First Galaxies and Reionization", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 455, Num 3, pp 2778-2791, 2015, doi:10.1093/mnras/stv2484


Joel B. Varley and André Schleife: "Bethe-Salpeter Calculation of Optical-Absorption Spectra of In2O3 and Ga2O3", Semiconductor Science and Technology, IOP Publishing, Vol 30, Num 2, pp 024010, 2015, doi:10.1088/0268-1242/30/2/024010


Boris Capitanu, Ted Underwood, Peter Organisciak, Timothy Cole, Maria Janina Sarol, and J. Stephen Downie: "The HathiTrust Research Center Extracted Feature Dataset (1.5)", HathiTrust Research Center, HathiTrust Research Center Documentation, 2015, doi:10.13012/J8X63JT3


Jing Li, Po-Chao Wen, Mahmoud Moradi, and Emad Tajkhorshid: "Computational Characterization of Structural Dynamics Underlying Function in Active Membrane Transporters", Current Opinion in Structural Biology, Elsevier BV, Vol 31, pp 96-105, 2015, doi:10.1016/j.sbi.2015.04.001


Mahmoud Moradi, Giray Enkavi, and Emad Tajkhorshid: "Atomic-Level Characterization of Transport Cycle Thermodynamics in the Glycerol-3-Phosphate:phosphate Antiporter", Nature Communications, Nature Publishing Group, Vol 6, pp 8393, 2015, doi:10.1038/ncomms9393


K. Jin, S. P. Vanka, and B. G. Thomas: "Three-Dimensional Flow in a Driven Cavity Subjected to an External Magnetic Field", Journal of Fluids Engineering, ASME International, Vol 137, Num 7, pp 071104, 2015, doi:10.1115/1.4029731


Kai Jin, Brian G. Thomas, and Xiaoming Ruan: "Modeling and Measurements of Multiphase Flow and Bubble Entrapment in Steel Continuous Casting", Metallurgical and Materials Transactions B, Springer Science + Business Media, Vol 47, Num 1, pp 548-565, 2015, doi:10.1007/s11663-015-0525-5


Xiao Chen, Xiongjie Yu, Gil Young Cho, Bryan K. Clark, and Eduardo Fradkin: "Many-Body Localization Transition in Rokhsar-Kivelson-Type Wave Functions", Physical Review B, American Physical Society, Vol 92, Num 21, pp 214204, 2015, doi:10.1103/physrevb.92.214204


Soohaeng Yoo Willow, Michael A. Salim, Kwang S. Kim, and So Hirata: "Ab Initio Molecular Dynamics of Liquid Water Using Embedded-Fragment Second-Order Many-Body Perturbation Theory Towards Its Accurate Property Prediction", Scientific Reports, Nature Publishing Group, Vol 5, pp 14358, 2015, doi:10.1038/srep14358


Andrew Sirjoosingh, Michael V. Pak, Kurt R. Brorsen, and Sharon Hammes-Schiffer: "Quantum Treatment of Protons with the Reduced Explicitly Correlated Hartree-Fock Approach", Journal of Chemical Physics, AIP Publishing, Vol 142, Num 21, pp 214107, 2015, doi:10.1063/1.4921303


Kurt R. Brorsen, Andrew Sirjoosingh, Michael V. Pak, and Sharon Hammes-Schiffer: "Nuclear-Electronic Orbital Reduced Explicitly Correlated Hartree-Fock Approach: Restricted Basis Sets and Open-Shell Systems", Journal of Chemical Physics, AIP Publishing, Vol 142, Num 21, pp 214108, 2015, doi:10.1063/1.4921304


William Gropp: "Algorithms for extreme-scale systems", 2016 Blue Waters Annual Report, pp 160-161, 2015


D. Guo, W. Gropp, and L. N. Olson: "A Hybrid Format for Better Performance of Sparse Matrix-Vector Multiplication on a GPU", International Journal of High Performance Computing Applications, SAGE Publications, Vol 30, Num 1, pp 103-120, 2015, doi:10.1177/1094342015593156


William Gropp: "Algorithms for extreme-scale systems", 2015 Blue Waters Annual Report, pp 124, 2015


Vivek Kale: "Low-Overhead Scheduling for Improving Performance of Scientific Applications", University of Illinois at Urbana-Champaign, Illinois Digital Environment for Access to Learning and Scholarship, Vol Doctoral dissertation, 2015


Martin Ostoja-Starzewski: "Mechanics of Random and Fractal Media", 2015 Blue Waters Annual Report, pp 102-103, 2015


Taishan Zhu and Elif Ertekin: "Resolving Anomalous Strain Effects on Two-Dimensional Phonon Flows: The Cases of Graphene, Boron Nitride, and Planar Superlattices", Physical Review B, American Physical Society, Vol 91, Num 20, pp 205429, 2015, doi:10.1103/physrevb.91.205429


Abhilash Harpale, Marco Panesi, and Huck Beng Chew: "Communication: Surface-to-Bulk Diffusion of Isolated Versus Interacting C Atoms in Ni(111) and Cu(111) Substrates: A First Principle Investigation", Journal of Chemical Physics, AIP Publishing, Vol 142, Num 6, pp 061101, 2015, doi:10.1063/1.4907716


Haoran Wang, Binyue Hou, Xueju Wang, Shuman Xia, and Huck Beng Chew: "Atomic-Scale Mechanisms of Sliding Along an Interdiffused Li-Si-Cu Interface", Nano Letters, American Chemical Society, Vol 15, Num 3, pp 1716-1721, 2015, doi:10.1021/nl5043837


Haoran Wang, Xueju Wang, Shuman Xia, and Huck Beng Chew: "Brittle-to-Ductile Transition of Lithiated Silicon Electrodes: Crazing to Stable Nanopore Growth", Journal of Chemical Physics, AIP Publishing, Vol 143, Num 10, pp 104703, 2015, doi:10.1063/1.4930856


Ruizhi Li and Huck Beng Chew: "Closed and Open-Ended Stacking Fault Tetrahedra Formation Along the Interfaces of Cu-Al Nanolayered Metals", Philosophical Magazine, Informa UK Limited, Vol 95, Num 25, pp 2747-2763, 2015, doi:10.1080/14786435.2015.1077283


Ruizhi Li and Huck Beng Chew: "Planar-to-Wavy Transition of Cu-Ag Nanolayered Metals: A Precursor Mechanism to Twinning", Philosophical Magazine, Informa UK Limited, Vol 95, Num 10, pp 1029-1048, 2015, doi:10.1080/14786435.2015.1006290


Jens Glaser, Trung Dac Nguyen, Joshua A. Anderson, Pak Lui, Filippo Spiga, Jaime A. Millan, David C. Morse, and Sharon C. Glotzer: "Strong Scaling of General-Purpose Molecular Dynamics Simulations on GPUs", Computer Physics Communications, Elsevier BV, Vol 192, pp 97--107, 2015, doi:10.1016/j.cpc.2015.02.028


Zhanpeng Zhang, Ryan L. Marson, Zhishen Ge, Sharon C. Glotzer, and Peter X. Ma: "Simultaneous Nano- and Microscale Control of Nanofibrous Microspheres Self-Assembled from Star-Shaped Polymers", Advanced Materials, Wiley-Blackwell, Vol 27, Num 26, pp 3947-3952, 2015, doi:10.1002/adma.201501329


Patrick Conry, Ashish Sharma, Mark J. Potosnak, Laura S. Leo, Edward Bensman, Jessica J. Hellmann, and Harindra J. S. Fernando: "Chicago's Heat Island and Climate Change: Bridging the Scales via Dynamical Downscaling", Journal of Applied Meteorology and Climatology, American Meteorological Society, Vol 54, Num 7, pp 1430-1448, 2015, doi:10.1175/jamc-d-14-0241.1


Poya Yasaei, Arman Fathizadeh, Reza Hantehzadeh, Arnab K. Majee, Ahmed El-Ghandour, David Estrada, Craig Foster, Zlatan Aksamija, Fatemeh Khalili-Araghi, and Amin Salehi-Khojin: "Bimodal Phonon Scattering in Graphene Grain Boundaries", Nano Letters, American Chemical Society, Vol 15, Num 7, pp 4532-4540, 2015, doi:10.1021/acs.nanolett.5b01100


Blakesley Burkhart, A. Lazarian, D. Balsara, C. Meyer, and J. Cho: "Alfvenic Turbulence Beyond the Ambipolar Diffusion Scale", Astrophysical Journal, The American Astronomical Society, Vol 805, Num 2, pp 118, 2015, doi:10.1088/0004-637x/805/2/118


Sudip Garain, Dinshaw S. Balsara, and John Reid: "Comparing Coarray Fortran (CAF) with MPI for Several Structured Mesh PDE Applications", Journal of Computational Physics, Elsevier BV, Vol 297, pp 237--253, 2015, doi:10.1016/j.jcp.2015.05.020


Gaurav Shukla, Zhongqing Wu, Han Hsu, Andrea Floris, Matteo Cococcioni, and Renata M. Wentzcovitch: "Thermoelasticity of Fe2+ -Bearing Bridgmanite", Geophysical Research Letters, Wiley-Blackwell, Vol 42, Num 6, pp 1741-1749, 2015, doi:10.1002/2014gl062888


Michel L. Marcondes and Renata M. Wentzcovitch: "Hybrid Ab-Initio/experimental High Temperature Equations of State: Application to the NaCl Pressure Scale", Journal of Applied Physics, AIP Publishing, Vol 117, Num 21, pp 215902, 2015, doi:10.1063/1.4921904


Ryan J. Wu, Mehmet Topsakal, Tony Low, Matthew C. Robbins, Nazila Haratipour, Jong Seok Jeong, Renata M. Wentzcovitch, Steven J. Koester, and K. Andre Mkhoyan: "Atomic and Electronic Structure of Exfoliated Black Phosphorus", Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, American Vacuum Society, Vol 33, Num 6, pp 060604, 2015, doi:10.1116/1.4926753


Edwin Mathews: "Large-Eddy Simulations of Aero-Optic Distortions", 2016 Blue Waters Annual Report, pp 262-263, 2015


Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper: "Numerical Investigation of Aero-Optical Distortions Over a Hemisphere-on-Cylinder Turret with Gaps", American Institute of Aeronautics and Astronautics, 46th AIAA Plasmadynamics and Lasers Conference, Dallas, Texas, U.S.A., 2015, doi:10.2514/6.2015-3248


Sara I. L. Kokkila Schumacher, Edward G. Hohenstein, Robert M. Parrish, Lee-Ping Wang, and Todd J. Martínez: "Tensor Hypercontraction Second-Order Moller-Plesset Perturbation Theory: Grid Optimization and Reaction Energies", Journal of Chemical Theory and Computation, American Chemical Society, Vol 11, Num 7, pp 3042-3052, 2015, doi:10.1021/acs.jctc.5b00272


Ariana Minot and Na Li: "A Fully Distributed State Estimation Using Matrix Splitting Methods", Institute of Electrical & Electronics Engineers, 2015 American Control Conference (ACC), pp 2488-2493, Chicago, Illinois, U.S.A., 2015, doi:10.1109/acc.2015.7171105


Ariana Minot, Yue M. Lu, and Na Li: "A Distributed Gauss-Newton Method for Power System State Estimation", IEEE Transactions on Power Systems, Institute of Electrical & Electronics Engineers, Vol 31, Num 5, pp 3804-3815, 2015, doi:10.1109/tpwrs.2015.2497330


J. Calhoun, L. Olson, M. Snir, and W. D. Gropp: "Towards a More Fault Resilient Multigrid Solver", Society for Computer Simulation International, HPC '15: Proceedings of the Symposium on High Performance Computing, pp 1-8, Alexandria, Virginia, U.S.A., 2015, doi:10.5555/2872599.2872600


David Radice, Sean M Couch, and Christian D Ott: "Implicit Large Eddy Simulations of Anisotropic Weakly Compressible Turbulence with Application to Core-Collapse Supernovae", Computational Astrophysics and Cosmology, Springer Science + Business Media, Vol 2, Num 1, 2015, doi:10.1186/s40668-015-0011-0


Philipp Mösta, Christian D. Ott, David Radice, Luke F. Roberts, Erik Schnetter, and Roland Haas: "A Large-Scale Dynamo and Magnetoturbulence in Rapidly Rotating Core-Collapse Supernovae", Nature, Nature Publishing Group, Vol 528, Num 7582, pp 376--379, 2015, doi:10.1038/nature15755


Sean M. Couch and Christian D. Ott: "The Role of Turbulence in Neutrino-Driven Core-Collapse Supernova Explosions", Astrophysical Journal, IOP Publishing, Vol 799, Num 1, pp 5, 2015, doi:10.1088/0004-637x/799/1/5


Viktoriya Morozova, Anthony L. Piro, Mathieu Renzo, Christian D. Ott, Drew Clausen, Sean M. Couch, Justin Ellis, and Luke F. Roberts: "Light Curves of Core-Collapse Supernovae with Substantial Mass Loss Using the New Open-Source Supernova Explosion Code (SNEC)", Astrophysical Journal, IOP Publishing, Vol 814, Num 1, pp 63, 2015, doi:10.1088/0004-637x/814/1/63


Varvara E. Zemskova, Brian L. White, and Alberto Scotti: "Available Potential Energy and the General Circulation: Partitioning Wind, Buoyancy Forcing, and Diapycnal Mixing", Journal of Physical Oceanography, American Meteorological Society, Vol 45, Num 6, pp 1510-1531, 2015, doi:10.1175/jpo-d-14-0043.1


George M. Slota and Kamesh Madduri: "Parallel Color-Coding", Parallel Computing, Elsevier BV, Vol 47, pp 51-69, 2015, doi:10.1016/j.parco.2015.02.004


George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri: "High-Performance Graph Analytics on Manycore Processors", Institute of Electrical & Electronics Engineers, 2015 IEEE International Parallel and Distributed Processing Symposium, pp 17-27, Hyderabad, India, 2015, doi:10.1109/ipdps.2015.54


Eugene Palovcak, Lucie Delemotte, Michael L. Klein, and Vincenzo Carnevale: "Comparative Sequence Analysis Suggests a Conserved Gating Mechanism for TRP Channels", Journal of General Physiology, Rockefeller University Press, Vol 146, Num 1, pp 37-50, 2015, doi:10.1085/jgp.201411329


Khaled Elokely, Phanindra Velisetty, Lucie Delemotte, Eugene Palovcak, Michael L. Klein, Tibor Rohacs, and Vincenzo Carnevale: "Understanding TRPV1 Activation by Ligands: Insights from the Binding Modes of Capsaicin and Resiniferatoxin", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 113, Num 2, pp E137-E145, 2015, doi:10.1073/pnas.1517288113


Luca Ponzoni, Guido Polles, Vincenzo Carnevale, and Cristian Micheletti: "SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets", Structure, Elsevier BV, Vol 23, Num 8, pp 1516-1525, 2015, doi:10.1016/j.str.2015.05.022


Saurabh S. Sawant, Burak Korkut, Ozgur Tumuklu, and Deborah A. Levin: "Development of an AMR Octree DSMC Approach for Shock Dominated Flows", American Institute of Aeronautics and Astronautics, 53rd AIAA Aerospace Sciences Meeting, Kissimmee, Florida, U.S.A., 2015, doi:10.2514/6.2015-0070


Junshik Um and Greg M. McFarquhar: "Formation of Atmospheric Halos and Applicability of Geometric Optics for Calculating Single-Scattering Properties of Hexagonal Ice Crystals: Impacts of Aspect Ratio and Ice Crystal Size", Journal of Quantitative Spectroscopy and Radiative Transfer, Elsevier BV, Vol 165, pp 134-152, 2015, doi:10.1016/j.jqsrt.2015.07.001


Eric Jakobsson: "Computational Approach to Designing Antibody for Ebola Virus", 2016 Blue Waters Annual Report, pp 217-218, 2015


Diwakar Shukla: "Understanding The Protein Allostery in Kinases and GPCRS", 2017 Blue Waters Annual Report, pp 236-237, 2015


C. D. Sudheer and Ashok Srinivasan: "Efficient Barrier Implementation on the POWER8 Processor", Institute of Electrical & Electronics Engineers, 2015 IEEE 22nd International Conference on High Performance Computing (HiPC), pp 165-173, Bangalore, India, 2015, doi:10.1109/hipc.2015.51


A. Barati Farimani, M. Heiranian, and N. R. Aluru: "Electromechanical Signatures for DNA Sequencing Through a Mechanosensitive Nanopore..", Journal of Physical Chemistry Letters, American Chemical Society, Vol 6, Num 4, pp 650-657, 2015, doi:10.1021/jz5025417


Yanbin Wu, Lucas K. Wagner, and Narayana R. Aluru: "The Interaction Between Hexagonal Boron Nitride and Water from First Principles", Journal of Chemical Physics, AIP Publishing, Vol 142, Num 23, pp 234702, 2015, doi:10.1063/1.4922491


Jaehyung Yu, Lucas K. Wagner, and Elif Ertekin: "Towards a systematic assessment of errors in diffusion Monte Carlo calculations of semiconductors: case study of zinc selenide and zinc oxide", Journal of Chemical Physics, AIP Publishing, Vol 143, Num 22, pp 224707, 2015, doi:10.1063/1.4937421


Miguel Zilhão, Scott C. Noble, Manuela Campanelli, and Yosef Zlochower: "Resolving the Relative Influence of Strong Field Spacetime Dynamics and MHD on Circumbinary Disk Physics", Physical Review D, American Physical Society, Vol 91, Num 2, pp 024034, 2015, doi:10.1103/PhysRevD.91.024034


S. Aseeri, O. Batrasev, M. Icardi, B. Leu, A. Liu, N. Li, B. K. Muite, E. Muller, B. Palen, M. Quell, H. Servat, P. Sheth, M. Van Moer, and J. Vienne: "Solving the Klein-Gordon equation using fourier spectral methods: a benchmark test for computer performance", Society for Computer Simulation International, HPC '15: Proceedings of the Symposium on High Performance Computing, pp 182-191, Alexandria, Virginia, U.S.A., 2015, doi:10.5555/2872599.2872622


Jon Calhoun, Marc Snir, Luke Olson, and Maria Garzaran: "Understanding the Propagation of Error Due to a Silent Data Corruption in a Sparse Matrix Vector Multiply", Institute of Electrical & Electronics Engineers, 2015 IEEE International Conference on Cluster Computing, pp 541-542, Chicago, Illinois, U.S.A., 2015, doi:10.1109/cluster.2015.101


Constantin Schoeler, Rafael C. Bernardi, Klara H. Malinowska, Ellis Durner, Wolfgang Ott, Edward A. Bayer, Klaus Schulten, Michael A. Nash, and Hermann E. Gaub: "Mapping Mechanical Force Propagation Through Biomolecular Complexes", Nano Letters, American Chemical Society, Vol 15, Num 11, pp 7370-7376, 2015, doi:10.1021/acs.nanolett.5b02727


Celso L. Mendes, Brett Bode, Gregory H. Bauer, Jeremy Enos, Cristina Beldica, and William T. Kramer: "Deployment and Testing of the Sustained Petascale Blue Waters System", Journal of Computational Science, Elsevier BV, Vol 10, pp 327-337, 2015, doi:10.1016/j.jocs.2015.03.007


Robert Sisneros: "A Feature-First Approach to Clustering for Highlighting Regions of Interest in Scientific Data", Elsevier BV, Procedia Computer Science (15th annual International Conference On Computational Science, ICCS 2015), Vol 51, pp 2207-2216, Reykjavík, Iceland, 2015, doi:10.1016/j.procs.2015.05.497


Catello Di Martino, William Kramer, Zbigniew Kalbarczyk, and Ravishankar Iyer: "Measuring and Understanding Extreme-Scale Application Resilience: A Field Study of 5,000,000 HPC Application Runs", Institute of Electrical & Electronics Engineers, 2015 45th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, pp 25-36, Rio de Janeiro, Brazil, 2015, doi:10.1109/dsn.2015.50


S. Byna, R. Sisneros, K. Chadalavada, Q. Koziol: "Tuning Parallel I/O on Blue Waters for Writing 10 Trillion Particles", presented at CUG 2015, Chicago, Illinois, U.S.A., 2015


Adam Burrows: "Three-Dimensional Core-Collapse Supernova Simulations", 2015 Blue Waters Annual Report, pp 36-37, 2015


Eric J. Lentz and Stephen W. Bruenn and W. Raphael Hix and Anthony Mezzacappa and O. E. Bronson Messer and Eirik Endeve and John M. Blondin and J. Austin Harris and Pedro Marronetti and Konstantin N. Yakunin: "Three-dimensional Core-collapse Supernova Simulated Using a 15 M-circle dot Progenitor", Astrophysical Journal Letters, The American Astronomical Society, Vol 807, Num 2, pp L31, 2015, doi:10.1088/2041-8205/807/2/L31


Rommie Amaro: "Virtual Flu, A Different Kind of Computer Virus", 2015 Blue Waters Annual Report, pp 128-129, 2015


David Ceperley: "Hydrogen under Extreme Conditions", 2015 Blue Waters Annual Report, pp 76-77, 2015


Narayana Aluru: "Large-Scale Simulations of Biological–Synthetic Interface Materials for Sensing Applications", 2015 Blue Waters Annual Report, pp 70-71, 2015


Kristin Muterspaw, Tara Urner, Ruth Lewis, Ivan Babic, Deeksha Srinath, and Charles Peck: "Multidisciplinary Research and Education with Open Tools", ACM Press, XSEDE '15: Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure, pp 22:1-22:8, St. Louis, Missouri, U.S.A., 2015, doi:10.1145/2792745.2792767


Daniel Bodony: "Reducing jet aircraft noise by harnessing the hetergeneous XK nodes on Blue Waters", 2015 Blue Waters Annual Report, pp 74-75, 2015


Mohammad Heiranian, Amir Barati Farimani, and Narayana R. Aluru: "Water Desalination with a Single-Layer MoS2 Nanopore", Nature Communications, Springer Nature, Vol 6, pp 8616, 2015, doi:10.1038/ncomms9616


Dinshaw S. Balsara: "Comparing CAF and MPI-3 and Simulating Molecular Cloud Turbulence with Two-Fluid MHD", 2015 Blue Waters Annual Report, pp 72-73, 2015


Alexander Priest, E. Davis Oldham, Lynn Lewis, and David Toth: "Identification of Inhibitors of Fatty Acid Synthesis Enzymes in Mycobacterium Smegmatis", Journal of Computational Science Education, Shodor Education Foundation Inc., Vol 6, Num 1, pp 25-31, 2015, doi:10.22369/issn.2153-4136/6/1/3


Dinshaw S. Balsara: "Comparing CAF and MPI-3 and Simulating Molecular Cloud Turbulence with Two-Fluid MHD", 2016 Blue Waters Annual Report, pp 24-25, 2015


Bryan Clark: "Strongly Correlated Systems through Computation: From Bad Metals to Perfect Insulators", 2015 Blue Waters Annual Report, pp 78-79, 2015


Thomas Cheatham: "Convergence and Reproducibility in Simulations of Nucleic Acids", 2015 Blue Waters Annual Report, pp 132-133, 2015


Gustavo Caetano-Anolles: "Mining The Evolutionary Dynamics of Protein Loop Structure and its Role in Biological Functions", 2015 Blue Waters Annual Report, pp 130-131, 2015


Scott Althaus: "Computational Strategies for Applying Quality Scoring and Error Modeling Strategies to Extreme-Scale Text Archives", 2015 Blue Waters Annual Report, pp 180-181, 2015


Aleksei Aksimentiev: "Ionic Conductivity, Structural Deformation, and Programmable Anistrophy of DNA Origami in An Electric Field", 2015 Blue Waters Annual Report, pp 68-69, 2015


Elif Ertekin: "Simulating Thermal Transport in Nanostructures from The Ballistic to The Diffusive Regime", 2015 Blue Waters Annual Report, pp 84-85, 2015


Nilufer Ertekin-Taner: "Epistatic Interactions for Brain Expression GWAS in Alzheimer's Disease", 2015 Blue Waters Annual Report, pp 134-135, 2015


Paul Fischer: "High-Order Methods for Turbulent Transport in Engineering and Geosciences", 2015 Blue Waters Annual Report, pp 86-87, 2015


Marcelo Garcia: "Large Eddy Simulation of Sediment Transport and Hydrodynamics at River Bifurcations", 2015 Blue Waters Annual Report, pp 42-43, 2015


John Gerlt: "Sequence Similarity Networks for the Protein "Universe"", 2015 Blue Waters Annual Report, pp 136-137, 2015


Sharon Glotzer: "Many-GPU Simulations of Soft Matter Design", 2015 Blue Waters Annual Report, pp 88-89, 2015


Claudio Grosman: "Elucidating The Molecular Basis of Charge Selectivity in Pentametric Ligand-Gated Ion Channels", 2015 Blue Waters Annual Report, pp 138-139, 2015


Sharon Hammes-Schiffer: "Non-Born-Oppenheimer Effects between Electrons and Protons", 2015 Blue Waters Annual Report, pp 140-141, 2015


Lars Hansen: "Policy Responses to Climate Change in a Dynamic Stochastic Economy", 2015 Blue Waters Annual Report, pp 178-180, 2015


Eric Jakobsson: "Effect of Confinement on Protein Dynamic and Structure", 2015 Blue Waters Annual Report, pp 144-145, 2015


Curtis Johnson: "High-Resolution MR Elastography of The Brain in A Clinical Setting", 2015 Blue Waters Annual Report, pp 148-149, 2015


Thomas Jordan: "Earthquake System Science Research", 2015 Blue Waters Annual Report, pp 44-46, 2015


Peter Kasson: "Simulating Influenza Hemagglutinin Membrane Assemblies", 2015 Blue Waters Annual Report, pp 157-158, 2015


Fatemeh Khalili-Araghi: "Functional Mechanism of The Bacterial Efflux Pump", 2015 Blue Waters Annual Report, pp 150-151, 2015


Michael Klein: "Functional Mechanics of Voltage Gated Like Ion Channels", 2015 Blue Waters Annual Report, pp 152-153, 2015


Seid Koric: "Sparse Matrix Factorization in Solid Mechanics and Geophysics on CPUs and GPUs", 2015 Blue Waters Annual Report, pp 94-95, 2015


Sonia Lasher-Trapp: "Simulating Cumulus Entrainment: A Resolution Problem or Conceptual?", 2015 Blue Waters Annual Report, pp 46-47, 2015


Sanjiva Lele: "Shock-induced turbulent mixing", 2015 Blue Waters Annual Report, pp 96-97, 2015


Eric Lentz: "Core-Collapse Supernovae Through Cosmic Time", 2015 Blue Waters Annual Report, pp 22-23, 2015


Deborah Levin: "High-performance Computing of Hypersonic, Shock-shock Interactions using Kinetic, Particle Approaches", 2015 Blue Waters Annual Report, pp 98-99, 2015


Zaida Luthey-Schulten: "Simulating Ribosome Biogenesis in Whole Cells", 2015 Blue Waters Annual Report, pp 154-156, 2015


Nancy Makri: "Quantum-Classical Path Integral Simulation of Proton Transfer in Solution", 2015 Blue Waters Annual Report, pp 160-161, 2015


Liudmila Mainzer: "Instrumenting Human Variant Calling Workflow", 2015 Blue Waters Annual Report, pp 158-159, 2015


Arif Masud: "Blood–Artery Interactions in Patient-Specific Geometries", 2015 Blue Waters Annual Report, pp 162-163, 2015


Kiritkumar Makwana: "Simulating Magnetized Plasma Turbulence from Macro to Micro Scales", 2015 Blue Waters Annual Report, pp 24-25, 2015


Brian O'Shea: "Exploring The First Generations of Galaxies", 2015 Blue Waters Annual Report, pp 26-27, 2015


Christian Ott: "High-Resolution 3-D Simulations of Core-Collapse Supernovae", 2015 Blue Waters Annual Report, pp 104-105, 2015


Nikolai Pogorelov: "Modeling Heliophysics and Astrophysics Phenomena with a Multi-Scale Fluid-Kinetic Simulation Suite", 2015 Blue Waters Annual Report, pp 28-29, 2015


Vijay Pande: "Understanding P53, A Protein “Shape Shifter” Responsible for Many Cancer Tumors", 2015 Blue Waters Annual Report, pp 164-165, 2015


Thomas Quinn: "Evolution of the Small Galaxy Population From High Redshift to the Present", 2015 Blue Waters Annual Report, pp 106-107, 2015


Patrick Reed: "Design and Management of Satellite Assets to Advance Space Based Earth Science", 2015 Blue Waters Annual Report, pp 48-49, 2015


Benoit Roux: "Molecular Details of The Luminal Exit of Calcium Ions in The Calcium Pump of The Sarco/Endoplasmic Reticulum", 2015 Blue Waters Annual Report, pp 168-169, 2015


Chad Rienstra: "Protein structure determination and refinement from raw NMR data", 2015 Blue Waters Annual Report, pp 166-167, 2015


Andre Schleife: "Theoretical Spectroscopy for Transparent Conducting Oxides", 2015 Blue Waters Annual Report, pp 108-109, 2015


Stuart Shapiro: "Relativistic Jet Formation in Black-Hole–Neutron Star Mergers", 2015 Blue Waters Annual Report, pp 30-31, 2015


Jamesina Simpson: "Location-Specific Space-Weather Hazards to Electric-Power Grids Calculated on A Global Scale", 2015 Blue Waters Annual Report, pp 30-31, 2015


Ryan Sriver: "Scaling The CESM to Ultra-High Resolutions for Analyzing Tropical Cyclone–Climate Feedbacks", 2015 Blue Waters Annual Report, pp 52-53, 2015


Robert Sugar: "Lattice QCD on Blue Waters", 2015 Blue Waters Annual Report, pp 115-117, 2015


Ahmed Taha: "Software Extreme Benchmarking", 2015 Blue Waters Annual Report, pp 122-123, 2015


Emad Tajkhorshid: "Characterizing Structural Transitions of Membrane Transport Proteins at Atomic Detail", 2015 Blue Waters Annual Report, pp 172-173, 2015


Klaus Schulten: "The Computational Microscope", 2015 Blue Waters Annual Report, pp 170-171, 2015


Brian Thomas: "Dynamics of Argon Bubbles in Steel Continuous Casting with A Magnetic Field", 2015 Blue Waters Annual Report, pp 112-114, 2015


Robert Trapp: "Petascale modeling of convective storms under climate change and variability", 2015 Blue Waters Annual Report, pp 54-55, 2015


Gregory Voth: "Ultra-Coarse-Grained Biomolecular Simulations", 2015 Blue Waters Annual Report, pp 174-175, 2015


Shaowen Wang: "An Extreme-Scale Computational Approach to Redistricting Optimization", 2015 Blue Waters Annual Report, pp 182-185, 2015


Stan Woosley: "Modeling Type IA Supernova Progenitors", 2015 Blue Waters Annual Report, pp 118-119, 2015


Renata Wentzcovitch: "Computational Mineral Physics", 2015 Blue Waters Annual Report, pp 58-60, 2015


Kodi Collins and Tandy Warnow: "PASTA For Proteins Data (BALiBASE)", University of Illinois at Urbana-Champaign, Illinois Data Bank, 2015, doi:10.13012/B2IDB-4074787_V1


Lijun Liu and Jin S. Zhang: "Differential Contraction of Subducted Lithosphere Layers Generates Deep Earthquakes", Earth and Planetary Science Letters, Elsevier BV, Vol 421, pp 98-106, 2015, doi:10.1016/j.epsl.2015.03.053


Justin C. Kasper, Robert Abiad, Gerry Austin, Marianne Balat-Pichelin, Stuart D. Bale, John W. Belcher, Peter Berg, Henry Bergner, Matthieu Berthomier, Jay Bookbinder, Etienne Brodu, David Caldwell, Anthony W. Case, Benjamin D. G. Chandran, Peter Cheimets, Jonathan W. Cirtain, Steven R. Cranmer, David W. Curtis, Peter Daigneau, Greg Dalton, Brahmananda Dasgupta, David DeTomaso, Millan Diaz-Aguado, Blagoje Djordjevic, Bill Donaskowski, Michael Effinger, Vladimir Florinski, Nichola Fox, Mark Freeman, Dennis Gallagher, S. Peter Gary, Tom Gauron, Richard Gates, Melvin Goldstein, Leon Golub, Dorothy A. Gordon, Reid Gurnee, Giora Guth, Jasper Halekas, Ken Hatch, Jacob Heerikuisen, George Ho, Qiang Hu, Greg Johnson, Steven P. Jordan, Kelly E. Korreck, Davin Larson, Alan J. Lazarus, Gang Li, Roberto Livi, Michael Ludlam, Milan Maksimovic, James P. McFadden, William Marchant, Bennet A. Maruca, David J. McComas, Luciana Messina, Tony Mercer, Sang Park, Andrew M. Peddie, Nikolai Pogorelov, Matthew J. Reinhart, John D. Richardson, Miles Robinson, Irene Rosen, Ruth M. Skoug, Amanda Slagle, John T. Steinberg, Michael L. Stevens, Adam Szabo, Ellen R. Taylor, Chris Tiu, Paul Turin, Marco Velli, Gary Webb, Phyllis Whittlesey, Ken Wright, S. T. Wu, and Gary Zank: "Solar Wind Electrons Alphas and Protons (SWEAP) Investigation: Design of the Solar Wind and Coronal Plasma Instrument Suite for Solar Probe Plus", Space Science Reviews, Springer Nature, Vol 204, Num 1-4, pp 131-186, 2015, doi:10.1007/s11214-015-0206-3


Jon A. Linker, Ronald M. Caplan, Cooper Downs, Roberto Lionello, Pete Riley, Zoran Mikic, Carl J. Henney, Charles N. Arge, Tae Kim, and Nikolai Pogorelov: "An Empirically Driven Time-Dependent Model of the Solar Wind", IOP Publishing Ltd, Journal of Physics: Conference Series (10th International Conference on Numerical Modeling of Space Plasma Flows, ASTRONUM 2015), Vol 719, Num 1, pp 012012, Avignon, France, 2015, doi:10.1088/1742-6596/719/1/012012


Warren Mori: "Particle-in-Cell Simulations of Kinetic Effects in HED Plasmas", 2015 Blue Waters Annual Report, pp 100-101, 2015


Kim, Jinho and Balsara, Dinshaw S. and Lyutikov, Maxim and Komissarov, Sergei S. and George, Daniel and Siddireddy, Prasanna Kumar: "On the linear stability of magnetized jets without current sheets non-relativistic case", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 450, Num 1, pp 982-997, 2015, doi:10.1093/mnras/stv606


Dinshaw S. Balsara, and Michael Dumbser: "Divergence-Free MHD on Unstructured Meshes Using High Order Finite Volume Schemes Based on Multidimensional Riemann Solvers", Journal of Computational Physics, Elsevier BV, Vol 299, pp 687-715, 2015, doi:10.1016/j.jcp.2015.07.012


B. R. Ryan and J. C. Dolence, and C. F. Gammie: "bhlight: General Relativistic Radiation Magnetohydrodynamics with Monte Carlo Transport", Astrophysical Journal, The American Astronomical Society, Vol 807, Num 1, pp 31, 2015, doi:10.1088/0004-637X/807/1/31


Sherwood Richers and Daniel Kasen and Evan O’Connor and Rodrigo Fernández and Christian D. Ott: "Monte Carlo Neutrino Transport through Remnant Disks from Neutron Star Mergers", Astrophysical Journal, The American Astronomical Society, Vol 813, Num 1, pp 38, 2015, doi:10.1088/0004-637X/813/1/38


Ryan J. Wu, Mehmet Topsakal, Matt C. Robbins, Nazila Haratipour, Jong Seok. Jeong, Renata M. M. Wentzcovich, Steven J. Koester, and K. Andre Mkhoyan: "Measuring the Atomic and Electronic Structure of Black Phosphorus with STEM", Microscopy and Microanalysis, Cambridge University Press, Vol 21, Num S3, pp 109-110, 2015, doi:10.1017/s1431927615001348


Jonas Lippuner and Luke F. Roberts: "r-process Lanthanide Production and Heating Rates in Kilonovae", Astrophysical Journal, The American Astronomical Society, Vol 815, Num 2, pp 82, 2015, doi:10.1088/0004-637X/815/2/82


Paul R. Woodward: "3-D Simulations of i-Process Nucleosynthesis in the Early Universe", 2015 Blue Waters Annual Report, pp 34-36, 2015


Manman Lu, Guangjin Hou, Huilan Zhang, Christopher L. Suiter, Jinwoo Ahn, In-Ja L. Byeon, Juan R. Perilla, Christopher J. Langmead, Ivan Hung, Peter L. Gor'kov, Zhehong Gan, William Brey, Christopher Aiken, Peijun Zhang, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova: "Dynamic Allostery Governs Cyclophilin A-HIV Capsid Interplay", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 112, Num 47, pp 14617-14622, 2015, doi:10.1073/pnas.1516920112


Brian K. Radak, Tai-Sung Lee, Michael E. Harris, and Darrin M. York: "Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM", RNA, Cold Spring Harbor Laboratory, Vol 21, Num 9, pp 1566-1577, 2015, doi:10.1261/rna.051466.115


Maria T. Panteva, George M. Giambaşu, and Darrin M. York: "Comparison of Structural, Thermodynamic, Kinetic and Mass Transport Properties of Mg2+ion Models Commonly Used in Biomolecular Simulations", Journal of Computational Chemistry, Wiley, Vol 36, Num 13, pp 970-982, 2015, doi:10.1002/jcc.23881


Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambaşu, Tai-Sung Lee, and Darrin M. York: "Multiscale Methods for Computational RNA Enzymology", Elsevier, Methods in Enzymology, pp 335-374, 2015, doi:10.1016/bs.mie.2014.10.064


Peicheng Yu, Xinlu Xu, Adam Tableman, Viktor K. Decyk, Frank S. Tsung, Frederico Fiuza, Asher Davidson, Jorge Vieira, Ricardo A. Fonseca, Wei Lu, Luis O. Silva, and Warren B. Mori: "Mitigation of Numerical Cerenkov Radiation and Instability Using a Hybrid Finite Difference-FFT Maxwell Solver and a Local Charge Conserving Current Deposit", Computer Physics Communications, Elsevier BV, Vol 197, pp 144-152, 2015, doi:10.1016/j.cpc.2015.08.026


D. Buaria, Brian L. Sawford, and P. K. Yeung: "Characteristics of Backward and Forward Two-Particle Relative Dispersion in Turbulence at Different Reynolds Numbers", Physics of Fluids, AIP Publishing, Vol 27, Num 10, pp 105101, 2015, doi:10.1063/1.4931602


Bikan Tan, Miroslav Hodak, Wenchang Lu, and J. Bernholc: "Charge Transport in DNA Nanowires Connected to Carbon Nanotubes", Physical Review B, American Physical Society, Vol 92, Num 7, pp 075429, 2015, doi:10.1103/physrevb.92.075429


Minseung Kim, Violeta Zorraquino, and Ilias Tagkopoulos: "Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles", PLoS Computational Biology, PLoS, Vol 11, Num 3, pp e1004127, 2015, doi:10.1371/journal.pcbi.1004127


Xianming Liu, Rongrong Ji, Changhu Wang, Wei Liu, Bineng Zhong, and Thomas S. Huang: "Understanding image structure via hierarchical shape parsing", Institute of Electrical & Electronics Engineers, 2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp 5042-5050, Boston, Massachusetts, U.S.A., 2015, doi:10.1109/CVPR.2015.7299139


Chunshui Cao, Xianming Liu, Yi Yang, Yinan Yu, Jiang Wang, Zilei Wang, Yongzhen Huang, Liang Wang, Chang Huang, Wei Xu, Deva Ramanan, and Thomas S. Huang: "Look and Think Twice: Capturing Top-Down Visual Attention with Feedback Convolutional Neural Networks", Institute of Electrical & Electronics Engineers, 2015 IEEE International Conference on Computer Vision (ICCV), pp 2956-2964, Santiago, Chile, 2015, doi:10.1109/ICCV.2015.338


Hiroyuki Nakano, James Healy, Carlos O. Lousto, and Yosef Zlochower: "Perturbative extraction of gravitational waveforms generated with numerical relativity", Physical Review D, American Physical Society, Vol 91, Num 10, pp 104022, 2015, doi:10.1103/PhysRevD.91.104022


Yosef Zlochower and Carlos O. Lousto: "Modeling the remnant mass, spin, and recoil from unequal-mass, precessing black-hole binaries: The intermediate mass ratio regime", Physical Review D, American Physical Society, Vol 92, Num 2, pp 024022, 2015, doi:10.1103/PhysRevD.92.024022


Renato Prata de Moraes Frasson, Gil Bohrer, David Medvigy, Ashley M. Matheny, Timothy H. Morin, Christoph S. Vogel, Christopher M. Gough, Kyle D. Maurer, and Peter S. Curtis: "Modeling forest carbon cycle response to tree mortality: Effects of plant functional type and disturbance intensity", Journal of Geophysical Research: Biogeosciences, American Geophysical Union, Vol 120, Num 11, pp 2178-2193, 2015, doi:10.1002/2015JG003035


2014

Constantin Schoeler, Klara H. Malinowska, Rafael C. Bernardi, Lukas F. Milles, Markus A. Jobst, Ellis Durner, Wolfgang Ott, Daniel B. Fried, Edward A. Bayer, Klaus Schulten, Hermann E. Gaub, and Michael A. Nash: "Ultrastable Cellulosome-Adhesion Complex Tightens Under Load", Nature Communications, Springer Nature, Vol 5, pp 5635, 2014, doi:10.1038/ncomms6635


M. Litos, E. Adli, W. An, C. I. Clarke, C. E. Clayton, S. Corde, J. P. Delahaye, R. J. England, A. S. Fisher, J. Frederico, S. Gessner, S. Z. Green, M. J. Hogan, C. Joshi, W. Lu, K. A. Marsh, W. B. Mori, P. Muggli, N. Vafaei-Najafabadi, D. Walz, G. White: "High-Efficiency Acceleration of an Electron Beam in a Plasma Wakefield Accelerator", Nature, Nature Publishing Group, Vol 515, Num 7525, pp 92-95, 2014, doi:10.1038/nature13882


M. Tzoufras, F. S. Tsung, W. B. Mori, and A. A. Sahai: "Improving the Self-Guiding of an Ultraintense Laser by Tailoring Its Longitudinal Profile", Physical Review Letters, American Physical Society, Vol 113, Num 24, pp 245001, 2014, doi:10.1103/physrevlett.113.245001


Christina Bergonzo, Niel M. Henriksen, Daniel R. Roe, Jason M. Swails, Adrian E. Roitberg, and Thomas E. Cheatham: "Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide", Journal of Chemical Theory and Computation, American Chemical Society, Vol 10, Num 1, pp 492-499, 2014, doi:10.1021/ct400862k


Daniel R. Roe, Christina Bergonzo, and Thomas E. Cheatham: "Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics With Hamiltonian Replica Exchange Methods", Journal of Physical Chemistry B, American Chemical Society, Vol 118, Num 13, pp 3543-3552, 2014, doi:10.1021/jp4125099


Rodrigo Galindo-Murillo, Daniel R. Roe, and Thomas E. Cheatham: "On the absence of intrahelical DNA dynamics on the mu s to ms timescale", Nature Communications, Nature Publishing Group, Vol 5, pp 5152, 2014, doi:10.1038/ncomms6152


Paul R. Woodward, Falk Herwig, and Pei-Hung Lin: "Hydrodynamic Simulations of H Entrainment at the Top of He-Shell Flash Convection", Astrophysical Journal, The American Astronomical Society, Vol 798, Num 1, pp 49, 2014, doi:10.1088/0004-637x/798/1/49


Renyue Cen, Ana Roxana Pop, and Neta A. Bahcall: "Gas Loss in Simulated Galaxies as They Fall Into Clusters", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 111, Num 22, pp 7914-7919, 2014, doi:10.1073/pnas.1407300111


Renyue Cen: "Evolution of Cold Streams and Emergence of the Hubble Sequence", Astrophysical Journal Letters, The American Astronomical Society, Vol 789, Num 1, pp L21, 2014, doi:10.1088/2041-8205/789/1/l21


Renyue Cen: "Frequent Spin Reorientation of Galaxies Due to Local Interactions", Astrophysical Journal Letters, The American Astronomical Society, Vol 785, Num 1, pp L15, 2014, doi:10.1088/2041-8205/785/1/l15


Renyue Cen: "On the Origin of the Hubble Sequence: I. Insights on Galaxy Color Migration from Cosmological Simulations", Astrophysical Journal, The American Astronomical Society, Vol 781, Num 1, pp 38, 2014, doi:10.1088/0004-637x/781/1/38


Renyue Cen: "Temporal Self-Organization in Galaxy Formation", Astrophysical Journal Letters, The American Astronomical Society, Vol 785, Num 2, pp L21, 2014, doi:10.1088/2041-8205/785/2/l21


Renyue Cen and Taysun Kimm: "Infrared Properties of Z=7 Galaxies from Cosmological Simulations", Astrophysical Journal, The American Astronomical Society, Vol 782, Num 1, pp 32, 2014, doi:10.1088/0004-637x/782/1/32


Stephanie Tonnesen and Renyue Cen: "On the Reversal of SFR-Density Relation at Z=1: Insights from Simulations", Astrophysical Journal, The American Astronomical Society, Vol 788, Num 2, pp 133, 2014, doi:10.1088/0004-637x/788/2/133


Taysun Kimm and Renyue Cen: "Escape Fraction of Ionizing Photons During Reionization: Effects Due to Supernova Feedback and Runaway OB Stars", Astrophysical Journal, The American Astronomical Society, Vol 788, Num 2, pp 121, 2014, doi:10.1088/0004-637x/788/2/121


Nakul Jindal, Victor Lotrich, Erik Deumens, and Beverly A. Sanders: "Exploiting GPUs with the Super Instruction Architecture", International Journal of Parallel Programming, Springer Science + Business Media, Vol 44, Num 2, pp 309-324, 2014, doi:10.1007/s10766-014-0319-4


Lukasz Wesolowski, Ramprasad Venkataraman, Abhishek Gupta, Jae-Seung Yeom, Keith Bisset, Yanhua Sun, Pritish Jetley, Thomas R. Quinn, and Laxmikant V. Kale: "TRAM: Optimizing Fine-Grained Communication with Topological Routing and Aggregation of Messages", Institute of Electrical & Electronics Engineers, 2014 43rd International Conference on Parallel Processing (ICPP), pp 211-220, Minneapolis, Minnesota, U.S.A., 2014, doi:10.1109/icpp.2014.30


D. Buaria and P. K. Yeung: "Challenges in Particle Tracking in Turbulence on a Massive Scale", Association for Computing Machinery, XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment, Atlanta, Georgia, U.S.A., 2014, doi:10.1145/2616498.2616526


K. P. Iyer and P. K. Yeung: "Structure Functions and Applicability of Yaglom's Relation in Passive-Scalar Turbulent Mixing at Low Schmidt Numbers with Uniform Mean Gradient", Physics of Fluids, AIP Publishing, Vol 26, Num 8, pp 085107, 2014, doi:10.1063/1.4892581


Pui-kuen Yeung: "Intermittency, Resolution Effects and High Schmidt Number Mixing in Turbulence", 2017 Blue Waters Annual Report, pp 166-167, 2014


P. K. Yeung and K. R. Sreenivasan: "Direct Numerical Simulation of Turbulent Mixing at Very Low Schmidt Number with a Uniform Mean Gradient", Physics of Fluids, AIP Publishing, Vol 26, Num 1, pp 015107, 2014, doi:10.1063/1.4861070


Pui-kuen Yeung: "The Complexities of High Reynolds Number Turbulence", 2016 Blue Waters Annual Report, pp 134-136, 2014


Doriam Restrepo and Jacobo Bielak: "Virtual Topography: A Fictitious Domain Approach for Analyzing Free-Surface Irregularities in Large-Scale Earthquake Ground Motion Simulation", International Journal for Numerical Methods in Engineering, Wiley-Blackwell, Vol 100, Num 7, pp 504-533, 2014, doi:10.1002/nme.4756


Efecan Poyraz, Heming Xu, and Yifeng Cui: "Application-Specific I/O Optimizations on Petascale Supercomputers", Elsevier BV, Procedia Computer Science (2014 International Conference on Computational Science, ICCS 2014), Vol 29, pp 910-923, Cairns, Australia, 2014, doi:10.1016/j.procs.2014.05.082


En-Jui Lee, Po Chen, Thomas H. Jordan, Phillip B. Maechling, Marine A. M. Denolle, and Gregory C. Beroza: "Full-3-D Tomography for Crustal Structure in Southern California Based on the Scattering-Integral and the Adjoint-Wavefield Methods", Journal of Geophysical Research: Solid Earth, Wiley-Blackwell, Vol 119, Num 8, pp 6421-6451, 2014, doi:10.1002/2014jb011346


F. Wang and T. H. Jordan: "Comparison of Probabilistic Seismic-Hazard Models Using Averaging-Based Factorization", Bulletin of the Seismological Society of America, Seismological Society of America, Vol 104, Num 3, pp 1230-1257, 2014, doi:10.1785/0120130263


Heming Xu, Yifeng Cui, James H. Dieterich, Keith Richards-Dinger, Efecan Poyraz, and Dong Ju Choi: "Aftershock Sequence Simulations Using Synthetic Earthquakes and Rate-State Seismicity Formulation", Earthquake Science, Springer Science + Business Media, Vol 27, Num 4, pp 401--410, 2014, doi:10.1007/s11589-014-0087-7


M. Böse, R. W. Graves, D. Gill, S. Callaghan, and P. J. Maechling: "CyberShake-Derived Ground-Motion Prediction Models for the Los Angeles Region with Application to Earthquake Early Warning", Geophysical Journal International, Oxford University Press, Vol 198, Num 3, pp 1438-1457, 2014, doi:10.1093/gji/ggu198


Philipp Mösta, Sherwood Richers, Christian D. Ott, Roland Haas, Anthony L. Piro, Kristen Boydstun, Ernazar Abdikamalov, Christian Reisswig, and Erik Schnetter: "Magnetorotational Core-Collapse Supernovae in Three Dimensions", Astrophysical Journal Letters, The American Astronomical Society, Vol 785, Num 2, pp L29, 2014, doi:10.1088/2041-8205/785/2/l29


Bruno C. Mundim, Hiroyuki Nakano, Nicolás Yunes, Manuela Campanelli, Scott C. Noble, and Yosef Zlochower: "Approximate Black Hole Binary Spacetime via Asymptotic Matching", Physical Review D, American Physical Society, Vol 89, Num 8, pp 084008, 2014, doi:10.1103/physrevd.89.084008


Carlos O. Lousto and Yosef Zlochower: "Black Hole Binary Remnant Mass and Spin: A New Phenomenological Formula", Physical Review D, American Physical Society, Vol 89, Num 10, 2014, doi:10.1103/physrevd.89.104052


Carlos O. Lousto and Yosef Zlochower: "Where Angular Momentum Goes in a Precessing Black-Hole Binary", Physical Review D, American Physical Society, Vol 89, Num 2, 2014, doi:10.1103/physrevd.89.021501


J Aasi et al. (LIGO Scientific Collaboration and Virgo Collaboration), and M Boyle and B Brügmann and L T Buchman and M Campanelli and T Chu and Z B Etienne and M Hannam and J Healy and I Hinder and L E Kidder and P Laguna and Y T Liu and L London and C O Lousto and G Lovelace and I MacDonald and P Marronetti and P Mösta and D Müller and B C Mundim and H Nakano and V Paschalidis and L Pekowsky and D Pollney and H P Pfeiffer and M Ponce and M Pürrer and G Reifenberger and C Reisswig and L Santamaría and M A Scheel and S L Shapiro and D Shoemaker and C F Sopuerta and U Sperhake and B Szilágyi and N W Taylor and W Tichy and P Tsatsin and Y Zlochower: "The NINJA-2 Project: Detecting and Characterizing Gravitational Waveforms Modelled Using Numerical Binary Black Hole Simulations", Classical and Quantum Gravity, IOP Publishing, Vol 31, Num 11, pp 115004, 2014, doi:10.1088/0264-9381/31/11/115004


Miguel Zilhão and Scott C Noble: "Dynamic Fisheye Grids for Binary Black Hole Simulations", Classical and Quantum Gravity, IOP Publishing, Vol 31, Num 6, pp 065013, 2014, doi:10.1088/0264-9381/31/6/065013


John. M. A. Grime and Gregory A. Voth: "Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations", Journal of Chemical Theory and Computation, American Chemical Society, Vol 10, Num 1, pp 423-431, 2014, doi:10.1021/ct400727q


Hai Nguyen, James Maier, He Huang, Victoria Perrone, and Carlos Simmerling: "Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent", Journal of the American Chemical Society, American Chemical Society, Vol 136, Num 40, pp 13959-13962, 2014, doi:10.1021/ja5032776


Jason M. Swails, Darrin M. York, and Adrian E. Roitberg: "Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation", Journal of Chemical Theory and Computation, American Chemical Society, Vol 10, Num 3, pp 1341-1352, 2014, doi:10.1021/ct401042b


Julien C. Thibault, Daniel R. Roe, Julio C. Facelli, and Thomas E. Cheatham: "Data Model, Dictionaries, and Desiderata for Biomolecular Simulation Data Indexing and Sharing", Journal of Cheminformatics, Springer Nature, Vol 6, Num 1, pp 4, 2014, doi:10.1186/1758-2946-6-4


Julien C. Thibault, Thomas E. Cheatham, and Julio C. Facelli: "iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings", Journal of Chemical Information and Modeling, American Chemical Society, Vol 54, Num 6, pp 1810-1819, 2014, doi:10.1021/ci500173w


Natali V. Di Russo, Marcelo A. Marti, and Adrian E. Roitberg: "Underlying Thermodynamics of pH-Dependent Allostery", Journal of Physical Chemistry B, American Chemical Society, Vol 118, Num 45, pp 12818-12826, 2014, doi:10.1021/jp507971v


Niel M. Henriksen, Hamed S. Hayatshahi, Darrell R. Davis, and Thomas E. Cheatham: "Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations", Journal of Chemical Information and Modeling, American Chemical Society, Vol 54, Num 6, pp 1758-1772, 2014, doi:10.1021/ci500132c


T. Dwight McGee, Jesse Edwards, and Adrian E. Roitberg: "pH-REMD Simulations Indicate That the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Monoprotonated State", Journal of Physical Chemistry B, American Chemical Society, Vol 118, Num 44, pp 12577-12585, 2014, doi:10.1021/jp504011c


Lee-Ping Wang, Alexey Titov, Robert McGibbon, Fang Liu, Vijay S. Pande, and Todd J. Martinez: "Discovering Chemistry with an Ab Initio Nanoreactor", Nature Chemistry, Nature Publishing Group, Vol 6, Num 12, pp 1044-1048, 2014, doi:10.1038/nchem.2099


Ganesh Hegde, Michael Povolotskyi, Tillmann Kubis, James Charles, and Gerhard Klimeck: "An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. II. Application-Effect of quantum confinement and homogeneous strain on Cu conductance", Journal of Applied Physics, AIP Publishing, Vol 115, Num 12, pp 123704, 2014, doi:10.1063/1.4868979


Ganesh Hegde, Michael Povolotskyi, Tillmann Kubis, Timothy Boykin, and Gerhard Klimeck: "An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation", Journal of Applied Physics, AIP Publishing, Vol 115, Num 12, pp 123703, 2014, doi:10.1063/1.4868977


M. Salmani-Jelodar, S. Kim, K. Ng, and G. Klimeck: "Transistor Roadmap Projection Using Predictive Full-Band Atomistic Modeling", Applied Physics Letters, AIP Publishing, Vol 105, Num 8, pp 083508, 2014, doi:10.1063/1.4894217


Pengyu Long, Michael Povolotskyi, Bozidar Novakovic, Tillmann Kubis, Gerhard Klimeck, and Mark J. W. Rodwell: "Design and Simulation of Two-Dimensional Superlattice Steep Transistors", IEEE Electron Device Letters, Institute of Electrical & Electronics Engineers, Vol 35, Num 12, pp 1212-1214, 2014, doi:10.1109/led.2014.2364593


Yu He, Yu Wang, Gerhard Klimeck, and Tillmann Kubis: "Non-Equilibrium Green's Functions Method: Non-Trivial and Disordered Leads", Applied Physics Letters, AIP Publishing, Vol 105, Num 21, pp 213502, 2014, doi:10.1063/1.4902504


Bazavov, A. and Bernard, C. and Bouchard, C. M. and DeTar, C. and Du, Daping and El-Khadra, A. X. and Foley, J. and Freeland, E. D. and Gámiz, E. and Gottlieb, Steven and Heller, U. M. and Kim, Jongjeong and Kronfeld, A. S. and Laiho, J. and Levkova, L. and Mackenzie, P. B. and Neil, E. T. and Oktay, M. B. and Qiu, Si-Wei and Simone, J. N. and Sugar, R. and Toussaint, D. and Van de Water, R. S. and Zhou, Ran (Fermilab Lattice and MILC Collaborations): "Determination of |Vus| from a Lattice QCD Calculation of the K→πℓν Semileptonic Form Factor with Physical Quark Masses", Physical Review Letters, American Physical Society, Vol 112, Num 11, pp 112001, 2014, doi:10.1103/physrevlett.112.112001


Bazavov, A. and Bernard, C. and Komijani, J. and Bouchard, C. M. and DeTar, C. and Foley, J. and Levkova, L. and Du, D. and Laiho, J. and El-Khadra, A. X. and Freeland, E. D. and Gámiz, E. and Gottlieb, Steven and Heller, U. M. and Kim, J. and Toussaint, D. and Kronfeld, A. S. and Mackenzie, P. B. and Simone, J. N. and Van de Water, R. S. and Zhou, R. and Neil, E. T. and Sugar, R. (Fermilab Lattice and MILC Collaborations): "Charmed and Light Pseudoscalar Meson Decay Constants from Four-Flavor Lattice QCD with Physical Light Quarks", Physical Review D, American Physical Society, Vol 90, Num 7, pp 074509, 2014, doi:10.1103/physrevd.90.074509


A. Bazavov, C. Bernard, N. Brown, C. DeTar, J. Foley, S. Gottlieb, U.M. Heller, J.E. Hetrick, J. Komijani, J. Laiho, L. Levkova, M. Oktay, R.L. Sugar, D. Toussaint, R.S. Van de Water, R. Zhou: "Gradient Flow Analysis on MILC HISQ Ensembles", Proceedings of Science, Proceedings, 32nd International Symposium on Lattice Field Theory (Lattice 2014), Vol 214, pp 090, Brookhaven, New York, U.S.A., 2014, doi:10.22323/1.214.0090


A. Bazavov, C. Bernard, C. Bouchard, C. DeTar, D. Du, A.X. El-Khadra, J. Foley, E.D. Freeland, E. Gámiz, Steven Gottlieb, U.M. Heller, J. Kim, J. Komijani, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint, R.S. Van de Water, R. Zhou: "Charmed and Light Pseudoscalar Meson Decay Constants from HISQ Simulations", Proceedings of Science, Proceedings, 32nd International Symposium on Lattice Field Theory (Lattice 2014), Vol 214, pp 382, Brookhaven, New York, U.S.A., 2014, doi:10.22323/1.214.0382


Daniel Mohler, Carleton DeTar, Andreas S. Kronfeld, Song-haeng Lee, Ludmila Levkova, J. N. Simone: "Low Lying Charmonium States at the Physical Point", Proceedings of Science, Proceedings, 32nd International Symposium on Lattice Field Theory (Lattice 2014), Vol 214, pp 085, Brookhaven, New York, U.S.A., 2014, doi:10.22323/1.214.0085


F.T. Winter, M.A. Clark, R.G. Edwards, and B. Joo: "A Framework for Lattice QCD Calculations on GPUs", Institute of Electrical & Electronics Engineers, 2014 IEEE 28th International Parallel and Distributed Processing Symposium, pp 1073-1082, Phoenix, Arizona, U.S.A., 2014, doi:10.1109/ipdps.2014.112


Jozef J. Dudek, Robert G. Edwards, Christopher E. Thomas, and David J. Wilson: "Resonances in Coupled πK-ηK Scattering From Quantum Chromodynamics", Physical Review Letters, American Physical Society, Vol 113, Num 18, pp 182001, 2014, doi:10.1103/physrevlett.113.182001


Thomas Primer, Doug Toussaint, Aida El-Khadra, Elvira Gámiz, and James Simone: "Kaon and D Meson Semileptonic Form Factors from Lattice QCD", Proceedings of Science, Proceedings, 32nd International Symposium on Lattice Field Theory (Lattice 2014), Vol 214, pp 374, Brookhaven, New York, U.S.A., 2014, doi:10.22323/1.214.0374


Fan Guo, Hui Li, William Daughton, and Yi-Hsin Liu: "Formation of Hard Power Laws in the Energetic Particle Spectra Resulting from Relativistic Magnetic Reconnection", Physical Review Letters, American Physical Society, Vol 113, Num 15, pp 155005, 2014, doi:10.1103/physrevlett.113.155005


J. Jara-Almonte, W. Daughton, and H. Ji: "Debye Scale Turbulence Within the Electron Diffusion Layer During Magnetic Reconnection", Physics of Plasmas, AIP Publishing, Vol 21, Num 3, pp 032114, 2014, doi:10.1063/1.4867868


H. Karimabadi, V. Roytershteyn, H. X. Vu, Y. A. Omelchenko, J. Scudder, W. Daughton, A. Dimmock. K. Nykyri, M. Wan, D. Sibeck, M. Tatineni, A. Majumdar, B. Loring, and B. Geveci: "The link between shocks, turbulence, and magnetic reconnection in collisionless plasmas", Physics of Plasmas, AIP Publishing, Vol 21, Num 6, pp 062308, 2014, doi:10.1063/1.4882875


Homayoun Karimabadi: "Enabling Breakthrough Kinetic Simulations of the Magnetosphere", 2015 Blue Waters Annual Report, pp 18-20, 2014


W. H. Matthaeus, S. Oughton, K. T. Osman, S. Servidio, M. Wan, S. P. Gary, M. A. Shay, F. Valentini, V. Roytershteyn, H. Karimabadi, and S. C. Chapman: "Nonlinear and Linear Timescales Near Kinetic Scales in Solar Wind Turbulence", Astrophysical Journal, The American Astronomical Society, Vol 790, Num 2, pp 155, 2014, doi:10.1088/0004-637x/790/2/155


Yi-Hsin Liu, Joachim Birn, William Daughton, Michael Hesse, and Karl Schindler: "Onset of Reconnection in the Near Magnetotail: PIC Simulations", Journal of Geophysical Research: Space Physics, Wiley-Blackwell, Vol 119, Num 12, pp 9773-9789, 2014, doi:10.1002/2014ja020492


C. M. Malone, A. Nonaka, S. E. Woosley, A. S. Almgren, J. B. Bell, S. Dong, and M. Zingale: "The Deflagration Stage of Chandrasekhar Mass Models for Type Ia Supernovae. I. Early Evolution", Astrophysical Journal, The American Astronomical Society, Vol 782, Num 1, pp 11, 2014, doi:10.1088/0004-637x/782/1/11


Greg L. Bryan and Michael L. Norman and Brian W. O'Shea and Tom Abel and John H. Wise and Matthew J. Turk and Daniel R. Reynolds and David C. Collins and Peng Wang and Samuel W. Skillman and Britton Smith and Robert P. Harkness and James Bordner and Ji-hoon Kim and Michael Kuhlen and Hao Xu and Nathan Goldbaum and Cameron Hummels and Alexei G. Kritsuk and Elizabeth Tasker and Stephen Skory and Christine M. Simpson and Oliver Hahn and Jeffrey S. Oishi and Geoffrey C. So and Fen Zhao and Renyue Cen and Yuan Li and The Enzo Collaboration: "Enzo: An Adaptive Mesh Refinement Code for Astrophysics", Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 211, Num 2, pp 19, 2014, doi:10.1088/0067-0049/211/2/19


Hao Xu, Kyungjin Ahn, John H. Wise, Michael L. Norman, and Brian W. O'Shea: "Heating the Intergalactic Medium by X-Rays from Population III Binaries in High-Redshift Galaxies", Astrophysical Journal, The American Astronomical Society, Vol 791, Num 2, pp 110, 2014, doi:10.1088/0004-637x/791/2/110


Pengfei Chen, John H. Wise, Michael L. Norman, Hao Xu, and Brian W. O'Shea: "Scaling Relations for Galaxies Prior to Reionization", Astrophysical Journal, The American Astronomical Society, Vol 795, Num 2, pp 144, 2014, doi:10.1088/0004-637x/795/2/144


Danielle E. Chandler, Johan Strümpfer, Melih Sener, Simon Scheuring, and Klaus Schulten: "Light Harvesting by Lamellar Chromatophores in Rhodospirillum Photometricum", Biophysical Journal, Elsevier BV, Vol 106, Num 11, pp 2503--2510, 2014, doi:10.1016/j.bpj.2014.04.030


James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten: "Petascale Tcl with NAMD, VMD, and Swift/T", Institute of Electrical & Electronics Engineers, 2014 First Workshop for High Performance Technical Computing in Dynamic Languages, pp 6-17, New Orleans, Louisiana, U.S.A., 2014, doi:10.1109/hptcdl.2014.7


James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laxmikant V. Kale: "Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation", Institute of Electrical & Electronics Engineers, SC '14: International Conference for High Performance Computing, Networking, Storage and Analysis, pp 81-91, New Orleans, Louisiana, U.S.A., 2014, doi:10.1109/sc.2014.12


John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten: "GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting", Faraday Discussions, Royal Society of Chemistry, Vol 169, pp 265-283, 2014, doi:10.1039/c4fd00005f


Mark D. Klein and John E. Stone: "Unlocking the Full Potential of the Cray XK7 Accelerator", presented at CUG 2014, Lugano, Switzerland, 2014


Michaël L. Cartron, John D. Olsen, Melih Sener, Philip J. Jackson, Amanda A. Brindley, Pu Qian, Mark J. Dickman, Graham J. Leggett, Klaus Schulten, and C. Neil Hunter: "Integration of Energy and Electron Transfer Processes in the Photosynthetic Membrane of Rhodobacter Sphaeroides", Biochimica et Biophysica Acta (BBA) - Bioenergetics, Elsevier BV, Vol 1837, Num 10, pp 1769-1780, 2014, doi:10.1016/j.bbabio.2014.02.003


Milana Fraiberg, Oshri Afanzar, C. Keith Cassidy, Alexandra Gabashvili, Klaus Schulten, Yishai Levin, and Michael Eisenbach: "CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli", Molecular Microbiology, Wiley-Blackwell, Vol 95, Num 2, pp 231-244, 2014, doi:10.1111/mmi.12858


Ramya Gamini, Wei Han, John E. Stone, and Klaus Schulten: "Assembly of Nsp1 Nucleoporins Provides Insight Into Nuclear Pore Complex Gating", PLoS Computational Biology, Public Library of Science, Vol 10, Num 3, pp e1003488, 2014, doi:10.1371/journal.pcbi.1003488


Shanmugapriya Sothiselvam, Bo Liu, Wei Han, Haripriya Ramu, Dorota Klepacki, Gemma Catherine Atkinson, Age Brauer, Maido Remm, Tanel Tenson, Klaus Schulten, Nora Vázquez-Laslop, and Alexander S. Mankin: "Macrolide Antibiotics Allosterically Predispose the Ribosome for Translation Arrest", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 111, Num 27, pp 9804-9809, 2014, doi:10.1073/pnas.1403586111


Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, and Benoît Roux: "Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD", Computer Physics Communications, Elsevier BV, Vol 185, Num 3, pp 908-916, 2014, doi:10.1016/j.cpc.2013.12.014


Zhe Wu and Klaus Schulten: "Synaptotagmin's Role in Neurotransmitter Release Likely Involves Ca2+-induced Conformational Transition", Biophysical Journal, Elsevier BV, Vol 107, Num 5, pp 1156-1166, 2014, doi:10.1016/j.bpj.2014.07.041


Thomas Quinn: "Unified Modeling of Galaxy Populations in Clusters", 2017 Blue Waters Annual Report, pp 48-49, 2014


Sarah Loebman, Jennifer Ortiz, Lee Lee Choo, Laurel Orr, Lauren Anderson, Daniel Halperin, Magdalena Balazinska, Thomas Quinn, and Fabio Governato: "Big-Data Management Use-Case", Association for Computing Machinery, Proceedings of Workshop on Data analytics in the Cloud (DanaC'14), pp 9:1-9:4, Snowbird, Utah, U.S.A., 2014, doi:10.1145/2627770.2627774


E. J. Zirnstein, J. Heerikhuisen, G. P. Zank, N. V. Pogorelov, D. J. McComas, and M. I. Desai: "Charge-Exchange Coupling Between Pickup Ions Across the Heliopause and Its Effect on Energetic Neutral Hydrogen Flux", Astrophysical Journal, The American Astronomical Society, Vol 783, Num 2, pp 129, 2014, doi:10.1088/0004-637x/783/2/129


J. Heerikhuisen, E. J. Zirnstein, H. O. Funsten, N. V. Pogorelov, and G. P. Zank: "The Effect of New Interstellar Medium Parameters on the Heliosphere and Energetic Neutral Atoms from the Interstellar Boundary", Astrophysical Journal, The American Astronomical Society, Vol 784, Num 1, pp 73, 2014, doi:10.1088/0004-637x/784/1/73


Ming Zhang, Pingbing Zuo, and Nikolai Pogorelov: "Heliospheric Influence on the Anisotropy of TeV Cosmic Rays", Astrophysical Journal, The American Astronomical Society, Vol 790, Num 1, pp 5, 2014, doi:10.1088/0004-637x/790/1/5


N. V. Pogorelov, S. N. Borovikov, J. Heerikhuisen, T. K. Kim, G. P. Zank: "Time-dependent Processes in the Sheath between the Heliospheric Termination Shock and the Heliopause", Astronomical Society of the Pacific, ASP Conference Series: 8th International Conference of Numerical Modeling of Space Plasma Flows (ASTRONUM 2013), Vol 488, pp 167, Biarritz, France, 2014


Nikolai Pogorelov, Sergey Borovikov, Jacob Heerikhuisen, Tae Kim, Igor Kryukov, and Gary Zank: "MS-FLUKSS and Its Application to Modeling Flows of Partially Ionized Plasma in the Heliosphere", Association for Computing Machinery, XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment, Atlanta, Georgia, U.S.A., 2014, doi:10.1145/2616498.2616499


S. N. Borovikov and N. V. Pogorelov: "Voyager 1 Near the Heliopause", Astrophysical Journal Letters, The American Astronomical Society, Vol 783, Num 1, pp L16, 2014, doi:10.1088/2041-8205/783/1/l16


T. K. Kim, N. V. Pogorelov, S. N. Borovikov, B. V. Jackson, H.-S. Yu, and M. Tokumaru: "MHD Heliosphere with Boundary Conditions from a Tomographic Reconstruction Using Interplanetary Scintillation Data", Journal of Geophysical Research: Space Physics, Wiley-Blackwell, Vol 119, Num 10, pp 7981-7997, 2014, doi:10.1002/2013ja019755


Kaori Nagashima, Björn Löptien, Laurent Gizon, Aaron C. Birch, Robert Cameron, Sebastien Couvidat, Sanja Danilovic, Bernhard Fleck, and Robert Stein: "Interpreting the Helioseismic and Magnetic Imager (HMI) Multi-Height Velocity Measurements", Solar Physics, Springer Science + Business Media, Vol 289, Num 9, pp 3457-3481, 2014, doi:10.1007/s11207-014-0543-5


Robert F. Stein: "Ab Initio Models of Solar Activity", 2015 Blue Waters Annual Report, pp 32-33, 2014


Matthew Ferringer, Marc DiPrinzio, Timothy Thompson, Kyle Hanifen, and Patrick Reed: "A Framework for the Discovery of Passive-Control, Minimum Energy Satellite Constellations", American Institute of Aeronautics and Astronautics, AIAA/AAS Astrodynamics Specialist Conference, San Diego, California, U.S.A., 2014, doi:10.2514/6.2014-4158


Patrick M. Reed and David Hadka: "Evolving Many-Objective Water Management to Exploit Exascale Computing", Water Resources Research, Wiley-Blackwell, Vol 50, Num 10, pp 8367-8373, 2014, doi:10.1002/2014wr015976


Daniel Langr, Pavel Tvrdík, Tomáš Dytrych, and Jerry P. Draayer: "Algorithm 947", ACM Transactions on Mathematical Software, Association for Computing Machinery, Vol 41, Num 1, pp 1-26, 2014, doi:10.1145/2669372


G. K. Tobin, M. C. Ferriss, K. D. Launey, T. Dytrych, J. P. Draayer, A. C. Dreyfuss, and C. Bahri: "Symplectic No-Core Shell-Model Approach to Intermediate-Mass Nuclei", Physical Review C, American Physical Society, Vol 89, Num 3, pp 034312, 2014, doi:10.1103/physrevc.89.034312


K. D. Launey, A. C. Dreyfuss, J. P. Draayer, T. Dytrych, and R. Baker: "Emergence of Cluster Structures and Collectivity Within a No-Core Shell-Model Framework", IOP Publishing, Journal of Physics: Conference Series (3rd International Workshop on "State of the Art in Nuclear Cluster Physics", SOTANCP3), Vol 569, pp 012061, Yokohama, Japan, 2014, doi:10.1088/1742-6596/569/1/012061


K.D. Launey, S. Sarbadhicary, T. Dytrych, and J.P. Draayer: "Program in C for Studying Characteristic Properties of Two-Body Interactions in the Framework of Spectral Distribution Theory", Computer Physics Communications, Elsevier BV, Vol 185, Num 1, pp 254-267, 2014, doi:10.1016/j.cpc.2013.08.007


T. Dytrych, K. D. Launey, and J. P. Draayer: "Symmetry-Adapted No-Core Shell Model", McGraw-Hill Education, McGraw-Hill Yearbook of Science & Technology, 2014, doi:10.1036/1097-8542.YB140314


Y. Cai, J. Steinbuks, J. W. Elliott, and T. W. Hertel: "The Effect of Climate and Technological Uncertainty in Crop Yields on the Optimal Path of Global Land Use", The World Bank Group, Policy Research Working Paper, Vol 1, Num WPS7009, 2014


Scott J. Krieder, Justin M. Wozniak, Timothy Armstrong, Michael Wilde, Daniel S. Katz, Benjamin Grimmer, Ian T. Foster, and Ioan Raicu: "Design and Evaluation of the Gemtc Framework for GPU-Enabled Many-Task Computing", Association for Computing Machinery, Proceedings of the 23rd International Symposium on High-performance parallel and distributed computing (HPDC '14), pp 153-164, Vancouver, British Columbia, Canada, 2014, doi:10.1145/2600212.2600228


Galen Arnold, Manisha Gajbe, Seid Koric, and John Urbanic: "XSEDE OpenACC Workshop Enables Blue Waters Researchers to Accelerate Key Algorithms", Association for Computing Machinery, XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment, pp 28:1-28:6, Atlanta, Georgia, U.S.A., 2014, doi:10.1145/2616498.2616530


Seid Koric, Qiyue Lu, and Erman Guleryuz: "Evaluation of Massively Parallel Linear Sparse Solvers on Unstructured Finite Element Meshes", Computers & Structures, Elsevier BV, Vol 141, pp 19-25, 2014, doi:10.1016/j.compstruc.2014.05.009


Wen Huang, Seid Koric, Xin Yu, K. Jimmy Hsia, and Xiuling Li: "Precision Structural Engineering of Self-Rolled-Up 3D Nanomembranes Guided by Transient Quasi-Static FEM Modeling", Nano Letters, American Chemical Society, Vol 14, Num 11, pp 6293-6297, 2014, doi:10.1021/nl5026369


Milton Ruiz, Vasileios Paschalidis, and Stuart L. Shapiro: "Pulsar Spin-Down Luminosity: Simulations in General Relativity", Physical Review D, American Physical Society (APS), Vol 89, Num 8, pp 084045, 2014, doi:10.1103/physrevd.89.084045


Roman Gold, Vasileios Paschalidis, Milton Ruiz, Stuart L. Shapiro, Zachariah B. Etienne, and Harald P. Pfeiffer: "Accretion Disks Around Binary Black Holes of Unequal Mass: General Relativistic MHD Simulations of Postdecoupling and Merger", Physical Review D, American Physical Society, Vol 90, Num 10, pp 104030, 2014, doi:10.1103/physrevd.90.104030


Roman Gold, Vasileios Paschalidis, Zachariah B. Etienne, Stuart L. Shapiro, and Harald P. Pfeiffer: "Accretion Disks Around Binary Black Holes of Unequal Mass: General Relativistic Magnetohydrodynamic Simulations Near Decoupling", Physical Review D, American Physical Society, Vol 89, Num 6, pp 064060, 2014, doi:10.1103/physrevd.89.064060


Zachariah B. Etienne, John G. Baker, Vasileios Paschalidis, Bernard J. Kelly, and Stuart L. Shapiro: "Improved Moving Puncture Gauge Conditions for Compact Binary Evolutions", Physical Review D, American Physical Society, Vol 90, Num 6, pp 064032, 2014, doi:10.1103/physrevd.90.064032


C Maffeo, J Yoo, J Comer, D B Wells, B Luan, and A Aksimentiev: "Close Encounters with DNA", Journal of Physics: Condensed Matter, IOP Publishing, Vol 26, Num 41, pp 413101, 2014, doi:10.1088/0953-8984/26/41/413101


Manish Shankla and Aleksei Aksimentiev: "Conformational Transitions and Stop-and-Go Nanopore Transport of Single-Stranded DNA on Charged Graphene", Nature Communications, Nature Publishing Group, Vol 5, pp 5171, 2014, doi:10.1038/ncomms6171


Maxim Belkin, Shu-Han Chao, Gino Giannetti, and Aleksei Aksimentiev: "Modeling Thermophoretic Effects in Solid-State Nanopores", Journal of Computational Electronics, Springer Science + Business Media, Vol 13, Num 4, pp 826-838, 2014, doi:10.1007/s10825-014-0594-8


Shouvik Banerjee, James Wilson, Jiwook Shim, Manish Shankla, Elise A. Corbin, Aleksei Aksimentiev, and Rashid Bashir: "Slowing DNA Transport Using Graphene-DNA Interactions", Advanced Functional Materials, Wiley-Blackwell, Vol 25, Num 6, pp 936-946, 2014, doi:10.1002/adfm.201403719


Spencer Carson, James Wilson, Aleksei Aksimentiev, and Meni Wanunu: "Smooth DNA Transport Through a Narrowed Pore Geometry", Biophysical Journal, Elsevier BV, Vol 107, Num 10, pp 2381-2393, 2014, doi:10.1016/j.bpj.2014.10.017


Lijun Liu: "Rejuvenation of Appalachian Topography Caused by Subsidence-Induced Differential Erosion", Nature Geoscience, Nature Publishing Group, Vol 7, Num 7, pp 518-523, 2014, doi:10.1038/ngeo2187


Haihu Liu, Albert J. Valocchi, Charles Werth, Qinjun Kang, and Mart Oostrom: "Pore-Scale Simulation of Liquid CO2 Displacement of Water Using a Two-Phase Lattice Boltzmann Model", Advances in Water Resources, Elsevier BV, Vol 73, pp 144-158, 2014, doi:10.1016/j.advwatres.2014.07.010


Larry Di Girolamo: "Global Observations of Cloud Microphysics through Terra Data Fusion", 2015 Blue Waters Annual Report, pp 40-41, 2014


Andre Schleife, Erik W. Draeger, Victor M. Anisimov, Alfredo A. Correa, and Yosuke Kanai: "Quantum Dynamics Simulation of Electrons in Materials on High-Performance Computers", Computing in Science & Engineering, Institute of Electrical & Electronics Engineers, Vol 16, Num 5, pp 54-60, 2014, doi:10.1109/mcse.2014.55


Lucas K. Wagner and Peter Abbamonte: "Effect of Electron Correlation on the Electronic Structure and Spin-Lattice Coupling of High-Tc Cuprates: Quantum Monte Carlo Calculations", Physical Review B, American Physical Society, Vol 90, Num 12, 2014, doi:10.1103/physrevb.90.125129


Robert Wilhelmson: "Long-Track EF5 Tornado Simulation", 2015 Blue Waters Annual Report, pp 64-65, 2014


David Buchta, Aaron Anderson, and Jonathan B. Freund: "Near-Field Shocks Radiated by High-Speed Free-Shear-Flow Turbulence", American Institute of Aeronautics and Astronautics, 20th AIAA/CEAS Aeroacoustics Conference, Atlanta, Georgia, U.S.A., 2014, doi:10.2514/6.2014-3201


Mahmoud Moradi and Emad Tajkhorshid: "Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems", Journal of Chemical Theory and Computation, American Chemical Society, Vol 10, Num 7, pp 2866-2880, 2014, doi:10.1021/ct5002285


So Hirata: "Ice and Water", 2015 Blue Waters Annual Report, pp 142-142, 2014


So Hirata: "Ice and Water", 2016 Blue Waters Annual Report, pp 214-216, 2014


Athol Kemball: "New Techniques for Pixel-Level Fidelity Assessment in Interferometric Images", 2015 Blue Waters Annual Report, pp 90-91, 2014


Taishan Zhu and Elif Ertekin: "Phonon Transport on Two-Dimensional Graphene/boron Nitride Superlattices", Physical Review B, American Physical Society, Vol 90, Num 19, pp 195209, 2014, doi:10.1103/physrevb.90.195209


Jens Glaser, Pavani Medapuram, Thomas M. Beardsley, Mark W. Matsen, and David C. Morse: "Universality of Block Copolymer Melts", Physical Review Letters, American Physical Society, Vol 113, Num 6, pp 068302, 2014, doi:10.1103/physrevlett.113.068302


Mohammad Zaved Kaiser Khan, Rajeshwar Mehrotra, Ashish Sharma, and A. Sankarasubramanian: "Global Sea Surface Temperature Forecasts Using an Improved Multimodel Approach", Journal of Climate, American Meteorological Society, Vol 27, Num 10, pp 3505-3515, 2014, doi:10.1175/jcli-d-13-00486.1


C. D. Meyer, D. S. Balsara, B. Burkhart, and A. Lazarian: "Observational Diagnostics for Two-Fluid Turbulence in Molecular Clouds as Suggested by Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 439, Num 3, pp 2197-2210, 2014, doi:10.1093/mnras/stt1893


Jon Calhoun, Luke Olson, and Marc Snir: "FlipIt: An LLVM Based Fault Injector for HPC", Springer Science + Business Media, Lecture Notes in Computer Science: Euro-Par 2014, Parallel Processing Workshops, pp 547-558, Porto, Portugal, 2014, doi:10.1007/978-3-319-14325-5_47


Kris Beckwith, Seth Veitzer, Stephen F. McCormick, John W. Ruge, Luke N. Olson, and Jon C. Calhoun: "Fully-Implicit Ultrascale Physics Solvers and Application to Ion Source Modelling", Institute of Electrical & Electronics Engineers (IEEE), 2014 IEEE 41st International Conference on Plasma Sciences (ICOPS) held with 2014 IEEE International Conference on High-Power Particle Beams (BEAMS), pp 1-8, Washington, D.C., U.S.A., 2014, doi:10.1109/plasma.2014.7012726


Amir Barati Farimani, Kyoungmin Min, and Narayana R. Aluru: "DNA Base Detection Using a Single-Layer MoS2", ACS Nano, American Chemical Society, Vol 8, Num 8, pp 7914-7922, 2014, doi:10.1021/nn5029295


R. Sisneros: "Visualizing the Big (and Large) Data from an HPC Resource", Astronomical Society of the Pacific, ASP Conference Series: 9th Annual International Conference on Numerical Modeling of Space Plasma Flows (ASTRONUM 2014), Vol 498, pp 240, Long Beach, California, U.S.A., 2014


Anthony Agelastos, Benjamin Allan, Jim Brandt, Paul Cassella, Jeremy Enos, Joshi Fullop, Ann Gentile, Steve Monk, Nichamon Naksinehaboon, Jeff Ogden, Mahesh Rajan, Michael Showerman, Joel Stevenson, Narate Taerat, and Tom Tucker: "The Lightweight Distributed Metric Service: A Scalable Infrastructure for Continuous Monitoring of Large Scale Computing Systems and Applications", Institute of Electrical & Electronics Engineers, SC '14: International Conference for High Performance Computing, Networking, Storage and Analysis, pp 154-165, New Orleans, Louisiana, U.S.A., 2014, doi:10.1109/sc.2014.18


Jeremy Enos, Greg Bauer, Robert Brunner, Sharif Islam, Robert A. Fiedler, Michael Steed, and David Jackson: "Topology-Aware Job Scheduling Strategies for Torus Networks", presented at CUG 2014, Lugano, Switzerland, 2014, doi:10.13140/2.1.2693.6001


B. D. Semeraro, Robert Sisneros, Joshi Fullop, and Gregory H. Bauer: "It Takes a Village: Monitoring the Blue Waters Supercomputer", Institute of Electrical & Electronics Engineers, 2014 IEEE International Conference on Cluster Computing (CLUSTER), pp 392-399, Madrid, Spain, 2014, doi:10.1109/cluster.2014.6968671


Robert Sisneros, Joshi Fullop, B. David Semeraro, and Greg Bauer: "Ribbons: Enabling the Effective Use of HPC Utilization Data for System Support Staff", The Eurographics Association, EuroVis Workshop on Visual Analytics (EuroVA 2014), Swansea, Wales, U.K., 2014, doi:10.2312/eurova.20141139


R. Sisneros, K. Chadalavada: "Toward Understanding Congestion Protection Events on Blue Waters Via Visual Analytics", presented at CUG 2014, Lugano, Switzerland, 2014


J. Fullop, R. Sisneros: "A Diagnostic Utility For Analyzing Periods Of Degraded Job Performance", presented at CUG 2014, Lugano, Switzerland, 2014


Andy Loftus, Alex Parga: "Clearing the Obstacles to Backup PiB-Size Filesystems", presented at CUG 2014, Lugano, Switzerland, 2014


Celso L. Mendes, Brett Bode, Gregory H. Bauer, Jeremy Enos, Cristina Beldica, and William T. Kramer: "Deploying a Large Petascale System: The Blue Waters Experience", Elsevier BV, Procedia Computer Science (2014 International Conference on Computational Science, ICCS 2014), Vol 29, pp 198-209, Cairns, Australia, 2014, doi:10.1016/j.procs.2014.05.018


Gregory Bauer, Celso Mendes, William Kramer, and Robert Fiedler: "Expanding Blue Waters with Improved Acceleration Capability", presented at CUG 2014, Lugano, Switzerland, 2014


Anisimov, Victor M. and Bauer, Gregory H. and Chadalavada, Kalyana and Olson, Ryan M. and Glenski, Joseph W. and Kramer, William T. C. and Aprà, Edoardo and Kowalski, Karol: "Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures", Journal of Chemical Theory and Computation, American Chemical Society, Vol 10, Num 10, pp 4307-4316, 2014, doi:10.1021/ct500404c


Franck Cappello, Geist Al, William Gropp, Sanjay Kale, Bill Kramer, and Marc Snir: "Toward Exascale Resilience: 2014 Update", Supercomputing Frontiers and Innovations, FSAEIHE South Ural State University (National Research University), Vol 1, Num 1, pp 5-28, 2014, doi:10.14529/jsfi140101


Catello Di Martino, Zbigniew Kalbarczyk, Ravishankar K. Iyer, Fabio Baccanico, Joseph Fullop, and William Kramer: "Lessons Learned from the Analysis of System Failures at Petascale: The Case of Blue Waters", IEEE, 2014 44th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, pp 610-621, Atlanta, Georgia, U.S.A., 2014, doi:10.1109/dsn.2014.62


Kramer, William, Butler, Michelle, Bauer, Gregory, Chadalavada, Kalyana and Mendes, Celso: "National Center for Supercomputing Applications", Chapman and Hall/CRC, High Performance Parallel I/O, pp 17-31, 2014


Brian H. Solis and Sharon Hammes-Schiffer: "Proton-Coupled Electron Transfer in Molecular Electrocatalysis: Theoretical Methods and Design Principles", Inorganic Chemistry, American Chemical Society (ACS), Vol 53, Num 13, pp 6427--6443, 2014, doi:10.1021/ic5002896


Xu, X. L. and Hua, J. F. and Li, F. and Zhang, C. J. and Yan, L. X. and Du, Y. C. and Huang, W. H. and Chen, H. B. and Tang, C. X. and Lu, W. and Yu, P. and An, W. and Joshi, C. and Mori, W. B.: "Phase-Space Dynamics of Ionization Injection in Plasma-Based Accelerators", Physical Review Letters, American Physical Society, Vol 112, Num 3, pp 035003, 2014, doi:10.1103/PhysRevLett.112.035003


Lijun Liu: "Constraining Cretaceous Subduction Polarity in Eastern Pacific from Seismic Tomography and Geodynamic Modeling", Geophysical Research Letters, Wiley-Blackwell, Vol 41, Num 22, pp 8029-8036, 2014, doi:10.1002/2014gl061988


Paul R. Woodward, Jagan Jayaraj, and Richard Barrett: "mPPM Viewed as a Co-Design Effort", Institute of Electrical & Electronics Engineers, Proceedings of the 1st International Workshop on Hardware-Software Co-Design for High Performance Computing (Co-HPC '14), pp 33-40, New Orleans, Louisiana, U.S.A., 2014, doi:10.1109/co-hpc.2014.13


Liang, Lichen, Durier, Fabrice, Babul, Arif, Davé, Romeel, Oppenheimer, Benjamin D., Katz, Neal, Fardal, Mark, and Quinn, Tom: "The growth and enrichment of intragroup gas", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 456, Num 4, pp 4266-4290, 2014, doi:10.1093/mnras/stv2840


Viktor K. Decyk and Tajendra V. Singh: "Particle-in-Cell Algorithms for Emerging Computer Architectures", Computer Physics Communications, Elsevier BV, Vol 185, Num 3, pp 708-719, 2014, doi:10.1016/j.cpc.2013.10.013


Yingzhen Yang, Feng Liang, Shuicheng Yan, Zhangyang Wang, and Thomas S. Huang: "On a Theory of Nonparametric Pairwise Similarity for Clustering: Connecting Clustering to Classification", MIT Press, Proceedings of the 27th International Conference on Neural Information Processing Systems (NIPS '14), Vol 1, pp 145-153, Montreal, Canada, 2014, doi:10.5555/2968826.2968843


Falk Herwig, Paul R. Woodward, Pei-Hung Lin, Mike Knox, and Chris Fryer: "Global non-spherical oscillations in three-dimensional 4 pi simulations of the H-ingestion flash", Astrophysical Journal Letters, The American Astronomical Society, Vol 792, Num 1, pp L3, 2014, doi:10.1088/2041-8205/792/1/l3


Ricardo Taborda and Jacobo Bielak: "Ground‐Motion Simulation and Validation of the 2008 Chino Hills, California, Earthquake Using Different Velocity Models", Bulletin of the Seismological Society of America, Vol 104, Num 4, pp 1876-1898, 2014, doi:10.1785/0120130266


Kai J. Kohlhoff, Diwakar Shukla, Morgan Lawrenz, Gregory R. Bowman, David E. Konerding, Dan Belov, Russ B. Altman, and Vijay S. Pande: "Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways", Nature Chemistry, Springer Nature Limited, Vol 6, Num 1, pp 15-21, 2014, doi:10.1038/nchem.1821


Patricia Jacobs, Phillip List, Mobeen Ludin, Aaron Weeden, and Robert Michael Panoff: "The Blue Waters Student Internship Program: Promoting Competence and Confidence for next Generation Researchers in High-Performance Computing", Institute of Electrical & Electronics Engineers, EduHPC '14: Proceedings of the Workshop on Education for High-Performance Computing, pp 49–55, New Orleans, Louisiana, U.S.A., 2014, doi:10.1109/EduHPC.2014.6


2013

Paul R. Woodward, Jagan Jayaraj, Pei-Hung Lin, Michael Knox, Simon D. Hammond, James Greensky, and Sarah E. Anderson: "Scaling the Multifluid PPM Code on Blue Waters and Intel MIC", Institute of Electrical & Electronics Engineers, 2013 Extreme Scaling Workshop (XSW 2013), pp 64-72, Boulder, Colorado, U.S.A., 2013, doi:10.1109/xsw.2013.13


Ji-hoon Kim and Tom Abel and Oscar Agertz and Greg L. Bryan and Daniel Ceverino and Charlotte Christensen and Charlie Conroy and Avishai Dekel and Nickolay Y. Gnedin and Nathan J. Goldbaum and Javiera Guedes and Oliver Hahn and Alexander Hobbs and Philip F. Hopkins and Cameron B. Hummels and Francesca Iannuzzi and Dusan Keres and Anatoly Klypin and Andrey V. Kravtsov and Mark R. Krumholz and Michael Kuhlen and Samuel N. Leitner and Piero Madau and Lucio Mayer and Christopher E. Moody and Kentaro Nagamine and Michael L. Norman and Jose Onorbe and Brian W. O'Shea and Annalisa Pillepich and Joel R. Primack and Thomas Quinn and Justin I. Read and Brant E. Robertson and Miguel Rocha and Douglas H. Rudd and Sijing Shen and Britton D. Smith and Alexander S. Szalay and Romain Teyssier and Robert Thompson and Keita Todoroki and Matthew J. Turk and James W. Wadsley and John H. Wise and and Adi Zolotov: "The AGORA High-Resolution Galaxy Simulations Comparison Project", Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 210, Num 1, pp 14, 2013, doi:10.1088/0067-0049/210/1/14


Ludwig Oser, Manisha Gajbe, Kentaro Nagamine, Greg Bryan, Jeremiah P. Ostriker, and Renyue Cen: "Alleviating the Scaling Problem of Cosmological Hydrodynamic Simulations with HECA", Association for Computing Machinery, XSEDE '13: Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery, pp 9:1-9:4, San Diego, California, U.S.A., 2013, doi:10.1145/2484762.2484776


M. Hirschmann, T. Naab, R. Dave, B. D. Oppenheimer, J. P. Ostriker, R. S. Somerville, L. Oser, R. Genzel, L. J. Tacconi, N. M. Forster-Schreiber, A. Burkert, and S. Genel: "The Effect of Metal Enrichment and Galactic Winds on Galaxy Formation in Cosmological Zoom Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 436, Num 4, pp 2929-2949, 2013, doi:10.1093/mnras/stt1770


Renyue Cen and Zheng Zheng: "The Nature of Lyα Blobs: Powered by Extreme Starbursts", Astrophysical Journal, The American Astronomical Society, Vol 775, Num 2, pp 112, 2013, doi:10.1088/0004-637x/775/2/112


Taysun Kimm and Renyue Cen: "Heavy Dust Obscuration of Z=7 Galaxies in a Cosmological Hydrodynamic Simulation", Astrophysical Journal, The American Astronomical Society, Vol 776, Num 1, pp 35, 2013, doi:10.1088/0004-637x/776/1/35


Nakul Jindal, Victor Lotrich, Erik Deumens, and Beverly A. Sanders: "SIPMaP: A Tool for Modeling Irregular Parallel Computations in the Super Instruction Architecture", Institute of Electrical & Electronics Engineers (IEEE), 2013 IEEE 27th International Symposium on Parallel and Distributed Processing, Boston, Massachusetts, U.S.A., 2013, doi:10.1109/ipdps.2013.35


Fengjie Ma, Shiwei Zhang, and Henry Krakauer: "Excited State Calculations in Solids by Auxiliary-Field Quantum Monte Carlo", New Journal of Physics, IOP Publishing and Deutsche Physikalische Gesellschaft, Vol 15, Num 9, pp 093017, 2013, doi:10.1088/1367-2630/15/9/093017


Hao Shi and Shiwei Zhang: "Symmetry in Auxiliary-Field Quantum Monte Carlo Calculations", Physical Review B, American Physical Society, Vol 88, Num 12, 2013, doi:10.1103/physrevb.88.125132


Shiwei Zhang: "Auxiliary-Field Quantum Monte Carlo for Correlated Electron Systems", Verlag des Forschungszentrum Jülich, Emergent Phenomena in Correlated Matter Modeling and Simulation, Vol. 3 (Lecture notes of the Autumn School on Correlated Electrons 2013), Jülich, Germany, 2013


Wirawan Purwanto, Shiwei Zhang, and Henry Krakauer: "Frozen-Orbital and Downfolding Calculations with Auxiliary-Field Quantum Monte Carlo", Journal of Chemical Theory and Computation, American Chemical Society, Vol 9, Num 11, pp 4825-4833, 2013, doi:10.1021/ct4006486


Andreas Pavlogiannis, Vadim Mozhayskiy, and Ilias Tagkopoulos: "A Flood-Based Information Flow Analysis and Network Minimization Method for Gene Regulatory Networks", BMC Bioinformatics, Springer Nature, Vol 14, Num 1, pp 137, 2013, doi:10.1186/1471-2105-14-137


Vadim Mozhayskiy and Ilias Tagkopoulos: "Microbial Evolution in Vivo and in Silico: Methods and Applications", Integrative Biology, Royal Society of Chemistry, Vol 5, Num 2, pp 262-277, 2013, doi:10.1039/c2ib20095c


Jun Zhou, Yifeng Cui, Efecan Poyraz, Dong Ju Choi, and Clark C. Guest: "Multi-GPU Implementation of a 3D Finite Difference Time Domain Earthquake Code on Heterogeneous Supercomputers", Elsevier BV, Procedia Computer Science (2013 International Conference on Computational Science, ICCS 2013), Vol 18, pp 1255-1264, Barcelona, Spain, 2013, doi:10.1016/j.procs.2013.05.292


Ricardo Taborda and Jacobo Bielak: "Ground-Motion Simulation and Validation of the 2008 Chino Hills, California, Earthquake", Bulletin of the Seismological Society of America, Seismological Society of America (SSA), Vol 103, Num 1, pp 131-156, 2013, doi:10.1785/0120110325


Y. Cui, A. Chourasia, Z. Shi, S. M. Day, P. J. Maechling, T. H. Jordan, E. Poyraz, K. B. Olsen, J. Zhou, K. Withers, S. Callaghan, J. Larkin, C. Guest, and D. Choi: "Physics-Based Seismic Hazard Analysis on Petascale Heterogeneous Supercomputers", Association for Computing Machinery, SC '13: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, Denver, Colorado, U.S.A., 2013, doi:10.1145/2503210.2503300


Y. Cui, E. Poyraz, J. Zhou, S. Callaghan, P. Maechling, T.H. Jordan, L. Shih, and P. Chen: "Accelerating CyberShake Calculations on the XE6/XK7 Platform of Blue Waters", Institute of Electrical & Electronics Engineers, 2013 Extreme Scaling Workshop (XSW 2013), pp 8-17, Boulder, Colorado, U.S.A., 2013, doi:10.1109/xsw.2013.6


Zheqiang Shi, and Steven M. Day: "Rupture Dynamics and Ground Motion from 3-D Rough-Fault Simulations", Journal of Geophysical Research: Solid Earth, Wiley-Blackwell, Vol 118, Num 3, pp 1122-1141, 2013, doi:10.1002/jgrb.50094


Erik Schnetter: "Performance and Optimization Abstractions for Large Scale Heterogeneous Systems in the Cactus/Chemora Framework", Institute of Electrical & Electronics Engineers, 2013 Extreme Scaling Workshop (XSW 2013), pp 33-42, Boulder, Colorado, U.S.A., 2013, doi:10.1109/xsw.2013.9


Carlos O. Lousto, and Yosef Zlochower: "Exploring the Outer Limits of Numerical Relativity", Physical Review D, American Physical Society (APS), Vol 88, Num 2, 2013, doi:10.1103/physrevd.88.024001


Carlos O. Lousto, and Yosef Zlochower: "Nonlinear Gravitational Recoil from the Mergers of Precessing Black-Hole Binaries", Physical Review D, American Physical Society (APS), Vol 87, Num 8, 2013, doi:10.1103/physrevd.87.084027


Ian Hinder and Alessandra Buonanno and Michael Boyle and Zachariah B Etienne and James Healy and Nathan K Johnson-McDaniel and Alessandro Nagar and Hiroyuki Nakano and Yi Pan and Harald P Pfeiffer and Michael Pürrer and Christian Reisswig and Mark A Scheel and Erik Schnetter and Ulrich Sperhake and Bela Szilágyi and Wolfgang Tichy and Barry Wardell and Anıl Zenginoğlu and Daniela Alic and Sebastiano Bernuzzi and Tanja Bode and Bernd Brügmann and Luisa T Buchman and Manuela Campanelli and Tony Chu and Thibault Damour and Jason D Grigsby and Mark Hannam and Roland Haas and Daniel A Hemberger and Sascha Husa and Lawrence E Kidder and Pablo Laguna and Lionel London and Geoffrey Lovelace and Carlos O Lousto and Pedro Marronetti and Richard A Matzner and Philipp Mösta and Abdul Mroué and Doreen Müller and Bruno C Mundim and Andrea Nerozzi and Vasileios Paschalidis and Denis Pollney and George Reifenberger and Luciano Rezzolla and Stuart L Shapiro and Deirdre Shoemaker and Andrea Taracchini and Nicholas W Taylor and Saul A Teukolsky and Marcus Thierfelder and Helvi Witek and Yosef Zlochower: "Error-Analysis and Comparison to Analytical Models of Numerical Waveforms Produced by the NRAR Collaboration", Classical and Quantum Gravity, IOP Publishing, Vol 31, Num 2, pp 025012, 2013, doi:10.1088/0264-9381/31/2/025012


Miguel Zilhão and Frank Löffler: "An Introduction to the Einstein Toolkit", International Journal of Modern Physics A, World Scientific Pub Co Pte Lt, Vol 28, Num 22n23, pp 1340014, 2013, doi:10.1142/s0217751x13400149


Philipp Mösta, Bruno C Mundim, Joshua A Faber, Roland Haas, Scott C Noble, Tanja Bode, Frank Löffler, Christian D Ott, Christian Reisswig, and Erik Schnetter: "GRHydro: A New Open-Source General-Relativistic Magnetohydrodynamics Code for the Einstein Toolkit", Classical and Quantum Gravity, IOP Publishing, Vol 31, Num 1, pp 015005, 2013, doi:10.1088/0264-9381/31/1/015005


Dawei Mu, Po Chen, and Liqiang Wang: "Accelerating the Discontinuous Galerkin Method for Seismic Wave Propagation Simulations Using Multiple GPUs with CUDA and MPI", Earthquake Science, Springer Science + Business Media, Vol 26, Num 6, pp 377-393, 2013, doi:10.1007/s11589-013-0047-7


Dawei Mu, Po Chen, and Liqiang Wang: "Accelerating the Discontinuous Galerkin Method for Seismic Wave Propagation Simulations Using the Graphic Processing Unit (GPU)--Single-GPU Implementation", Computers & Geosciences, Elsevier BV, Vol 51, pp 282-292, 2013, doi:10.1016/j.cageo.2012.07.017


En-Jui Lee, He Huang, John M. Dennis, Po Chen, and Liqiang Wang: "An Optimized Parallel LSQR Algorithm for Seismic Tomography", Computers & Geosciences, Elsevier BV, Vol 61, pp 184-197, 2013, doi:10.1016/j.cageo.2013.08.013


He Huang, John M. Dennis, Liqiang Wang, and Po Chen: "A Scalable Parallel LSQR Algorithm for Solving Large-Scale Linear System for Tomographic Problems: A Case Study in Seismic Tomography", Elsevier BV, Procedia Computer Science (2013 International Conference on Computational Science, ICCS 2013), Vol 18, pp 581-590, Barcelona, Spain, 2013, doi:10.1016/j.procs.2013.05.222


James F. Dama, Anton V. Sinitskiy, Martin McCullagh, Jonathan Weare, Benoît Roux, Aaron R. Dinner, and Gregory A. Voth: "The Theory of Ultra-Coarse-Graining. 1. General Principles", Journal of Chemical Theory and Computation, American Chemical Society, Vol 9, Num 5, pp 2466-2480, 2013, doi:10.1021/ct4000444


Daniel R. Roe and Thomas E. Cheatham: "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data", Journal of Chemical Theory and Computation, American Chemical Society, Vol 9, Num 7, pp 3084-3095, 2013, doi:10.1021/ct400341p


R. A. Fonseca, J. Vieira, F. Fiuza, A. Davidson, F. S. Tsung, W. B. Mori, and L. O. Silva: "Exploiting Multi-Scale Parallelism for Large Scale Numerical Modelling of Laser Wakefield Accelerators", Plasma Physics and Controlled Fusion, IOP Publishing, Vol 55, Num 12, pp 124011, 2013, doi:10.1088/0741-3335/55/12/124011


J. E. Fonseca, T. Kubis, M. Povolotskyi, B. Novakovic, A. Ajoy, G. Hegde, H. Ilatikhameneh, Z. Jiang, P. Sengupta, Y. Tan, and G. Klimeck: "Efficient and Realistic Device Modeling from Atomic Detail to the Nanoscale", Journal of Computational Electronics, Springer Science + Business Media, Vol 12, Num 4, pp 592-600, 2013, doi:10.1007/s10825-013-0509-0


Lang Zeng, Yu He, Michael Povolotskyi, XiaoYan Liu, Gerhard Klimeck, and Tillmann Kubis: "Low Rank Approximation Method for Efficient Green's Function Calculation of Dissipative Quantum Transport", Journal of Applied Physics, AIP Publishing, Vol 113, Num 21, pp 213707, 2013, doi:10.1063/1.4809638


Parijat Sengupta, Tillmann Kubis, Yaohua Tan, Michael Povolotskyi, and Gerhard Klimeck: "Design Principles for HgTe Based Topological Insulator Devices", Journal of Applied Physics, AIP Publishing, Vol 114, Num 4, pp 043702, 2013, doi:10.1063/1.4813877


Yaohua Tan, Michael Povolotskyi, Tillmann Kubis, Yu He, Zhengping Jiang, Gerhard Klimeck, and Timothy B. Boykin: "Empirical Tight Binding Parameters for GaAs and MgO with Explicit Basis Through DFT Mapping", Journal of Computational Electronics, Springer Science + Business Media, Vol 12, Num 1, pp 56-60, 2013, doi:10.1007/s10825-013-0436-0


A. Bazavov, C. Bernard, C. Bouchard, C. DeTar, D. Du, A.X. El-Khadra, J. Foley, E.D. Freeland, E. Gamiz, Steven Gottlieb, U.M. Heller, J. Kim, J. Komijani, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint, R.S. Van de Water, R. Zhou: "Charmed and Strange Pseudoscalar Meson Decay Constants from HISQ Simulations", Proceedings of Science, Proceedings, 31st International Symposium on Lattice Field Theory (Lattice 2013), Vol 187, pp 405, Mainz, Germany, 2013, doi:10.22323/1.187.0405


A. Bazavov, C. Bernard, C. Bouchard, C. DeTar, D. Du, A.X. El-Khadra, J. Foley, E.D. Freeland, E. Gámiz, Steven Gottlieb, U.M. Heller, J. Kim, J. Komijani, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, D. Mohler, E.T. Neil, M.B. Oktay, S. Qiu, J.N. Simone, R.L. Sugar, D. Toussaint, R.S. Van de Water, R. Zhou: "The Ds, D+, Bs and B decay constants from 2+1 flavor lattice QCD", Proceedings of Science, Proceedings, 31st International Symposium on Lattice Field Theory (Lattice 2013), Vol 187, pp 394, Mainz, Germany, 2013, doi:10.22323/1.187.0394


A. Bazavov, C. Bernard, C. DeTar, J. Foley, S. Gottlieb, U. M. Heller, J. E. Hetrick, J. Laiho, L. Levkova, J. Osborn, R. Sugar, D. Toussaint, R. S. Van de Water, and R. Zhou: "Update on the 2+1+1 Flavor QCD Equation of State with HISQ", Proceedings of Science, Proceedings, 31st International Symposium on Lattice Field Theory (Lattice 2013), Vol 187, pp 154, Mainz, Germany, 2013, doi:10.22323/1.187.0154


A. Bazavov, C. Bernard, C. DeTar, J. Foley, W. Freeman, Steven Gottlieb, U. M. Heller, J. E. Hetrick, J. Kim, J. Laiho, L. Levkova, M. Lightman, J. Osborn, S. Qiu, R. L. Sugar, D. Toussaint, R. S. Van de Water, and R. Zhou: "Leptonic-Decay-Constant Ratio fK+/fπ+ from Lattice QCD with Physical Light Quarks", Physical Review Letters, American Physical Society, Vol 110, Num 17, pp 172003, 2013, doi:10.1103/physrevlett.110.172003


A. Bazavov, C. Bernard, J. Komijani, C. DeTar, L. Levkova, W. Freeman, Steven Gottlieb, Ran Zhou, U. M. Heller, J. E. Hetrick, J. Laiho, J. Osborn, R. L. Sugar, D. Toussaint, and R. S. Van de Water: "Lattice QCD Ensembles with Four Flavors of Highly Improved Staggered Quarks", Physical Review D, American Physical Society, Vol 87, Num 5, pp 054505, 2013, doi:10.1103/physrevd.87.054505


A. Bazavov, C. Bernard, N. Brown, C. DeTar, J. Foley, Steven Gottlieb, U. M. Heller, J. E. Hetrick, J. Laiho, L. Levkova, M. Oktay, R. L. Sugar, D. Toussaint, R. S. Van de Water, R. Zhou: "Symanzik Flow on HISQ Ensembles", Proceedings of Science, Proceedings, 31st International Symposium on Lattice Field Theory (Lattice 2013), Vol 187, pp 269, Mainz, Germany, 2013, doi:10.22323/1.187.0269


E. Gámiz, A. Bazavov, C. Bernard, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, Steven Gottlieb, U.M. Heller, J. Komijani, A.S. Kronfeld, J. Laiho, P.B. Mackenzie, E.T. Neil, T. Primer, J.N. Simone, R. Sugar, D. Toussaint, R.S. Van de Water, and Ran Zhou: "Kaon semileptonic form factors with Nf = 2+1+1 HISQ fermions and physical light quark masses", Proceedings of Science, Proceedings, 31st International Symposium on Lattice Field Theory (Lattice 2013), Vol 187, pp 395, Mainz, Germany, 2013, doi:10.22323/1.187.0395


Yi-Hsin Liu, W. Daughton, H. Karimabadi, H. Li, and V. Roytershteyn: "Bifurcated Structure of the Electron Diffusion Region in Three-Dimensional Magnetic Reconnection", Physical Review Letters, American Physical Society, Vol 110, Num 26, pp 265004, 2013, doi:10.1103/physrevlett.110.265004


Hao Xu, John H. Wise, and Michael L. Norman: "Population III Stars and Remnants in High-Redshift Galaxies", Astrophysical Journal, The American Astronomical Society, Vol 773, Num 2, pp 83, 2013, doi:10.1088/0004-637x/773/2/83


Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang: "Mature HIV-1 Capsid Structure by Cryo-Electron Microscopy and All-Atom Molecular Dynamics", Nature, Nature Publishing Group, Vol 497, Num 7451, pp 643--646, 2013, doi:10.1038/nature12162


John E. Stone, Barry Isralewitz, and Klaus Schulten: "Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters", Institute of Electrical & Electronics Engineers, 2013 Extreme Scaling Workshop (XSW 2013), pp 43-50, Boulder, Colorado, U.S.A., 2013, doi:10.1109/xsw.2013.10


John E. Stone, Kirby L. Vandivort, and Klaus Schulten: "GPU-Accelerated Molecular Visualization on Petascale Supercomputing Platforms", Association for Computing Machinery, Proceedings of the 8th International Workshop on Ultrascale Visualization (UltraVis '13), pp 6:1-6:8, Denver, Colorado, U.S.A., 2013, doi:10.1145/2535571.2535595


Xue Wang, Fengting Xu, Jiasen Liu, Bingquan Gao, Yanxin Liu, Yujia Zhai, Jun Ma, Kai Zhang, Timothy S. Baker, Klaus Schulten, Dong Zheng, Hai Pang, and Fei Sun: "Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography", PLOS Pathogens, Public Library of Science (PLoS), Vol 9, Num 1, pp e1003132, 2013, doi:10.1371/journal.ppat.1003132


Antonio J. Peña, Ralf G. Correa Carvalho, James Dinan, Pavan Balaji, Rajeev Thakur, and William Gropp: "Analysis of Topology-Dependent MPI Performance on Gemini Networks", Association for Computing Machinery, Proceedings of the 20th European MPI Users' Group Meeting (EuroMPI '13), pp 61-66, Madrid, Spain, 2013, doi:10.1145/2488551.2488564


Said Elghobashi: "Direct Simulation of Dispersed Liquid Droplets in Isotropic Turbulence", 2015 Blue Waters Annual Report, pp 83-83, 2013


H. Kucharek, S. A. Fuselier, P. Wurz, N. Pogorelov, S. Borovikov, M. A. Lee, E. Moebius, D. Reisenfeld, H. Funsten, N. Schwadron, and D. McComas: "The Solar Wind as a Possible Source of Fast Temporal Variations of the Heliospheric Ribbon", Astrophysical Journal, The American Astronomical Society, Vol 776, Num 2, pp 109, 2013, doi:10.1088/0004-637x/776/2/109


N. V. Pogorelov, S. N. Borovikov, M. C. Bedford, J. Heerikhuisen, T. K. Kim, I. A. Kryukov, and G. P. Zank: "Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite", Astronomical Society of the Pacific, ASP Conference Series: 7th Annual International Conference on Numerical Modeling of Space Plasma Flows (ASTRONUM 2012), Vol 474, pp 165, Big Island, Hawai'i, U.S.A., 2013


N. V. Pogorelov, S. T. Suess, S. N. Borovikov, R. W. Ebert, D. J. McComas, and G. P. Zank: "Three-Dimensional Features of the Outer Heliosphere Due to Coupling Between the Interstellar and Interplanetary Magnetic Fields; IV: Solar Cycle Model Based on Ulysses Observations", Astrophysical Journal, The American Astronomical Society, Vol 772, Num 1, pp 2, 2013, doi:10.1088/0004-637x/772/1/2


Sergey N. Borovikov, Jacob Heerikhuisen, and Nikolai V. Pogorelov: "Hybrid Parallelization of Adaptive MHD-Kinetic Module in Multi-Scale Fluid-Kinetic Simulation Suite", Astronomical Society of the Pacific, ASP Conference Series: 7th Annual International Conference on Numerical Modeling of Space Plasma Flows (ASTRONUM 2012), Vol 474, pp 219-225, Big Island, Hawai'i, U.S.A., 2013


Xi Luo, Ming Zhang, Hamid K. Rassoul, Nikolai V. Pogorelov, and Jacob Heerikhuisen: "Galactic Cosmic-Ray Modulation in a Realistic Global Magnetohydrodynamic Heliosphere", Astrophysical Journal, The American Astronomical Society, Vol 764, Num 1, pp 85, 2013, doi:10.1088/0004-637x/764/1/85


Matthew J. Woodruff, Patrick M. Reed, and Timothy W. Simpson: "Many Objective Visual Analytics: Rethinking the Design of Complex Engineered Systems", Structural and Multidisciplinary Optimization, Springer Science + Business Media, Vol 48, Num 1, pp 201-219, 2013, doi:10.1007/s00158-013-0891-z


Alison C. Dreyfuss, Kristina D. Launey, Tomáš Dytrych, Jerry P. Draayer, and Chairul Bahri: "Hoyle State and Rotational Features in Carbon-12 Within a No-Core Shell-Model Framework", Physics Letters B, Elsevier BV, Vol 727, Num 4-5, pp 511-515, 2013, doi:10.1016/j.physletb.2013.10.048


Jerry P. Draayer, Tomáš Dytrych, Kristina D. Launey, Alison C. Dreyfuss, Mia C. Ferriss, Gregory K. Tobin, Feng Pan, and Xin Guan: "Unraveling Mysteries of the Strong Interaction - 'Top Down' Versus 'Bottom Up' Considerations", Pacific Nat. U., Proceedings, International Conference on Nuclear Theory in the Supercomputing Era (NTSE-2013), pp 47, Ames, Iowa, U.S.A., 2013


K. D. Launey, A. C. Dreyfuss, T. Dytrych, J. P. Draayer, D. Langr, P. Maris, J. P. Vary, and C. Bahri: "Symmetry-Adapted Ab Initio No-Core Shell Model Calculations for 12 C", IOP Publishing, Journal of Physics: Conference Series (10th International Conference on Clustering Aspects of Nuclear Structure and Dynamics, CLUSTER '12), Vol 436, pp 012023, Debrecen, Hungary, 2013, doi:10.1088/1742-6596/436/1/012023


K. D. Launey, T. Dytrych, J. P. Draayer, G. K. Tobin, M. C. Ferriss, D. Langr, A. C. Dreyfuss, P. Maris, J. P. Vary, and C. Bahri: "Symmetry-Adapted No-Core Shell Model for Light Nuclei", World Scientific Pub Co Pte Lt, Fission and Properties of Neutron-Rich Nuclei: Proceedings of 5th International Conference on Fission and Properties of Neutron-Rich Nuclei (ICFN5), pp 29-38, Sanibel Island, Florida, U.S.A., 2013, doi:10.1142/9789814525435_0003


T. Dytrych, J. P. Draayer, K. D. Launey, P. Maris, J. P. Vary, and D. Langr: "Utilizing Symmetry Coupling Schemes in Ab Initio Nuclear Structure Calculations", Pacific Nat. U., Proceedings, International Conference on Nuclear Theory in the Supercomputing Era (NTSE-2013), pp 62, Ames, Iowa, U.S.A., 2013


T. Dytrych, K. D. Launey, J. P. Draayer, P. Maris, J. P. Vary, E. Saule, U. Catalyurek, M. Sosonkina, D. Langr, and M. A. Caprio: "Collective Modes in Light Nuclei from First Principles", Physical Review Letters, American Physical Society, Vol 111, Num 25, pp 252501, 2013, doi:10.1103/physrevlett.111.252501


JaeHyuk Kwack and Arif Masud: "A Stabilized Mixed Finite Element Method for Shear-Rate Dependent Non-Newtonian Fluids: 3D Benchmark Problems and Application to Blood Flow in Bifurcating Arteries", Computational Mechanics, Springer Science + Business Media, Vol 53, Num 4, pp 751-776, 2013, doi:10.1007/s00466-013-0928-6


Junshik Um and Greg M. McFarquhar: "Optimal Numerical Methods for Determining the Orientation Averages of Single-Scattering Properties of Atmospheric Ice Crystals", Journal of Quantitative Spectroscopy and Radiative Transfer, Elsevier BV, Vol 127, pp 207-223, 2013, doi:10.1016/j.jqsrt.2013.05.020


N. Battaglia, H. Trac, R. Cen, and A. Loeb: "Reionization on Large Scales. I. A Parametric Model Constructed from Radiation-Hydrodynamic Simulations", Astrophysical Journal, The American Astronomical Society, Vol 776, Num 2, pp 81, 2013, doi:10.1088/0004-637x/776/2/81


Mahmoud Moradi and Emad Tajkhorshid: "Mechanistic Picture for Conformational Transition of a Membrane Transporter at Atomic Resolution", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 110, Num 47, pp 18916-18921, 2013, doi:10.1073/pnas.1313202110


Soohaeng Yoo Willow, Matthew R. Hermes, Kwang S. Kim, and So Hirata: "Convergence Acceleration of Parallel Monte Carlo Second-Order Many-Body Perturbation Calculations Using Redundant Walkers", Journal of Chemical Theory and Computation, American Chemical Society, Vol 9, Num 10, pp 4396-4402, 2013, doi:10.1021/ct400557z


Dahai Guo and William Gropp: "Applications of the Streamed Storage Format for Sparse Matrix Operations", International Journal of High Performance Computing Applications, SAGE Publications, Vol 28, Num 1, pp 3-12, 2013, doi:10.1177/1094342012470469


Gengbin Zheng and Laxmikant Kale: "The Charm++ Programming Model", CRC Press, Parallel Science and Engineering Applications: The Charm++ Approach, pp 1-16, 2013, doi:10.1201/b16251-2


Matthieu Dorier, Robert Sisneros, Tom Peterka, Gabriel Antoniu, and Dave Semeraro: "Damaris/Viz: A Nonintrusive, Adaptable and User-Friendly in Situ Visualization Framework", IEEE, 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), pp 67-75, Atlanta, Georgia, U.S.A., 2013, doi:10.1109/ldav.2013.6675160


K. Chadalavada, R. Sisneros: "Analysis of the Blue Waters File System Architecture for Application I/O Performance", presented at CUG 2013, Napa Valley, California, U.S.A., 2013


Peter Johnsen, Mark Straka, Melvyn Shapiro, Alan Norton, and Thomas Galarneau: "Petascale WRF Simulation of Hurricane Sandy Deployment of NCSA's Cray XE6 Blue Waters", Association for Computing Machinery, SC '13: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, Denver, Colorado, U.S.A., 2013, doi:10.1145/2503210.2503231


Ana Gainaru, Franck Cappello, Marc Snir, and William Kramer: "Failure Prediction for HPC Systems and Applications", International Journal of High Performance Computing Applications, SAGE Publications, Vol 27, Num 3, pp 273-282, 2013, doi:10.1177/1094342013488258


Celso L. Mendes, Brett Bode, Gregory H. Bauer, Joseph R. Muggli, Cristina Beldica and William T. Kramer: "Blue Waters Acceptance: Challenges and Accomplishments", presented at CUG 2013, Napa Valley, California, U.S.A., 2013


William T. Kramer: "Sustained Performance on Blue Waters with the SPP Metric", presented at CUG 2013, Napa Valley, California, U.S.A., 2013


Weiming An, Viktor K. Decyk, Warren B. Mori, and Thomas M. Antonsen: "An Improved Iteration Loop for the Three Dimensional Quasi-Static Particle-in-Cell Algorithm: QuickPIC", Journal of Computational Physics, Elsevier BV, Vol 250, pp 165-177, 2013, doi:10.1016/j.jcp.2013.05.020


W. An, M. Zhou, N. Vafaei-Najafabadi, K. A. Marsh, C. E. Clayton, C. Joshi, W. B. Mori, W. Lu, E. Adli, S. Corde, M. Litos, S. Li, S. Gessner, J. Frederico, M. J. Hogan, D. Walz, J. England, J. P. Delahaye, and P. Muggli: "Strategies for mitigating the ionization-induced beam head erosion problem in an electron-beam-driven plasma wakefield accelerator", Physical Review Special Topics - Accelerators and Beams, American Physical Society, Vol 16, Num 10, pp 101301, 2013, doi:10.1103/physrevstab.16.101301


Brett Bode, Michelle Butler, Thom Dunning, Torsten Hoefler, William Kramer, William Gropp, and Wen-mei Hwu: "The Blue Waters Super-System for Super-Science", Taylor & Francis, Contemporary high performance computing : from petascale toward exascale, Vol 1, pp 339-366, 2013, doi:10.1201/9781351104005


Robert Gerstenberger, Maciej Besta, and Torsten Hoefler: "Enabling Highly-Scalable Remote Memory Access Programming with MPI-3 One Sided", Association for Computing Machinery, SC '13: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, Denver, Colorado, U.S.A., 2013, doi:10.1145/2503210.2503286


2012

P. R. Woodward, J. Jayaraj, P.-H. Lin, M. Knox, D. H. Porter, C. L. Fryer, G. Dimonte, C. Joggerst, G.M. Rockefeller, W. Dai, R. J. Kares, and V. A. Thomas: "Simulating Turbulent Mixing from Richtmyer-Meshkov and Rayleigh-Taylor Instabilities in Converging Geometries Using Moving Cartesian Grids", Los Alamos National Laboratory, 2012 Nuclear Explosive Code Development Conference (NECDC 2012), Num LA-UR-13-20949, Livermore, California, U.S.A., 2012


Jeongnim Kim, Kenneth P. Esler, Jeremy McMinis, Miguel A. Morales, Bryan K. Clark, Luke Shulenburger, and David M. Ceperley: "Hybrid Algorithms in Quantum Monte Carlo", IOP Publishing, Journal of Physics: Conference Series (IUPAP C20 Conference on Computational Physics, CCP 2011), Vol 402, pp 012008, Gatlinburg, Tennessee, U.S.A., 2012, doi:10.1088/1742-6596/402/1/012008


Kenneth Esler, Jeongnim Kim, David Ceperley, and Luke Shulenburger: "Accelerating Quantum Monte Carlo Simulations of Real Materials on GPU Clusters", Computing in Science & Engineering, Institute of Electrical & Electronics Engineers, Vol 14, Num 1, pp 40-51, 2012, doi:10.1109/mcse.2010.122


Pei-Hung Lin, Jagan Jayaraj, Paul Woodward, and Pen-Chung Yew: "A Study of Performance Portability Using Piecewise-Parabolic Method (PPM) Gas Dynamics Applications", Elsevier BV, Procedia Computer Science (Proceedings of the International Conference on Computational Science, ICCS 2012), Vol 9, pp 1988-1991, Omaha, Nebraska, U.S.A., 2012, doi:10.1016/j.procs.2012.04.217


Vadim Mozhayskiy and Ilias Tagkopoulos: "Guided Evolution of in Silico Microbial Populations in Complex Environments Accelerates Evolutionary Rates Through a Step-Wise Adaptation", BMC Bioinformatics, Springer Nature, Vol 13, Num Suppl 10, pp S10, 2012, doi:10.1186/1471-2105-13-s10-s10


Vadim Mozhayskiy, and Ilias Tagkopoulos: "Horizontal Gene Transfer Dynamics and Distribution of Fitness Effects During Microbial in Silico Evolution", BMC Bioinformatics, Springer Nature, Vol 13, Num Suppl 10, pp S13, 2012, doi:10.1186/1471-2105-13-s10-s13


Graham D. Fletcher, Dmitri G. Fedorov, Spencer R. Pruitt, Theresa L. Windus, and Mark S. Gordon: "Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method", Journal of Chemical Theory and Computation, American Chemical Society, Vol 8, Num 1, pp 75-79, 2012, doi:10.1021/ct200548v


Humayun Arafat, P. Sadayappan, James Dinan, Sriram Krishnamoorthy, and Theresa L. Windus: "Load Balancing of Dynamical Nucleation Theory Monte Carlo Simulations Through Resource Sharing Barriers", Institute of Electrical & Electronics Engineers, 2012 IEEE 26th International Parallel and Distributed Processing Symposium, pp 285-295, Shanghai, China, 2012, doi:10.1109/ipdps.2012.35


D. Roten, K. B. Olsen, and J. C. Pechmann: "3D Simulations of M 7 Earthquakes on the Wasatch Fault, Utah, Part II: Broadband (0-10 Hz) Ground Motions and Nonlinear Soil Behavior", Bulletin of the Seismological Society of America, Seismological Society of America (SSA), Vol 102, Num 5, pp 2008--2030, 2012, doi:10.1785/0120110286


A. Zebrowski, F. Löffler, and E. Schnetter: "The BL-Octree: An Efficient Data Structure for Discretized Block-Based Adaptive Mesh Refinement", IOS Press, Applications, Tools and Techniques on the Road to Exascale Computing (International Conference on Parallel Computing, ParCo 2011), Vol 22, pp 81-88, Ghent, Belgium, 2012, doi:10.3233/978-1-61499-041-3-81


Carlos O. Lousto, Hiroyuki Nakano, Yosef Zlochower, Bruno C. Mundim, and Manuela Campanelli: "Study of Conformally Flat Initial Data for Highly Spinning Black Holes and Their Early Evolutions", Physical Review D, American Physical Society, Vol 85, Num 12, 2012, doi:10.1103/physrevd.85.124013


Carlos O. Lousto, Yosef Zlochower, Massimo Dotti, and Marta Volonteri: "Gravitational Recoil from Accretion-Aligned Black-Hole Binaries", Physical Review D, American Physical Society, Vol 85, Num 8, 2012, doi:10.1103/physrevd.85.084015


Frank Löffler, Joshua Faber, Eloisa Bentivegna, Tanja Bode, Peter Diener, Roland Haas, Ian Hinder, Bruno C Mundim, Christian D. Ott, Erik Schnetter, Gabrielle Allen, Manuela Campanelli, and Pablo Laguna: "The Einstein Toolkit: A Community Computational Infrastructure for Relativistic Astrophysics", Classical and Quantum Gravity, IOP Publishing, Vol 29, Num 11, pp 115001, 2012, doi:10.1088/0264-9381/29/11/115001


Joshua A. Faber and Frederic A. Rasio: "Binary Neutron Star Mergers", Living Reviews in Relativity, Springer Science + Business Media, Vol 15, 2012, doi:10.12942/lrr-2012-8


P Ajith and Michael Boyle and Duncan A Brown and Bernd Brügmann and Luisa T Buchman and Laura Cadonati and Manuela Campanelli and Tony Chu and Zachariah B Etienne and Stephen Fairhurst and Mark Hannam and James Healy and Ian Hinder and Sascha Husa and Lawrence E Kidder and Badri Krishnan and Pablo Laguna and Yuk Tung Liu and Lionel London and Carlos O Lousto and Geoffrey Lovelace and Ilana MacDonald and Pedro Marronetti and Satya Mohapatra and Philipp Mösta and Doreen Müller and Bruno C Mundim and Hiroyuki Nakano and Frank Ohme and Vasileios Paschalidis and Larne Pekowsky and Denis Pollney and Harald P Pfeiffer and Marcelo Ponce and Michael Pürrer and George Reifenberger and Christian Reisswig and Lucía Santamaría and Mark A Scheel and Stuart L Shapiro and Deirdre Shoemaker and Carlos F Sopuerta and Ulrich Sperhake and Béla Szilágyi and Nicholas W Taylor and Wolfgang Tichy and Petr Tsatsin and Yosef Zlochower: "The NINJA-2 Catalog of Hybrid Post-Newtonian/numerical-Relativity Waveforms for Non-Precessing Black-Hole Binaries", Classical and Quantum Gravity, IOP Publishing, Vol 29, Num 12, pp 124001, 2012, doi:10.1088/0264-9381/29/12/124001


Scott C. Noble, Bruno C. Mundim, Hiroyuki Nakano, Julian H. Krolik, Manuela Campanelli, Yosef Zlochower, and Nicolás Yunes: "Circumbinary Magnetohydrodynamic Accretion into Inspiraling Binary Black Holes", Astrophysical Journal, The American Astronomical Society, Vol 755, Num 1, pp 51, 2012, doi:10.1088/0004-637x/755/1/51


Vitor Cardoso and Leonardo Gualtieri and Carlos Herdeiro and Ulrich Sperhake (editors) and Paul M Chesler and Luis Lehner and Seong Chan Park and Harvey S Reall and Carlos F Sopuerta (section coordinators) and Daniela Alic and Oscar J C Dias and Roberto Emparan and Valeria Ferrari and Steven B Giddings and Mahdi Godazgar and Ruth Gregory and Veronika E Hubeny and Akihiro Ishibashi and Greg Landsberg and Carlos O Lousto and David Mateos and Vicki Moeller and Hirotada Okawa and Paolo Pani and M Andy Parker and Frans Pretorius and Masaru Shibata and Hajime Sotani and Toby Wiseman and Helvi Witek and Nicolas Yunes and Miguel Zilhão: "NR/HEP: Roadmap for the Future", Classical and Quantum Gravity, IOP Publishing, Vol 29, Num 24, pp 244001, 2012, doi:10.1088/0264-9381/29/24/244001


Yosef Zlochower, Marcelo Ponce, and Carlos O. Lousto: "Accuracy Issues for Numerical Waveforms", Physical Review D, American Physical Society, Vol 86, Num 10, 2012, doi:10.1103/physrevd.86.104056


Carleton DeTar, A.S. Kronfeld, Song-Haeng Lee, L. Levkova, D. Mohler, J.N. Simone: "Charmonium Mass Splittings at the Physical Point", Proceedings of Science, Proceedings, 30th International Symposium on Lattice Field Theory (Lattice 2012), Vol 164, pp 257, Cairns, Australia, 2012, doi:10.22323/1.164.0257


R. Sisneros, C. Malone, A. Nonaka, and S. Woosley: "Investigation of Turbulence in the Early Stages of a High Resolution Supernova Simulation", Institute of Electrical & Electronics Engineers, 2012 SC Companion: High Performance Computing, Networking Storage and Analysis (SC '12), Num 1557-1558, Salt Lake City, Utah, U.S.A., 2012, doi:10.1109/sc.companion.2012.325


James Bordner, Michael L. Norman, and Brian W. O'Shea: "Enzo-P/Cello: Extreme Adaptive Mesh Refinement for Astrophysics and Cosmology", University of Illinois at Urbana-Champaign, XSEDE '12: Proceedings of the Extreme Scaling Workshop, pp 4:1-4:11, Chicago, Illinois, U.S.A., 2012, doi:10.5555/2462077.2462081


G. P. Zank, J. Heerikhuisen, B. E. Wood, N. V. Pogorelov, E. Zirnstein, and D. J. McComas: "Heliospheric Structure: The Bow Wave and the Hydrogen Wall", Astrophysical Journal, The American Astronomical Society, Vol 763, Num 1, pp 20, 2012, doi:10.1088/0004-637x/763/1/20


P. F. Hopkins: "A General Class of Lagrangian Smoothed Particle Hydrodynamics Methods and Implications for Fluid Mixing Problems", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 428, Num 4, pp 2840-2856, 2012, doi:10.1093/mnras/sts210


Aaron Anderson and Jonathan Freund: "Source Mechanisms of Jet Crackle", American Institute of Aeronautics and Astronautics (AIAA), 18th AIAA/CEAS Aeroacoustics Conference (33rd AIAA Aeroacoustics Conference), Colorado Springs, Colorado, U.S.A., 2012, doi:10.2514/6.2012-2251


Joseph Muggli, Brett Bode, Torsten Hoefler, William Kramer and Celso L. Mendes: "Blue Waters Testing Environment", presented at CUG 2012, Stuttgart, Germany, 2012


Dahai Guo and William Gropp: "Adaptive Thread Distributions for SpMV on a GPU", University of Illinois at Urbana-Champaign, XSEDE '12: Proceedings of the Extreme Scaling Workshop, pp 2:1-2:5, Chicago, Illinois, U.S.A., 2012, doi:10.5555/2462077.2462079


Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, James C. Phillips, Laximant V. Kale, and Terry R. Jones: "Optimizing Fine-Grained Communication in a Biomolecular Simulation Application on Cray XK6", IEEE, SC '12: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, pp 1-11, 2012, doi:10.1109/sc.2012.87


K. Chadalavada, M. Gajbe: "Understanding the effects of process placement on application performance on an AMD Interlagos processor", presented at CUG 2012, Stuttgart, Germany, 2012


B. O'Shea, M. Norman, B. Smith, M. Turk, M. Kuhlen, J. Wise, D. Reynolds, R. Harkness, M. Gajbe, and D. Semeraro: "Cosmology on the Blue Waters Early Science System", Institute of Electrical & Electronics Engineers (IEEE), 2012 SC Companion: High Performance Computing, Networking Storage and Analysis (SC '12), pp 1578, Salt Lake City, Utah, U.S.A., 2012, doi:10.1109/SC.Companion.2012.370


Ana Gainaru, Franck Cappello, Marc Snir, and William Kramer: "Fault Prediction Under the Microscope: A Closer Look into HPC Systems", IEEE Computer Society Press, SC '12: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, pp 77:1-77:11, Salt Lake City, Utah, U.S.A., 2012, doi:10.5555/2388996.2389101


William T. Kramer: "Top500 versus sustained performance - the top problems with the TOP500 list - and what to do about them", Institute of Electrical & Electronics Engineers, 2012 21st International Conference on Parallel Architectures and Compilation Techniques (PACT), pp 223-230, Minneapolis, Minnesota, U.S.A., 2012


Ana Gainaru, Franck Cappello, and William Kramer: "Taming of the Shrew: Modeling the Normal and Faulty Behaviour of Large-Scale HPC Systems", Institute of Electrical & Electronics Engineers, 2012 IEEE 26th International Parallel and Distributed Processing Symposium, pp 1168-1179, Shanghai, China, 2012, doi:10.1109/ipdps.2012.107


G. H. Bauer, T. Hoefler, W. T. Kramer, R. A. Fiedler: "Analyses and Modeling of Applications Used to Demonstrate Sustained Petascale Performance on Blue Waters", presented at CUG 2012, Stuttgart, Germany, 2012


Marek Blazewicz, Steven R. Brandt, Peter Diener, David M. Koppelman, Krzysztof Kurowski, Frank Löffler, Erik Schnetter, and Jian Tao: "A Massive Data Parallel Computational Framework for Petascale/Exascale Hybrid Computer Systems", IOS Press, Applications, Tools and Techniques on the Road to Exascale Computing (International Conference on Parallel Computing, ParCo 2011), Vol 22, pp 351-58, Ghent, Belgium, 2012, doi:10.3233/978-1-61499-041-3-351


William Kramer: "Blue Waters - A Super System for Super Challenges", presented at CUG 2012, Stuttgart, Germany, 2012


Matthieu Dorier, Gabriel Antoniu, Franck Cappello, Marc Snir, and Leigh Orf: "Damaris: How to Efficiently Leverage Multicore Parallelism to Achieve Scalable, Jitter-free I/O", Institute of Electrical & Electronics Engineers, 2012 IEEE International Conference on Cluster Computing, pp 155-163, Beijing, China, 2012, doi:10.1109/CLUSTER.2012.26


2011

D. C. Hambrick, J. P. Ostriker, P. H. Johansson, and T. Naab: "The Effects of X-Ray and UV Background Radiation on the Low-Mass Slope of the Galaxy Mass Function", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 413, Num 4, pp 2421-2428, 2011, doi:10.1111/j.1365-2966.2011.18312.x


D. Clay Hambrick, Jeremiah P. Ostriker, Thorsten Naab, and Peter H. Johansson: "The Effects of X-Ray Feedback from Active Galactic Nuclei on Host Galaxy Evolution", Astrophysical Journal, The American Astronomical Society, Vol 738, Num 1, pp 16, 2011, doi:10.1088/0004-637x/738/1/16


Gregory S. Novak, Jeremiah P. Ostriker, and Luca Ciotti: "Feedback from Central Black Holes in Elliptical Galaxies: Two-Dimensional Models Compared to One-Dimensional Models", Astrophysical Journal, The American Astronomical Society, Vol 737, Num 1, pp 26, 2011, doi:10.1088/0004-637x/737/1/26


Paramita Barai, Daniel Proga, and Kentaro Nagamine: "Smoothed Particle Hydrodynamics Simulations of Black Hole Accretion: A Step to Model Black Hole Feedback in Galaxies", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 418, Num 1, pp 591-611, 2011, doi:10.1111/j.1365-2966.2011.19508.x


Renyue Cen and Nora Elisa Chisari: "Star Formation Feedback and Metal Enrichment History of the Intergalactic Medium", Astrophysical Journal, The American Astronomical Society, Vol 731, Num 1, pp 11, 2011, doi:10.1088/0004-637x/731/1/11


Stephanie Tonnesen and Greg L. Bryan: "The Tail of the Stripped Gas That Cooled: HI, Halpha and X-Ray Observational Signatures of Ram Pressure Stripping", Astrophysical Journal, The American Astronomical Society, Vol 709, Num 2, pp 1203-1218, 2011, doi:10.1088/0004-637x/709/2/1203


Stephanie Tonnesen, Greg L. Bryan, and Rena Chen: "How to Light It Up: Simulating Ram-Pressure Stripped X-Ray Bright Tails", Astrophysical Journal, The American Astronomical Society, Vol 731, Num 2, pp 98, 2011, doi:10.1088/0004-637x/731/2/98


Dmitry I. Lyakh, Victor F. Lotrich, and Rodney J. Bartlett: "The `Tailored' CCSD(T) Description of the Automerization of Cyclobutadiene", Chemical Physics Letters, Elsevier BV, Vol 501, Num 4-6, pp 166-171, 2011, doi:10.1016/j.cplett.2010.11.058


Erik Deumens, Victor F. Lotrich, Ajith Perera, Mark J. Ponton, Beverly A. Sanders, and Rodney J. Bartlett: "Software Design of ACES III with the Super Instruction Architecture", Wiley Interdisciplinary Reviews: Computational Molecular Science, Wiley-Blackwell, Vol 1, Num 6, pp 895-901, 2011, doi:10.1002/wcms.77


Erik Deumens, Victor F. Lotrich, Ajith S. Perera, Rodney J. Bartlett, Nakul Jindal, and Beverly A. Sanders: "The Super Instruction Architecture", Elsevier BV, Annual Reports in Computational Chemistry, pp 179-191, 2011, doi:10.1016/b978-0-444-53835-2.00008-0


Monika Musiał, Ajith Perera, and Rodney J. Bartlett: "Multireference Coupled-Cluster Theory: The Easy Way", Journal of Chemical Physics, AIP Publishing, Vol 134, Num 11, pp 114108, 2011, doi:10.1063/1.3567115


Monika Musiał and Rodney J. Bartlett: "Charge-Transfer Separability and Size-Extensivity in the Equation-of-Motion Coupled Cluster Method: EOM-CCx", Journal of Chemical Physics, AIP Publishing, Vol 134, Num 3, pp 034106, 2011, doi:10.1063/1.3511783


Monika Musiał and Rodney J. Bartlett: "Multi-Reference Fock Space Coupled-Cluster Method in the Intermediate Hamiltonian Formulation for Potential Energy Surfaces", Journal of Chemical Physics, AIP Publishing, Vol 135, Num 4, pp 044121, 2011, doi:10.1063/1.3615500


Monika Musiał, Stanisław A. Kucharski, and Rodney J. Bartlett: "Multireference Double Electron Attached Coupled Cluster Method with Full Inclusion of the Connected Triple Excitations: MR-DA-CCSDT", Journal of Chemical Theory and Computation, American Chemical Society, Vol 7, Num 10, pp 3088-3096, 2011, doi:10.1021/ct200195q


Robert W. Molt, Thomas Watson, Victor F. Lotrich, and Rodney J. Bartlett: "RDX Geometries, Excited States, and Revised Energy Ordering of Conformers via MP2 and CCSD(T) Methodologies: Insights Into Decomposition Mechanism", Journal of Physical Chemistry A, American Chemical Society, Vol 115, Num 5, pp 884-890, 2011, doi:10.1021/jp109695v


V. Lotrich and Rodney J. Bartlett: "External Coupled-Cluster Perturbation Theory: Description and Application to Weakly Interaction Dimers. Corrections to the Random Phase Approximation", Journal of Chemical Physics, AIP Publishing, Vol 134, Num 18, pp 184108, 2011, doi:10.1063/1.3570573


Falk Herwig, Marco Pignatari, Paul R. Woodward, David H. Porter, Gabriel Rockefeller, Chris L. Fryer, Michael Bennett, and Raphael Hirschi: "Convective-Reactive Proton-C12 Combustion in Sakurai's Object (V4334 Sagittarii) and Implications for the Evolution and Yields from the First Generations of Stars", Astrophysical Journal, The American Astronomical Society, Vol 727, Num 2, pp 89, 2011, doi:10.1088/0004-637x/727/2/89


Pei-Hung Lin, Jagan Jayaraj, and Paul R. Woodward: "A Study of the Performance of Multifluid PPM Gas Dynamics on CPUs and GPUs", Institute of Electrical & Electronics Engineers, 2011 Symposium on Application Accelerators in High-Performance Computing, pp 42-51, Knoxville, Tennessee, U.S.A., 2011, doi:10.1109/saahpc.2011.27


Vadim Mozhayskiy and Ilias Tagkopoulos: "In Silico Evolution of Multi-Scale Microbial Systems in the Presence of Mobile Genetic Elements and Horizontal Gene Transfer", Springer Science + Business Media, Bioinformatics Research and Applications, Vol 7th International Symposium on Bioinformatics Research and Applications (ISBRA 2011), pp 262-273, Changsha, China, 2011, doi:10.1007/978-3-642-21260-4_26


Vadim Mozhayskiy, Bob Miller, Kwan-Liu Ma, and Ilias Tagkopoulos: "A Scalable Multi-Scale Framework for Parallel Simulation and Visualization of Microbial Evolution", Association for Computing Machinery, Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery (TG '11), pp 7:1-7:8, Salt Lake City, Utah, U.S.A., 2011, doi:10.1145/2016741.2016749


Alex B. Nielsen, Michael Jasiulek, Badri Krishnan, and Erik Schnetter: "Slicing Dependence of Nonspherically Symmetric Quasilocal Horizons in Vaidya Spacetimes", Physical Review D, American Physical Society, Vol 83, Num 12, pp 124022, 2011, doi:10.1103/physrevd.83.124022


C. D. Ott, C. Reisswig, E. Schnetter, E. O'Connor, U. Sperhake, F. Löffler,, P. Diener, E. Abdikamalov, I. Hawke, and A. Burrows: "Dynamics and Gravitational Wave Signature of Collapsar Formation", Physical Review Letters, American Physical Society, Vol 106, Num 16, pp 161103, 2011, doi:10.1103/physrevlett.106.161103


C. Reisswig, C. D. Ott, U. Sperhake, and E. Schnetter: "Gravitational Wave Extraction in Simulations of Rotating Stellar Core Collapse", Physical Review D, American Physical Society (APS), Vol 83, Num 6, pp 064008, 2011, doi:10.1103/physrevd.83.064008


Evan O'Connor and Christian D. Ott: "Black Hole Formation in Failing Core-Collapse Supernovae", Astrophysical Journal, The American Astronomical Society, Vol 730, Num 2, pp 70, 2011, doi:10.1088/0004-637x/730/2/70


Ian Vega, Barry Wardell, and Peter Diener: "Effective Source Approach to Self-Force Calculations", Classical and Quantum Gravity, IOP Publishing, Vol 28, Num 13, pp 134010, 2011, doi:10.1088/0264-9381/28/13/134010


Oleg Korobkin, Ernazar B. Abdikamalov, Erik Schnetter, Nikolaos Stergioulas, and Burkhard Zink: "Stability of General-Relativistic Accretion Disks", Physical Review D, American Physical Society, Vol 83, Num 4, pp 043007, 2011, doi:10.1103/physrevd.83.043007


Timothy D. Brandt, Adam Burrows, Christian D. Ott, and Eli Livne: "Results from Core-Collapse Simulations with Multi-Dimensional, Multi-Angle Neutrino Transport", Astrophysical Journal, The American Astronomical Society, Vol 728, Num 1, pp 8, 2011, doi:10.1088/0004-637x/728/1/8


Bruno C Mundim, Bernard J Kelly, Yosef Zlochower, Hiroyuki Nakano, and Manuela Campanelli: "Hybrid Black-Hole Binary Initial Data", Classical and Quantum Gravity, IOP Publishing, Vol 28, Num 13, pp 134003, 2011, doi:10.1088/0264-9381/28/13/134003


Carlos O. Lousto and Yosef Zlochower: "Hangup Kicks: Still Larger Recoils by Partial Spin-Orbit Alignment of Black-Hole Binaries", Physical Review Letters, American Physical Society, Vol 107, Num 23, pp 231102, 2011, doi:10.1103/physrevlett.107.231102


Carlos O. Lousto and Yosef Zlochower: "Modeling Maximum Astrophysical Gravitational Recoil Velocities", Physical Review D, American Physical Society, Vol 83, Num 2, pp 024003, 2011, doi:10.1103/physrevd.83.024003


Carlos O. Lousto and Yosef Zlochower: "Orbital Evolution of Extreme-Mass-Ratio Black-Hole Binaries with Numerical Relativity", Physical Review Letters, American Physical Society, Vol 106, Num 4, pp 041101, 2011, doi:10.1103/physrevlett.106.041101


Hiroyuki Nakano, Manuela Campanelli, Carlos O Lousto, and Yosef Zlochower: "Perturbative Effects of Spinning Black Holes in the Extreme Mass-Ratio Limit", Classical and Quantum Gravity, IOP Publishing, Vol 28, Num 13, pp 134005, 2011, doi:10.1088/0264-9381/28/13/134005


Hiroyuki Nakano, Yosef Zlochower, Carlos O. Lousto, and Manuela Campanelli: "Intermediate-Mass-Ratio Black Hole Binaries. II. Modeling Trajectories and Gravitational Waveforms", Physical Review D, American Physical Society, Vol 84, Num 12, pp 124006, 2011, doi:10.1103/physrevd.84.124006


M. C. Babiuc, J. Winicour, and Y. Zlochower: "Binary Black Hole Waveform Extraction at Null Infinity", Classical and Quantum Gravity, IOP Publishing, Vol 28, Num 13, pp 134006, 2011, doi:10.1088/0264-9381/28/13/134006


M. C. Babiuc, B. Szilágyi, J. Winicour, and Y. Zlochower: "Characteristic Extraction Tool for Gravitational Waveforms", Physical Review D, American Physical Society, Vol 84, Num 4, pp 044057, 2011, doi:10.1103/physrevd.84.044057


Marcelo Ponce, Carlos Lousto, and Yosef Zlochower: "Seeking for Toroidal Event Horizons from Initially Stationary BH Configurations", Classical and Quantum Gravity, IOP Publishing, Vol 28, Num 14, pp 145027, 2011, doi:10.1088/0264-9381/28/14/145027


Marcelo Ponce, Joshua A. Faber, and James C. Lombardi: "Accretion Disks Around Kicked Black Holes: Post-Kick Dynamics", Astrophysical Journal, The American Astronomical Society, Vol 745, Num 1, pp 71, 2011, doi:10.1088/0004-637x/745/1/71


Yosef Zlochower, Manuela Campanelli, and Carlos O Lousto: "Modeling Gravitational Recoil from Black-Hole Binaries Using Numerical Relativity", Classical and Quantum Gravity, IOP Publishing, Vol 28, Num 11, pp 114015, 2011, doi:10.1088/0264-9381/28/11/114015


En-Jui Lee, Po Chen, Thomas H. Jordan, and Liqiang Wang: "Rapid Full-Wave Centroid Moment Tensor (CMT) Inversion in a Three-Dimensional Earth Structure Model for Earthquakes in Southern California", Geophysical Journal International, Oxford University Press, Vol 186, Num 1, pp 311-330, 2011, doi:10.1111/j.1365-246x.2011.05031.x


Mikhail Smelyanskiy, Karthikeyan Vaidyanathan, Jee Choi, Bálint Joó, Jatin Chhugani, Michael A. Clark, and Pradeep Dubey: "High-Performance Lattice QCD for Multi-Core Based Parallel Systems Using a Cache-Friendly Hybrid Threaded-MPI Approach", Association for Computing Machinery, SC '11: Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis, pp 69:1-69:11, Seattle, Washington, U.S.A., 2011, doi:10.1145/2063384.2063477


R. Babich, M. A. Clark, B. Joó, G. Shi, R. C. Brower, and S. Gottlieb: "Scaling Lattice QCD Beyond 100 GPUs", Association for Computing Machinery, SC '11: Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis, pp 70:1-170:11, Seattle, Washington, U.S.A., 2011, doi:10.1145/2063384.2063478


Ron Babich, Richard Brower, Mike Clark, Steven Gottlieb, Balint Joo, and Guochun Shi: "Progress on the QUDA Code Suite", Proceedings of Science, 29th International Symposium on Lattice Field Theory (Lattice 2011), Vol 139, pp 033, Lake Tahoe, California, U.S.A., 2011, doi:10.22323/1.139.0033


H. Karimabadi, J. Dorelli, H. X. Vu, B. Loring, Y. Omelchenko, Dimitris Vassiliadis, Shing F. Fung, Xi Shao, Ioannis A. Daglis, and Joseph D. Huba: "Is Quadrupole Structure of Out-of-Plane Magnetic Field Evidence for Hall Reconnection?", AIP Publishing, AIP Conference Proceedings (Modern Challenges in Nonlinear Plasma Physics: A Festschrift Honoring the Career of Dennis Papadopoulos), Vol 1320, pp 137-143, Halkidiki, Greece, 2011, doi:10.1063/1.3544318


H. Karimabadi, J. Dorelli, V. Roytershteyn, W. Daughton, and L. Chacón: "Flux Pileup in Collisionless Magnetic Reconnection: Bursty Interaction of Large Flux Ropes", Physical Review Letters, American Physical Society, Vol 107, Num 2, pp 025002, 2011, doi:10.1103/physrevlett.107.025002


H. Karimabadi, V. Roytershteyn, C.G. Mouikis, L.M. Kistler, and W. Daughton: "Flushing Effect in Reconnection: Effects of Minority Species of Oxygen Ions", Planetary and Space Science, Elsevier BV, Vol 59, Num 7, pp 526-536, 2011, doi:10.1016/j.pss.2010.07.014


William Kramer: "How to Measure Useful, Sustained Performance", ACM Press, SC '11: State of the Practice Reports, pp 2:1-2:18, Seattle, Washington, U.S.A., 2011, doi:10.1145/2063348.2063351


Eric Heien, Derrick Kondo, Ana Gainaru, Dan LaPine, Bill Kramer, and Franck Cappello: "Modeling and Tolerating Heterogeneous Failures in Large Parallel Systems", ACM Press, SC '11: Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis, pp 45:1-45:11, Seattle, Washington, U.S.A., 2011, doi:10.1145/2063384.2063444


Ana Gainaru, Franck Cappello, Joshi Fullop, Stefan Trausan-Matu, and William Kramer: "Adaptive Event Prediction Strategy with Dynamic Time Window for Large-Scale HPC Systems", ACM Press, Managing Large-scale Systems via the Analysis of System Logs and the Application of Machine Learning Techniques (SLAML '11), pp 4:1-4:8, Cascais, Portugal, 2011, doi:10.1145/2038633.2038637


Ana Gainaru, Franck Cappello, Stefan Trausan-Matu, and Bill Kramer: "Event Log Mining Tool for Large Scale HPC Systems", Springer Berlin Heidelberg, Lecture Notes in Computer Science: Euro-Par 2011 Parallel Processing (17th International Conference), pp 52-64, Bordeaux, France, 2011, doi:10.1007/978-3-642-23400-2_6


Jack Dongarra, Pete Beckman, Terry Moore, Patrick Aerts, Giovanni Aloisio, Jean-Claude Andre, David Barkai, Jean-Yves Berthou, Taisuke Boku, Bertrand Braunschweig, Franck Cappello, Barbara Chapman, Xuebin Chi, Alok Choudhary, Sudip Dosanjh, Thom Dunning, Sandro Fiore, Al Geist, Bill Gropp, Robert Harrison, Mark Hereld, Michael Heroux, Adolfy Hoisie, Koh Hotta, Zhong Jin, Yutaka Ishikawa, Fred Johnson, Sanjay Kale, Richard Kenway, David Keyes, Bill Kramer, Jesus Labarta, Alain Lichnewsky, Thomas Lippert, Bob Lucas, Barney Maccabe, Satoshi Matsuoka, Paul Messina, Peter Michielse, Bernd Mohr, Matthias S. Mueller, Wolfgang E. Nagel, Hiroshi Nakashima, Michael E Papka, Dan Reed, Mitsuhisa Sato, Ed Seidel, John Shalf, David Skinner, Marc Snir, Thomas Sterling, Rick Stevens, Fred Streitz, Bob Sugar, Shinji Sumimoto, William Tang, John Taylor, Rajeev Thakur, Anne Trefethen, Mateo Valero, Aad van der Steen, Jeffrey Vetter, Peg Williams, Robert Wisniewski, and Kathy Yelick: "The International Exascale Software Project Roadmap", International Journal of High Performance Computing Applications, SAGE Publications, Vol 25, Num 1, pp 3-60, 2011, doi:10.1177/1094342010391989


2010

Hidenobu Yajima, Jun-Hwan Choi, and Kentaro Nagamine: "Escape Fraction of Ionizing Photons from High-Redshift Galaxies in Cosmological SPH Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 412, Num 1, pp 411-422, 2010, doi:10.1111/j.1365-2966.2010.17920.x


Jeremiah P. Ostriker, Ena Choi, Luca Ciotti, Gregory S. Novak, and Daniel Proga: "Momentum Driving: Which Physical Processes Dominate Active Galactic Nucleus Feedback?", Astrophysical Journal, The American Astronomical Society, Vol 722, Num 1, pp 642-652, 2010, doi:10.1088/0004-637x/722/1/642


Jun-Hwan Choi and Kentaro Nagamine: "Effects of Cosmological Parameters and Star Formation Models on the Cosmic Star Formation History in Lambda CDM Cosmological Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 407, Num 3, pp 1464-1476, 2010, doi:10.1111/j.1365-2966.2010.17029.x


Jun-Hwan Choi and Kentaro Nagamine: "Multicomponent and Variable Velocity Galactic Outflow in Cosmological Hydrodynamic Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 410, Num 4, pp 2579-2592, 2010, doi:10.1111/j.1365-2966.2010.17632.x


Kentaro Nagamine, Jun-Hwan Choi, and Hidenobu Yajima: "Effects of Ultraviolet Background and Local Stellar Radiation on the H I Column Density Distribution", Astrophysical Journal Letters, The American Astronomical Society, Vol 725, Num 2, pp L219-L222, 2010, doi:10.1088/2041-8205/725/2/l219


Luca Ciotti, Jeremiah P. Ostriker, and Daniel Proga: "Feedback from Central Black Holes in Elliptical Galaxies. III: Models with Both Radiative and Mechanical Feedback", Astrophysical Journal, The American Astronomical Society, Vol 717, Num 2, pp 708-723, 2010, doi:10.1088/0004-637x/717/2/708


Ludwig Oser, Jeremiah P. Ostriker, Thorsten Naab, Peter H. Johansson, and Andreas Burkert: "The Two Phases of Galaxy Formation", Astrophysical Journal, The American Astronomical Society, Vol 725, Num 2, pp 2312-2323, 2010, doi:10.1088/0004-637x/725/2/2312


Min-Su Shin, Jeremiah P. Ostriker, and Luca Ciotti: "Feedback from Central Black Holes in Elliptical Galaxies. II: Can Purely Mechanical Energy Feedback Models Work?", Astrophysical Journal, The American Astronomical Society, Vol 711, Num 1, pp 268-283, 2010, doi:10.1088/0004-637x/711/1/268


Beverly A. Sanders, Rod Bartlett, Erik Deumens, Victor Lotrich, and Mark Ponton: "A Block-Oriented Language and Runtime System for Tensor Algebra with Very Large Arrays", Institute of Electrical & Electronics Engineers, SC '10: Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, New Orleans, Louisiana, U.S.A., 2010, doi:10.1109/sc.2010.3


Dmitry I. Lyakh and Rodney J. Bartlett: "An Adaptive Coupled-Cluster Theory: @CC Approach", Journal of Chemical Physics, AIP Publishing, Vol 133, Num 24, pp 244112, 2010, doi:10.1063/1.3515476


V. F. Lotrich, J. M. Ponton, A. S. Perera, E. Deumens, R. J. Bartlett, and B. A. Sanders: "Super Instruction Architecture of Petascale Electronic Structure Software: The Story", Molecular Physics, Informa UK Limited, Vol 108, Num 21-23, pp 3323-3330, 2010, doi:10.1080/00268976.2010.512566


P. R. Woodward, D. H. Porter, W. Dai, T. Fuchs, T. Nowatzki, M. Knox, G. Dimonte, F. Herwig, and C. Freyer: "The Piecewise-Parabolic Boltzmann Advection Scheme (PPB) Applied to Multifluid Hydrodynamics", United States Department of Energy (Los Alamos National Laboratory), Los Alamos National Laboratory report, Num LA-UR-10-01823, 2010


Paul Woodward, P.-H. Lin, G. M. Rockefeller, C. L. Fryer, G. Dimonte, W. Dai, and R. J. Kares: "Simulating Rayleigh-Taylor (RT) Instability Using PPM Hydrodynamics at Scale on Roadrunner", Los Alamos National Laboratory, 2010 Nuclear Explosive Code Development Conference (NECDC 2010), Num LA-UR-11-00061, Los Alamos, New Mexico, U.S.A., 2010


Cristiana Stan, Marat Khairoutdinov, Charlotte A. DeMott, V. Krishnamurthy, David M. Straus, David A. Randall, James L. Kinter, and J. Shukla: "An Ocean-Atmosphere Climate Simulation with an Embedded Cloud Resolving Model", Geophysical Research Letters, Wiley-Blackwell, Vol 37, Num 1, 2010, doi:10.1029/2009gl040822


Christian Reisswig: "Binary Black Hole Mergers and Novel Approaches to Gravitational Wave Extraction in Numerical Relativity", Leibniz Universität Hannover, Institutional Repository of Leibniz Universität Hannover, Vol Doctoral dissertation, 2010, doi:10.15488/7496


J. Nordhaus, T. D. Brandt, A. Burrows, E. Livne, and C. D. Ott: "Theoretical Support for the Hydrodynamic Mechanism of Pulsar Kicks", Physical Review D, American Physical Society (APS), Vol 82, Num 10, pp 103016, 2010, doi:10.1103/physrevd.82.103016


Leonid Oliker, Jonathan Carter, Vincent Beckner, John Bell, Harvey Wasserman, Mark Adams, Stéphane Ethier, and Erik Schnetter: "Large-Scale Numerical Simulations on High-End Computational Platforms", CRC Press, Performance Tuning of Scientific Applications, pp 123-150, 2010, doi:10.1201/b10509-7


Oleg Korobkin: "Non-axisymmetric Instabilities in Self-Gravitating Tori around Black Holes, and Solving Einstein Constraints with Superconvergent Finite Element Methods", Louisiana State University, LSU Digital Commons, Vol Doctoral dissertations, 2010


Carlos O. Lousto, Hiroyuki Nakano, Yosef Zlochower, and Manuela Campanelli: "Intermediate-Mass-Ratio Black Hole Binaries: Intertwining Numerical and Perturbative Techniques", Physical Review D, American Physical Society (APS), Vol 82, Num 10, 2010, doi:10.1103/physrevd.82.104057


Carlos O. Lousto, Hiroyuki Nakano, Yosef Zlochower, and Manuela Campanelli: "Intermediate-Mass-Ratio Black-Hole Binaries: Numerical Relativity Meets Perturbation Theory", Physical Review Letters, American Physical Society (APS), Vol 104, Num 21, 2010, doi:10.1103/physrevlett.104.211101


Carlos O. Lousto, Hiroyuki Nakano, Yosef Zlochower, and Manuela Campanelli: "Statistical Studies of Spinning Black-Hole Binaries", Physical Review D, American Physical Society (APS), Vol 81, Num 8, 2010, doi:10.1103/physrevd.81.084023


Steven Gottlieb, Guochun Shi, Aaron Torok, and Volodymyr Kindratenko: "QUDA Programming for Staggered Quarks", Proceedings of Science, Proceedings, 28th International Symposium on Lattice Field Theory (Lattice 2010), Vol 105, pp 026, Villasimius, Italy, 2010, doi:10.22323/1.105.0026


H. Karimabadi, B. Loring, H. X. Vu, Y. Omelchenko, M. Tatineni, A. Majumdar, U. Ayachit and B. Geveci: "Petascale Global Kinetic Simulations of The Magnetosphere and Visualization Strategies for Analysis of Very Large Multi-Variate Data Sets", Astronomical Society of the Pacific, ASP Conference Series: 5th international conference of numerical modeling of space plasma flows (ASTRONUM 2010), Vol 444, pp 281, San Diego, California, U.S.A., 2010


Matthew J. Turk, Britton D. Smith, Jeffrey S. Oishi, Stephen Skory, Samuel W. Skillman, Tom Abel, and Michael L. Norman: "Yt: A Multi-Code Analysis Toolkit for Astrophysical Simulation Data", Astrophysical Journal Supplement Series, American Astronomical Society, Vol 192, Num 1, pp 9, 2010, doi:10.1088/0067-0049/192/1/9


D. Guo and W. Gropp: "Optimizing Sparse Data Structures for Matrix-Vector Multiply", International Journal of High Performance Computing Applications, SAGE Publications, Vol 25, Num 1, pp 115-131, 2010, doi:10.1177/1094342010374847


2009

M. Ryan Joung, Renyue Cen, and Greg L. Bryan: "Galaxy Size Problem at z=3: Simulated Galaxies Are Too Small", Astrophysical Journal Letters, The American Astronomical Society, Vol 692, Num 1, pp L1-L4, 2009, doi:10.1088/0004-637x/692/1/l1


Tomasz Kuś, Victor F. Lotrich, and Rodney J. Bartlett: "Parallel Implementation of the Equation-of-Motion Coupled-Cluster Singles and Doubles Method and Application for Radical Adducts of Cytosine", Journal of Chemical Physics, AIP Publishing, Vol 130, Num 12, pp 124122, 2009, doi:10.1063/1.3091293


Paul R. Woodward, Jagan Jayaraj, Pei-Hung Lin, and William Dai: "First Experience of Compressible Gas Dynamics Simulation on the Los Alamos Roadrunner Machine", Concurrency and Computation: Practice and Experience, Wiley-Blackwell, Vol 21, Num 17, pp 2160-2175, 2009, doi:10.1002/cpe.1494


Franck Cappello, Al Geist, Bill Gropp, Laxmikant Kale, Bill Kramer, and Marc Snir: "Toward Exascale Resilience", International Journal of High Performance Computing Applications, SAGE Publications, Vol 23, Num 4, pp 374-388, 2009, doi:10.1177/1094342009347767