Publications

PRAC Teams

Bartlett

  • Nakul Jindal, Victor Lotrich, Erik Deumens, and Beverly A. Sanders. "Exploiting GPUs with the Super Instruction Architecture", Int J Parallel Prog, Vol. 44(2): 309--324, 2014, doi:10.1007/s10766-014-0319-4
  • Nakul Jindal, Victor Lotrich, Erik Deumens, and Beverly A. Sanders. "SIPMaP: A Tool for Modeling Irregular Parallel Computations in the Super Instruction Architecture", 2013 IEEE 27th International Symposium on Parallel and Distributed Processing, Boston, MA, 2013, doi:10.1109/ipdps.2013.35
  • Robert W Molt, Victor Lotrich, and Rodney J. Bartlett. "Relative energies of cytochrome p450 intermediates using coupled cluster many-body methodologies", 2014, submitted
  • Robert W Molt, Victor Lotrich, and Rodney J. Bartlett. "The Mechanism of RDX Decomposition Using CCSD(T)", 2014, submitted

Bernholc

  • Rui Dong, V. Ranjan, Marco Buongiorno Nardelli, and J. Bernholc. "Atomistic Simulations of Aromatic Polyurea and Polyamide for Capacitive Energy Storage", Phys. Rev. B, Vol. 92(2), 2015, doi:10.1103/physrevb.92.024203
  • Yan Li, Miroslav Hodak, and J. Bernholc. "Enzymatic Mechanism of Copper-Containing Nitrite Reductase", Biochemistry, Vol. 54(5): 1233--1242, 2015, doi:10.1021/bi5007767
  • Yash Thakur, et al. "Optimizing Nanostructure to Achieve High Dielectric Response with Low Loss in Strongly Dipolar Polymers", Nano Energy, Vol. 16, 2015, doi:10.1016/j.nanoen.2015.06.021
  • E. Briggs, et al. "Petascale Electronic Structure Code with a New Parallel Eigensolver", APS March Meeting 2015, abstract #G23.007, 2015, url: http://adsabs.harvard.edu/abs/2015APS..MARG23007B
  • E. Briggs, W. Lu, M. Hodak, and J. Bernholc. "Electronic structure calculations on Thousands of CPU's and GPU's", The Twenty-Fifth Annual Workshop on Recent Developments in Electronic Structure Methods, Williamsburg, VA, 2013, url: http://es13.wm.edu/sfs/Briggs.pdf
  • E.L. Briggs, C.T. Kelley, and J. Bernholc. "Parallel Implementation of Electronic Structure Eigensolver Using a Partitioned Folded Spectrum Method", submitted

Bisset

  • Lukasz Wesolowski, et al. "TRAM: Optimizing Fine-Grained Communication with Topological Routing and Aggregation of Messages", 2014 43rd International Conference on Parallel Processing, Minneapolis, MN, 2014, doi:10.1109/icpp.2014.30

Burrows

  • Joshua Wallace, Adam Burrows, and Joshua C. Dolence. "Detecting the Supernova Breakout Burst in Terrestrial Neutrino Detectors", ApJ, Vol. 817(2): 182, 2016, doi:10.3847/0004-637x/817/2/182

Campanelli

  • 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", ApJ, Vol. 804(2): 85, 2015, doi:10.1088/0004-637x/804/2/85
  • 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, Vol. 91(2), 2015, doi:10.1103/physrevd.91.024034
  • Bruno C. Mundim, et al. "Approximate Black Hole Binary Spacetime via Asymptotic Matching", Physical Review D, Vol. 89(8), 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, Vol. 89(10), 2014, doi:10.1103/physrevd.89.104052
  • Miguel Zilhão, and Scott C Noble. "Dynamic Fisheye Grids for Binary Black Hole Simulations", Class. Quantum Grav., Vol. 31(6): 065013, 2014, doi:10.1088/0264-9381/31/6/065013
  • J Aasi, et al. "The NINJA-2 Project: Detecting and Characterizing Gravitational Waveforms Modelled Using Numerical Binary Black Hole Simulations", Class. Quantum Grav., Vol. 31(11): 115004, 2014, doi:10.1088/0264-9381/31/11/115004
  • Carlos O. Lousto, and Yosef Zlochower. "Where Angular Momentum Goes in a Precessing Black-Hole Binary", Physical Review D, Vol. 89(2), 2014, doi:10.1103/physrevd.89.021501
  • Miguel Zilhão, Frank Löffler. "An Introduction to the Einstein Toolkit", International Journal of Modern Physics A, Vol. 28(22n23): 1340014, 2013, doi:10.1142/s0217751x13400149
  • Ian Hinder, et al. "Error-Analysis and Comparison to Analytical Models of Numerical Waveforms Produced by the NRAR Collaboration", Class. Quantum Grav., Vol. 31(2): 025012, 2013, doi:10.1088/0264-9381/31/2/025012
  • Carlos O. Lousto, and Yosef Zlochower. "Exploring the Outer Limits of Numerical Relativity", Physical Review D, Vol. 88(2), 2013, doi:10.1103/physrevd.88.024001
  • Philipp Mösta, et al. "GRHydro: A New Open-Source General-Relativistic Magnetohydrodynamics Code for the Einstein Toolkit", Class. Quantum Grav., Vol. 31(1): 015005, 2013, doi:10.1088/0264-9381/31/1/015005
  • Carlos O. Lousto, and Yosef Zlochower. "Nonlinear Gravitational Recoil from the Mergers of Precessing Black-Hole Binaries", Physical Review D, Vol. 87(8), 2013, doi:10.1103/physrevd.87.084027
  • Yosef Zlochower, et al. "Inspiraling Black-Hole Binary Spacetimes: Transitioning from Analytical to Numerical Techniques", 2015, submitted

Cheatham

  • Rodrigo Galindo-Murillo, et al. "Assessing the Current State of Amber Force Field Modifications for DNA", J. Chem. Theory Comput., 2016, doi:10.1021/acs.jctc.6b00186
  • Christina Bergonzo, Kathleen B. Hall, and Thomas E. Cheatham. "Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics", J. Chem. Theory Comput., Vol. 12(7): 3382--3389, 2016, doi:10.1021/acs.jctc.6b00173
  • 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, Vol. 1860(3): 607--617, 2016, doi:10.1016/j.bbagen.2015.11.009
  • Lucía Álvarez, et al. "Structural Study of a Flexible Active Site Loop in Human Indoleamine 2, 3-Dioxygenase and Its Functional Implications", Biochemistry, Vol. 55(19): 2785--2793, 2016, doi:10.1021/acs.biochem.6b00077
  • James T. Waters, et al. "Transitions of Double-Stranded DNA Between the A- and B-Forms", The Journal of Physical Chemistry B, 2016, doi:10.1021/acs.jpcb.6b02155
  • 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, Vol. 1850(5): 1041--1058, 2015, doi:10.1016/j.bbagen.2014.09.007
  • James C. Robertson, and Thomas E Cheatham. "DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations", The Journal of Physical Chemistry B, Vol. 119(44): 14111--14119, 2015, doi:10.1021/acs.jpcb.5b08486
  • James A. Maier, et al. "ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB", J. Chem. Theory Comput., Vol. 11(8): 3696--3713, 2015, doi:10.1021/acs.jctc.5b00255
  • 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, Vol. 21(9): 1578--1590, 2015, doi:10.1261/rna.051102.115
  • Christina Bergonzo, and Thomas E. Cheatham. "Improved Force Field Parameters Lead to a Better Description of RNA Structure", J. Chem. Theory Comput., Vol. 11(9): 3969--3972, 2015, doi:10.1021/acs.jctc.5b00444
  • 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, Vol. 43(11): 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, Vol. 54(6): 1307--1313, 2015, doi:10.1021/bi5012833
  • Chad W. Hopkins, Scott Le Grand, Ross C. Walker, and Adrian E. Roitberg. "Long-Time-Step Molecular Dynamics Through Hydrogen Mass Repartitioning", J. Chem. Theory Comput., Vol. 11(4): 1864--1874, 2015, doi:10.1021/ct5010406
  • Cheng-Tsung Lai, et al. "Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium Tuberculosis InhA", Biochemistry, Vol. 54(30): 4683--4691, 2015, doi:10.1021/acs.biochem.5b00284
  • Hai Nguyen, Alberto Pérez, Sherry Bermeo, and Carlos Simmerling. "Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins", J. Chem. Theory Comput., Vol. 11(8): 3714--3728, 2015, doi:10.1021/acs.jctc.5b00271
  • 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", The Journal of Physical Chemistry B, Vol. 119(38): 12355--12364, 2015, doi:10.1021/acs.jpcb.5b05190
  • George M. Giambaşu, Darrin M. York, and David A. Case. "Structural Fidelity and NMR Relaxation Analysis in a Prototype RNA Hairpin", RNA, Vol. 21(5): 963--974, 2015, doi:10.1261/rna.047357.114
  • Thomas E. Cheatham, and Daniel R. Roe. "The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis", Comput. Sci. Eng., Vol. 17(2): 30--39, 2015, doi:10.1109/mcse.2015.7
  • 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", J. Chem. Theory Comput., Vol. 10(3): 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, Vol. 6(1): 4, 2014, doi:10.1186/1758-2946-6-4
  • D. R. Roe, J. M. Swails, R. Salomon-Ferrer, A. E. Roitberg, and C. E. Cheatham III. "Enhancing Amber for Use on the Blue Waters High-Performance Computing Resource", Tech. Rep., Blue Waters Project, University of Illinois, 2014
  • Daniel R. Roe, Christina Bergonzo, and Thomas E. Cheatham. "Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics With Hamiltonian Replica Exchange Methods", The Journal of Physical Chemistry B, Vol. 118(13): 3543--3552, 2014, doi:10.1021/jp4125099
  • 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", J. Am. Chem. Soc., Vol. 136(40): 13959--13962, 2014, doi:10.1021/ja5032776
  • 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, Vol. 54(6): 1810--1819, 2014, doi:10.1021/ci500173w
  • Christina Bergonzo, et al. "Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide", J. Chem. Theory Comput., Vol. 10(1): 492--499, 2014, doi:10.1021/ct400862k
  • Rodrigo Galindo-Murillo, Daniel R. Roe, and Thomas E. Cheatham. "On the Absence of Intrahelical DNA Dynamics on the μs to ms Timescale", Nature Communications, Vol. 5, 2014, doi:10.1038/ncomms6152
  • 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", The Journal of Physical Chemistry B, Vol. 118(44): 12577--12585, 2014, doi:10.1021/jp504011c
  • 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, Vol. 54(6): 1758--1772, 2014, doi:10.1021/ci500132c
  • Natali V. Di Russo, Marcelo A. Marti, and Adrian E. Roitberg. "Underlying Thermodynamics of pH-Dependent Allostery", The Journal of Physical Chemistry B, Vol. 118(45): 12818--12826, 2014, doi:10.1021/jp507971v
  • Daniel R. Roe, and Thomas E. Cheatham. "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data", J. Chem. Theory Comput., Vol. 9(7): 3084--3095, 2013, doi:10.1021/ct400341p

Di Matteo

  • Dacen Waters, et al. "Monsters in the Dark: Predictions for Luminous Galaxies in the Early Universe from the BlueTides Simulation", Monthly Notices of the Royal Astronomical Society: Letters, Vol. 461(1): L51--L55, 2016, doi:10.1093/mnrasl/slw100
  • Stephen M. Wilkins, et al. "The Lyman-Continuum Photon Production Efficiency in the High-Redshift Universe", Monthly Notices of the Royal Astronomical Society: Letters, Vol. 458(1): L6--L9, 2016, doi:10.1093/mnrasl/slw007
  • Stephen M. Wilkins, et al. "The Photometric Properties of Galaxies in the Early Universe", Mon. Not. R. Astron. Soc., Vol. 460(3): 3170--3178, 2016, doi:10.1093/mnras/stw1154
  • Tiziana Di Matteo. "AGN Feedback in Simulations of Structure Formation", IAU General Assembly, Meeting #29, 2015, url: http://adsabs.harvard.edu/abs/2015IAUGA..2257908D
  • Yu Feng, Mark Straka, Tiziana Di Matteo, and Rupert Croft. "MP-Sort: Sorting at Scale on Blue Waters – for a Cosmological Simulation", Proceedings of Cray User Group Conference 2015 (CUG 2015), Chicago, IL, 2015, url: https://cug.org/proceedings/cug2015_proceedings/includes/files/pap179.pdf
  • Rupert Croft, Tiziana Di Matteo, Nishikanta Khandai, and Yu Feng. "Petascale Cosmology: Simulations of Structure Formation", Comput. Sci. Eng., Vol. 17(2): 40--46, 2015, doi:10.1109/mcse.2015.5
  • Yu Feng, et al. "The BlueTides Simulation: First Galaxies and Reionization", Mon. Not. R. Astron. Soc., Vol. 455(3): 2778--2791, 2015, doi:10.1093/mnras/stv2484
  • Tiziana Di Matteo. "The First Quasars", IAU General Assembly, Meeting #29, 2015, url: http://adsabs.harvard.edu/abs/2015IAUGA..2257908D
  • Yu Feng, et al. "The Formation of Milky Way-Mass Disk Galaxies in the First 500 Million Years of a Cold Dark Matter Universe", ApJ, Vol. 808(1): L17, 2015, doi:10.1088/2041-8205/808/1/l17
  • N. Battaglia, H. Trac, R. Cen, and A. Loeb. "Reionization on Large Scales. I. A Parametric Model Constructed from Radiation-Hydrodynamic Simulations", ApJ, Vol. 776(2): 81, 2013, doi:10.1088/0004-637x/776/2/81
  • 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", 2016, submitted

Diener

  • Ernazar Abdikamalov, et al. "Neutrino-Driven Turbulent Convection and Standing Accretion Shock Instability in Three-Dimensional Core-Collapse Supernovae", ApJ, Vol. 808(1): 70, 2015, doi:10.1088/0004-637x/808/1/70
  • Philipp Mösta, et al. "Magnetorotational Core-Collapse Supernovae in Three Dimensions", ApJ, Vol. 785(2): L29, 2014, doi:10.1088/2041-8205/785/2/l29
  • Ian Hinder, et al. "Error-Analysis and Comparison to Analytical Models of Numerical Waveforms Produced by the NRAR Collaboration", Class. Quantum Grav., Vol. 31(2): 025012, 2013, doi:10.1088/0264-9381/31/2/025012
  • Erik Schnetter. "Performance and Optimization Abstractions for Large Scale Heterogeneous Systems in the Cactus/Chemora Framework", 2013 Extreme Scaling Workshop (xsw 2013), Boulder, CO, 2013, doi:10.1109/xsw.2013.9
  • Erik Schnetter, Marek Blazewicz, Steven R. Brandt, David M. Koppelman, and Frank Löffler. "Chemora: A PDE Solving Framework for Modern HPC Architectures", 2014, submitted

Elghobashi

  • M. Rosso, H. Wang, and S. Elghobashi. "Dispersion of finite size droplets and solid particles in isotropic turbulence", ICMF-2016 – 9th International Conference on Multiphase Flow, Firenze, Italy, 2016, url: http://www.aidic.it/icmf2016/webpapers/316rosso.pdf
  • Michele Rosso, and S. Elghobashi. "DNS of Droplet Motion in a Turbulent Flow", American Physical Society's 66th Annual Meeting of the Division of Fluid Dynamics, Pittsburgh, PA, 2013, url: http://meetings.aps.org/Meeting/DFD13/Event/204004

Gropp

  • Antonio J. Peña, et al. "Analysis of Topology-Dependent MPI Performance on Gemini Networks", Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13, 2013, doi:10.1145/2488551.2488564

Jordan

  • R. Taborda, N. Khoshnevis, S. Azizzadeh-Roodpish, and M. M. Huda. "Influence of the Source, Seismicvelocity, and Attenuation Models on the Validation of Ground Motion Simulations", Proceedings of the World Conference on Earthquake Engineering, Santiago de Chile, Chile, 2017
  • Ricardo Taborda, Shima Azizzadeh-Roodpish, Naeem Khoshnevis, and Keli Cheng. "Evaluation of the Southern California Seismic Velocity Models Through Simulation of Recorded Events", Geophys. J. Int., Vol. 205(3): 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", Geophys. J. Int., Vol. 205(2): 856--863, 2016, doi:10.1093/gji/ggw050
  • Yigit Isbiliroglu, Ricardo Taborda, and Jacobo Bielak. "Coupled Soil-Structure Interaction Effects of Building Clusters During Earthquakes", Earthquake Spectra, Vol. 31(1): 463--500, 2015, doi:10.1193/102412eqs315m
  • D. Roten, and Y. Cui. "GPU-Powered Simulations of Seismic Waves in Nonlinear Media", GPU Technology Conference 2015, San Jose, CA, 2015
  • Heming Xu, et al. "Aftershock Sequence Simulations Using Synthetic Earthquakes and Rate-State Seismicity Formulation", Earthquake Science, Vol. 27(4): 401--410, 2014, doi:10.1007/s11589-014-0087-7
  • Efecan Poyraz, Heming Xu, and Yifeng Cui. "Application-Specific I/O Optimizations on Petascale Supercomputers", Procedia Computer Science, Vol. 29, 2014, doi:10.1016/j.procs.2014.05.082
  • F. Wang, and T. H. Jordan. "Comparison of Probabilistic Seismic-Hazard Models Using Averaging-Based Factorization", Bulletin of the Seismological Society of America, Vol. 104(3): 1230--1257, 2014, doi:10.1785/0120130263
  • 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, Vol. 198(3): 1438--1457, 2014, doi:10.1093/gji/ggu198
  • D. Roten, K. B. Olsen, S. M. Day, Y. Cui, and D. Fäh. "Expected Seismic Shaking in Los Angeles Reduced by San Andreas Fault Zone Plasticity", Geophys. Res. Lett., Vol. 41(8): 2769--2777, 2014, doi:10.1002/2014gl059411
  • En-Jui Lee, et al. "Full-3-D Tomography for Crustal Structure in Southern California Based on the Scattering-Integral and the Adjoint-Wavefield Methods", J. Geophys. Res. Solid Earth, Vol. 119(8): 6421--6451, 2014, doi:10.1002/2014jb011346
  • 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, Vol. 100(7): 504--533, 2014, doi:10.1002/nme.4756
  • Y. Cui, et al. "Accelerating CyberShake Calculations on the XE6/XK7 Platform of Blue Waters", 2013 Extreme Scaling Workshop (xsw 2013), Boulder, CO, 2013, doi:10.1109/xsw.2013.6
  • Ricardo Taborda, and Jacobo Bielak. "Ground-Motion Simulation and Validation of the 2008 Chino Hills, California, Earthquake", Bulletin of the Seismological Society of America, Vol. 103(1): 131--156, 2013, doi:10.1785/0120110325
  • 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", Procedia Computer Science, Vol. 18, 2013, doi:10.1016/j.procs.2013.05.292
  • Y. Cui, et al. "Physics-Based Seismic Hazard Analysis on Petascale Heterogeneous Supercomputers", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13, Denver, CO, 2013, doi:10.1145/2503210.2503300
  • Zheqiang Shi, and Steven M. Day. "Rupture Dynamics and Ground Motion from 3-D Rough-Fault Simulations", J. Geophys. Res. Solid Earth, Vol. 118(3): 1122--1141, 2013, doi:10.1002/jgrb.50094
  • D. Roten, et al. "High-Frequency Nonlinear Earthquake Simulations on Petascale Heterogeneous Supercomputers", submitted to SC'16, Salt Lake City, UT, 2016, submitted

Karimabadi

  • Kai Germaschewski, et al. "The Plasma Simulation Code: A Modern Particle-in-Cell Code with Patch-Based Load-Balancing", Journal of Computational Physics, Vol. 318, 2016, doi:10.1016/j.jcp.2016.05.013
  • 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, Vol. 22(4): 042902, 2015, doi:10.1063/1.4916492
  • 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, Vol. 373(2041): 20140151--20140151, 2015, doi:10.1098/rsta.2014.0151
  • M. Wan, et al. "Intermittent Dissipation and Heating in 3D Kinetic Plasma Turbulence", Phys. Rev. Lett., Vol. 114(17), 2015, doi:10.1103/physrevlett.114.175002
  • Fan Guo, Yi-Hsin Liu, William Daughton, and Hui Li. "Particle Acceleration and Plasma Dynamics During Magnetic Reconnection in the Magnetically-Dominated Regime", ApJ, Vol. 806(2): 167, 2015, doi:10.1088/0004-637x/806/2/167
  • J. Jara-Almonte, W. Daughton, and H. Ji. "Debye Scale Turbulence Within the Electron Diffusion Layer During Magnetic Reconnection", Physics of Plasmas, Vol. 21(3): 032114, 2014, doi:10.1063/1.4867868
  • 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", Phys. Rev. Lett., Vol. 113(15), 2014, doi:10.1103/physrevlett.113.155005
  • W. H. Matthaeus, et al. "Nonlinear and Linear Timescales Near Kinetic Scales in Solar Wind Turbulence", ApJ, Vol. 790(2): 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", J. Geophys. Res. Space Physics, Vol. 119(12): 9773--9789, 2014, doi:10.1002/2014ja020492
  • H. Karimabadi, et al. "The Link Between Shocks, Turbulence, and Magnetic Reconnection in Collisionless Plasmas", Physics of Plasmas, Vol. 21(6): 062308, 2014, doi:10.1063/1.4882875
  • Yi-Hsin Liu, W. Daughton, H. Karimabadi, H. Li, and V. Roytershteyn. "Bifurcated Structure of the Electron Diffusion Region in Three-Dimensional Magnetic Reconnection", Phys. Rev. Lett., Vol. 110(26), 2013, doi:10.1103/physrevlett.110.265004
  • Roytershteyn et al. "The First 3D Fully Kinetic Simulations of Decaying Turbulence", 2014, submitted
  • Unknown. "Newly discovered electron scale turbulence", submitted
  • Karimabadi, et al. "Properties and Consequences of Turbulence Associated with Fast Collisionless Shocks: Structural Organization in Form of Flux Ropes, Fast Jets and Large Scale Vortices", Physics of Plasmas, submitted
  • Unknown. "Techniques for particle noise reduction", Physics of Plasmas journal, submitted
  • Unknown. "The first 3D fully kinetic simulations of cascading turbulence", submitted

Klein

  • Eugene Palovcak, Lucie Delemotte, Michael L. Klein, and Vincenzo Carnevale. "Comparative Sequence Analysis Suggests a Conserved Gating Mechanism for TRP Channels", The Journal of General Physiology, Vol. 146(1): 37--50, 2015, doi:10.1085/jgp.201411329
  • 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, Vol. 23(8): 1516--1525, 2015, doi:10.1016/j.str.2015.05.022
  • Khaled Elokely, et al. "Understanding TRPV1 Activation by Ligands: Insights from the Binding Modes of Capsaicin and Resiniferatoxin", Proceedings of the National Academy of Sciences, Vol. 113(2): E137--E145, 2015, doi:10.1073/pnas.1517288113

Klimeck

  • A. Tankasala, J. Salfi, S. Rogge, G. Klimeck, and R. Rahman. "Atomistic Simulations of Negatively Charged Donor States Probed In STM Experiments", APS March Meeting 2016, Baltimore, MD, 2016, url: http://meetings.aps.org/Meeting/MAR16/Session/P45.7
  • Yu Wang, et al. "Highly Tunable Exchange in Donor Qubits in Silicon", npj Quantum Information, Vol. 2, 2016, doi:10.1038/npjqi.2016.8
  • James Charles, et al. "Incoherent Transport in NEMO5: Realistic and Efficient Scattering on Phonons", J Comput Electron, 2016, doi:10.1007/s10825-016-0845-y
  • A. Tankasala, Y. Wang, G. Klimeck, and R. Rahman. "Atomistic Configuration Interaction Simulations of Two-electron States of Donors in Silicon", APS March Meeting 2015, San Antonio, TX, 2015, url: http://meetings.aps.org/Meeting/MAR15/Session/A37.11
  • Bozidar Novakovic, and Gerhard Klimeck. "Atomistic Quantum Transport Approach to Time-Resolved Device Simulations", 2015 International Conference on Simulation of Semiconductor Processes and Devices (SISPAD), 2015, doi:10.1109/sispad.2015.7292245
  • Mehdi Salmani-Jelodar, Saumitra R. Mehrotra, Hesameddin Ilatikhameneh, and Gerhard Klimeck. "Design Guidelines for Sub-12 Nm Nanowire MOSFETs", IEEE Transactions on Nanotechnology, Vol. 14(2): 210--213, 2015, doi:10.1109/tnano.2015.2395441
  • Fan W. Chen, et al. "In-Surface Confinement of Topological Insulator Nanowire Surface States", Appl. Phys. Lett., Vol. 107(12): 121605, 2015, doi:10.1063/1.4931975
  • A. Tankasala, et al. "Modeling Exchange Interaction in Bulk and Sub-Surface Donor Pairs In Silicon for Two-Qubit Gates,", Poster Session, ARO Quantum Computing Program Review, San Diego, CA, 2015
  • Ravi Pramod Vedula, et al. "Optimal Ge/SiGe Nanofin Geometries for Hole Mobility Enhancement: Technology Limit from Atomic Simulations", J. Appl. Phys., Vol. 117(17): 174312, 2015, doi:10.1063/1.4919091
  • 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", J. Appl. Phys., Vol. 117(4): 044304, 2015, doi:10.1063/1.4906842
  • 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", Phys. Rev. B, Vol. 92(8), 2015, doi:10.1103/physrevb.92.085301
  • 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", J. Appl. Phys., Vol. 115(12): 123703, 2014, doi:10.1063/1.4868977
  • 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\textemdashEffect of Quantum Confinement and Homogeneous Strain o", J. Appl. Phys., Vol. 115(12): 123704, 2014, doi:10.1063/1.4868979
  • Pengyu Long, et al. "Design and Simulation of Two-Dimensional Superlattice Steep Transistors", IEEE Electron Device Lett., Vol. 35(12): 1212--1214, 2014, doi:10.1109/led.2014.2364593
  • M. Salmani-Jelodar, J. D. Bermeol, S. Kim, and G. Klimeck. "ITRS Tool on NanoHUB", NanoHUB User Conf, Phoenix, AZ, 2014
  • Yu He, Yu Wang, Gerhard Klimeck, and Tillmann Kubis. "Non-Equilibrium Green's Functions Method: Non-Trivial and Disordered Leads", Appl. Phys. Lett., Vol. 105(21): 213502, 2014, doi:10.1063/1.4902504
  • M. Salmani-Jelodar, S. Kim, K. Ng, and G. Klimeck. "Transistor Roadmap Projection Using Predictive Full-Band Atomistic Modeling", Appl. Phys. Lett., Vol. 105(8): 083508, 2014, doi:10.1063/1.4894217
  • Parijat Sengupta, Tillmann Kubis, Yaohua Tan, Michael Povolotskyi, and Gerhard Klimeck. "Design Principles for HgTe Based Topological Insulator Devices", J. Appl. Phys., Vol. 114(4): 043702, 2013, doi:10.1063/1.4813877
  • J. E. Fonseca, et al. "Efficient and Realistic Device Modeling from Atomic Detail to the Nanoscale", J Comput Electron, Vol. 12(4): 592--600, 2013, doi:10.1007/s10825-013-0509-0
  • Yaohua Tan, et al. "Empirical Tight Binding Parameters for GaAs and MgO with Explicit Basis Through DFT Mapping", J Comput Electron, Vol. 12(1): 56--60, 2013, doi:10.1007/s10825-013-0436-0
  • Lang Zeng, et al. "Low Rank Approximation Method for Efficient Green's Function Calculation of Dissipative Quantum Transport", J. Appl. Phys., Vol. 113(21): 213707, 2013, doi:10.1063/1.4809638
  • H. Ilatikhameneh, T. Ameen, G. Klimeck, and R. Rahman. "Universal Behavior of Strain in Quantum Dots", 2015, submitted

Liu

  • Jiashun Hu, and Lijun Liu. "Abnormal Seismological and Magmatic Processes Controlled by the Tearing South American Flat Slabs", Earth and Planetary Science Letters, Vol. 450, 2016, doi:10.1016/j.epsl.2016.06.019
  • Paul L. Heller, and Lijun Liu. "Dynamic Topography and Vertical Motion of the U.S. Rocky Mountain Region Prior to and During the Laramide Orogeny", Geological Society of America Bulletin, Vol. 128(5-6): 973--988, 2016, doi:10.1130/b31431.1
  • 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, Vol. 438, 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", Geophys. Res. Lett., Vol. 43(3): 1132--1139, 2016, doi:10.1002/2015gl067131
  • Lijun Liu, and Quan Zhou. "Deep Recycling of Oceanic Asthenosphere Material During Subduction", Geophys. Res. Lett., Vol. 42(7): 2204--2211, 2015, doi:10.1002/2015gl063633
  • Lijun Liu. "The Ups and Downs of North America: Evaluating the Role of Mantle Dynamic Topography Since the Mesozoic", Rev. Geophys., Vol. 53(3): 1022--1049, 2015, doi:10.1002/2015rg000489
  • Q. Zhou, and L. Liu. "Formation of the Yellowstone Volcanic Province due to Intruding Hot Oceanic Asthenosphere", Nature, submitted
  • L. Liu, and D. Hasterok. "High–Resolution Lithosphere Viscosity and Dynamics Revealed by Magnetotelluric Imaging", Science, submitted
  • L. Liu, C. Chang, A. Kelbert, A. Anders, and J. Bass. "Stable Continental-scale drainage of North America: Implications for Deep Mantle Hydration", Nature Geoscience, submitted

Mori

  • F.S. Tsung, et al. "Controlling Laser Plasma Interactions with Temporal Bandwidths", The 2016 Anomalous Absorption Conference, Old Saybrook, CT, 2016, url: http://adsabs.harvard.edu/abs/2015APS..DPPBO8009X
  • Peicheng Yu, et al. "Enabling Lorentz Boosted Frame Particle-in-Cell Simulations of Laser Wakefield Acceleration in Quasi-3D Geometry", Journal of Computational Physics, Vol. 316, 2016, doi:10.1016/j.jcp.2016.04.014
  • X. Xu, et al. "Exact Phase Space Matching for Plasma and Traditional Acceleration Components Using Longitudinally Tailored Plasma Profiles", FACET Workshop, San Francisco, CA, 2015
  • B. B. Pollock, et al. "Formation of Ultrarelativistic Electron Rings from a Laser-Wakefield Accelerator", Phys. Rev. Lett., Vol. 115(5), 2015, doi:10.1103/physrevlett.115.055004
  • X. Xu, et al. "Intrinsic Phase Space Discretization of Charge in Laser-Triggered Ionization Injection", 57th Annual Meeting of the APS Division of Plasma Physics, Savannah, GA, 2015, url: http://adsabs.harvard.edu/abs/2015APS..DPPBO8009X
  • X. Xu, et al. "Lorentz Boosted Frame Simulation of Laser Wakefield Acceleration in 3D and Quasi-3D Geometry", The International Computational Accelerator Physics Conference 2015, Shanghai, China, 2015
  • S. Corde, et al. "Multi-Gigaelectronvolt Acceleration of Positrons in a Self-Loaded Plasma Wakefield", Nature, Vol. 524(7566): 442--445, 2015, doi:10.1038/nature14890
  • X. Xu, et al. "Phase Space Dynamics in Plasma Based Wakefield Acceleration", 2015 CPS Fall Meeting, Division of Plasma Physics, Changchun, Jilin, China, 2015
  • X. Xu, et al. "Phase Space Matching of Staging Plasma and Traditional Accelerator Using Longitudinally Tailored Plasma Structure", The 6th International Particle Accelerator Conference, Richmond, VA, 2015, url: http://accelconf.web.cern.ch/AccelConf/IPAC2015/talks/moac3_talk.pdf
  • X. Xu, et al. "Prospects for Generating Highbrightness and Low Energy Spread Electron Beams Through Self-Injection Schemes", FACET Workshop, San Francisco, CA, 2015
  • An W., et al. "QuickPIC Simulation of Plasma Wake Field Accelerator Experiments at FACET", 2015 International Conference on Numerical Simulation of Plasmas, Invited talk., 2015
  • An W., et al. "Simulations of Plasma Wakefield Acceleration at FACET and Beyond", 2015 Computational Accelerator Physics Conference. Invited plenary talk., 2015
  • W.B. Mori. "Synergy Between Experiments and Simulations in Laser and Beam-Driven Plasma Acceleration and Light Sources", Division of Plasma Physics APS 2015, Invited Plenary Talk, 2015
  • M. Litos, et al. "High-Efficiency Acceleration of an Electron Beam in a Plasma Wakefield Accelerator", Nature, Vol. 515(7525): 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", Phys. Rev. Lett., Vol. 113(24), 2014, doi:10.1103/physrevlett.113.245001
  • Viktor K. Decyk, and Tajendra V. Singh. "Particle-in-Cell Algorithms for Emerging Computer Architectures", Computer Physics Communications, Vol. 185(3): 708--719, 2014, doi:10.1016/j.cpc.2013.10.013
  • R A Fonseca, et al. "Exploiting Multi-Scale Parallelism for Large Scale Numerical Modelling of Laser Wakefield Accelerators", Plasma Phys. Control. Fusion, Vol. 55(12): 124011, 2013, doi:10.1088/0741-3335/55/12/124011
  • An W., et al. "Ion Motion Induced Emittance Growth of Matched Electron Beams in Plasma Wakefields", submitted to Physical Review Letters, 2016, submitted
  • X. Xu, et al. "Nano-Scale Electron Bunching in Laser-Triggered Ionization Injection in Plasma Accelerators", submitted to Physical Review Letters, 2015, submitted
  • B. J. Winjum et al. "Possible Interactions of Two Laser Speckles Due to Stimulated Raman Scattering", submitted

Nagamine

  • Jason Jaacks, Steven L. Finkelstein, and Kentaro Nagamine. "Connecting the Dots: Tracking Galaxy Evolution Using Constant Cumulative Number Density at 3≤z≤7", ApJ, Vol. 817(2): 174, 2016, doi:10.3847/0004-637x/817/2/174
  • E. Choi, J. P. Ostriker, T. Naab, L. Oser, and B. P. Moster. "The Impact of Mechanical AGN Feedback on the Formation of Massive Early-Type Galaxies", Monthly Notices of the Royal Astronomical Society, Vol. 449(4): 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 Λ Cold Dark Matter Simulations", Mon. Not. R. Astron. Soc., Vol. 452(3): 3030--3037, 2015, doi:10.1093/mnras/stv1433
  • Greg L. Bryan, et al. "Enzo: An Adaptive Mesh Refinement Code for Astrophysics", ApJS, Vol. 211(2): 19, 2014, doi:10.1088/0067-0049/211/2/19
  • Taysun Kimm, and Renyue Cen. "Escape Fraction of Ionizing Photons During Reionization: Effects Due to Supernova Feedback and Runaway OB Stars", ApJ, Vol. 788(2): 121, 2014, doi:10.1088/0004-637x/788/2/121
  • Renyue Cen. "Evolution of Cold Streams and Emergence of the Hubble Sequence", ApJ, Vol. 789(1): L21, 2014, doi:10.1088/2041-8205/789/1/l21
  • Renyue Cen. "Frequent Spin Reorientation of Galaxies Due to Local Interactions", ApJ, Vol. 785(1): L15, 2014, doi:10.1088/2041-8205/785/1/l15
  • R. Cen, A. R. Pop, and N. A. Bahcall. "Gas Loss in Simulated Galaxies as They Fall Into Clusters", Proceedings of the National Academy of Sciences, Vol. 111(22): 7914--7919, 2014, doi:10.1073/pnas.1407300111
  • Renyue Cen, and Taysun Kimm. "Infrared Properties of Z=7 Galaxies from Cosmological Simulations", ApJ, Vol. 782(1): 32, 2014, doi:10.1088/0004-637x/782/1/32
  • Renyue Cen. "On the Origin of the Hubble Sequence: I. Insights on Galaxy Color Migration from Cosmological Simulations", ApJ, Vol. 781(1): 38, 2014, doi:10.1088/0004-637x/781/1/38
  • Stephanie Tonnesen, and Renyue Cen. "On the Reversal of SFR-Density Relation at Z=1: Insights from Simulations", ApJ, Vol. 788(2): 133, 2014, doi:10.1088/0004-637x/788/2/133
  • Renyue Cen. "Temporal Self-Organization in Galaxy Formation", ApJ, Vol. 785(2): L21, 2014, doi:10.1088/2041-8205/785/2/l21
  • Ludwig Oser, et al. "Alleviating the Scaling Problem of Cosmological Hydrodynamic Simulations with HECA", Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13, San Diego, CA, 2013, doi:10.1145/2484762.2484776
  • Taysun Kimm, and Renyue Cen. "Heavy Dust Obscuration of Z=7 Galaxies in a Cosmological Hydrodynamic Simulation", ApJ, Vol. 776(1): 35, 2013, doi:10.1088/0004-637x/776/1/35
  • Ji-hoon Kim, et al. "The AGORA High-Resolution Galaxy Simulations Comparison Project", ApJS, Vol. 210(1): 14, 2013, doi:10.1088/0067-0049/210/1/14
  • M. Hirschmann, et al. "The Effect of Metal Enrichment and Galactic Winds on Galaxy Formation in Cosmological Zoom Simulations", Monthly Notices of the Royal Astronomical Society, Vol. 436(4): 2929--2949, 2013, doi:10.1093/mnras/stt1770
  • Renyue Cen, and Zheng Zheng. "The Nature of Ly? Blobs: Powered by Extreme Starbursts", ApJ, Vol. 775(2): 112, 2013, doi:10.1088/0004-637x/775/2/112


Ott

  • David Radice, et al. "Dynamical Mass Ejection from Binary Neutron Star Mergers", Mon. Not. R. Astron. Soc., Vol. 460(3): 3255--3271, 2016, doi:10.1093/mnras/stw1227
  • David Radice, et al. "Neutrino-Driven Convection in Core-Collapse Supernovae: High-Resolution Simulations", ApJ, Vol. 820(1): 76, 2016, doi:10.3847/0004-637x/820/1/76
  • Philipp Mösta, et al. "A Large-Scale Dynamo and Magnetoturbulence in Rapidly Rotating Core-Collapse Supernovae", Nature, Vol. 528(7582): 376--379, 2015, doi:10.1038/nature15755
  • David Radice, Sean M Couch, and Christian D Ott. "Implicit Large Eddy Simulations of Anisotropic Weakly Compressible Turbulence with Application to Core-Collapse Supernovae", Comput. Astrophys., Vol. 2(1), 2015, doi:10.1186/s40668-015-0011-0
  • Viktoriya Morozova, et al. "Light Curves of Core-Collapse Supernovae with Substantial Mass Loss Using the New Open-Source Supernova Explosion Code (SNEC)", ApJ, Vol. 814(1): 63, 2015, doi:10.1088/0004-637x/814/1/63
  • Ernazar Abdikamalov, et al. "Neutrino-Driven Turbulent Convection and Standing Accretion Shock Instability in Three-Dimensional Core-Collapse Supernovae", ApJ, Vol. 808(1): 70, 2015, doi:10.1088/0004-637x/808/1/70
  • Sean M. Couch, and Christian D. Ott. "The Role of Turbulence in Neutrino-Driven Core-Collapse Supernova Explosions", ApJ, Vol. 799(1): 5, 2015, doi:10.1088/0004-637x/799/1/5
  • Philipp Mösta, et al. "Magnetorotational Core-Collapse Supernovae in Three Dimensions", ApJ, Vol. 785(2): L29, 2014, doi:10.1088/2041-8205/785/2/l29
  • Luke F. Roberts, et al. "General Relativistic Three-Dimensional Multi-Group Neutrino Radiation-Hydrodynamics Simulations of Core-Collapse Supernovae", Submitted to ApJ, 2016, submitted
  • David Radice, Sebastiano Bernuzzi, and Christian D. Ott. "The One-Armed Spiral Instability in Neutron Star Mergers and its Detectability in Gravitational Waves", submitted for publication in Phys. Rev. D., 2016, submitted
  • Sebastiano Bernuzzi, et al. "How Loud Are Neutron Star Mergers?", submitted for publication in Mon. Not. Roy. Ast. Soc., 2015, submitted

Pande

  • Sheel C. Dodani, et al. "Discovery of a Regioselectivity Switch in Nitrating P450s Guided by Molecular Dynamics Simulations and Markov Models", Nature Chemistry, Vol. 8(5): 419--425, 2016, doi:10.1038/nchem.2474
  • Lee-Ping Wang, et al. "Discovering Chemistry with an Ab Initio Nanoreactor", Nature Chemistry, Vol. 6(12): 1044--1048, 2014, doi:10.1038/nchem.2099
  • Kai J. Kohlhoff, et al. "Cloud-Based Simulations on Google Exacycle Reveal Ligand Modulation of GPCR Activation Pathways", Nature Chemistry, Vol. 6(1): 15--21, 2013, doi:10.1038/nchem.1821

Pogorelov

  • E. J. Zirnstein, et al. "Local Interstellar Magnetic Field Determined from the Interstellar Boundary Explorer Ribbon", ApJ, Vol. 818(1): L18, 2016, doi:10.3847/2041-8205/818/1/l18
  • N. V. Pogorelov. "The Heliotail: Theory and Modeling", J. Phys.: Conf. Ser., Vol. 719, 2016, doi:10.1088/1742-6596/719/1/012013
  • Xi Luo, Ming Zhang, Marius Potgieter, Xueshang Feng, and N. V. Pogorelov. "A Numerical Simulation of Cosmic-Ray Modulation Near the Heliopause", ApJ, Vol. 808(1): 82, 2015, doi:10.1088/0004-637x/808/1/82
  • J. Heerikhuisen, Eric Zirnstein, and Nikolai Pogorelov. "κ-Distributed Protons in the Solar Wind and Their Charge-Exchange Coupling to Energetic Hydrogen", J. Geophys. Res. Space Physics, Vol. 120(3): 1516--1525, 2015, doi:10.1002/2014ja020636
  • N. V. Pogorelov, and S. N. Borovikov. "Mixing of the Interstellar and Solar Plasmas at the Heliospheric Interface", Numerical Modeling of Space Plasma Flows: ASTRONUM-2014, ASP Conference Series, 2015, url: http://aspbooks.org.proxy2.library.illinois.edu/custom/publications/paper/498-0160.html
  • P Manoharan, T Kim, N V Pogorelov, C N Arge, and P K Manoharan. "Modeling Solar Wind with Boundary Conditions from Interplanetary Scintillations", J. Phys.: Conf. Ser., Vol. 642, 2015, doi:10.1088/1742-6596/642/1/012016
  • N. V. Pogorelov, S. N. Borovikov, J. Heerikhuisen, and M. Zhang. "The Heliotail", ApJ, Vol. 812(1): L6, 2015, doi:10.1088/2041-8205/812/1/l6
  • R L Fermo, N V Pogorelov, and L F Burlaga. "Transient Shocks Beyond the Heliopause", J. Phys.: Conf. Ser., Vol. 642, 2015, doi:10.1088/1742-6596/642/1/012008
  • Ming Zhang, Xi Luo, and Nikolai Pogorelov. "Where Is the Cosmic-Ray Modulation Boundary of the Heliosphere?", Physics of Plasmas, Vol. 22(9): 091501, 2015, doi:10.1063/1.4928945
  • E. J. Zirnstein, et al. "Charge-Exchange Coupling Between Pickup Ions Across the Heliopause and Its Effect on Energetic Neutral Hydrogen Flux", ApJ, Vol. 783(2): 129, 2014, doi:10.1088/0004-637x/783/2/129
  • A. Bazavov, et al. "Determination of |Vus| from a Lattice QCD Calculation of the K→πℓν Semileptonic Form Factor with Physical Quark Masses", Phys. Rev. Lett., Vol. 112(11), 2014, doi:10.1103/physrevlett.112.112001
  • Ming Zhang, Pingbing Zuo, and Nikolai Pogorelov. "Heliospheric Influence on the Anisotropy of Tev Cosmic Rays", ApJ, Vol. 790(1): 5, 2014, doi:10.1088/0004-637x/790/1/5
  • T. K. Kim, et al. "MHD Heliosphere with Boundary Conditions from a Tomographic Reconstruction Using Interplanetary Scintillation Data", J. Geophys. Res. Space Physics, Vol. 119(10): 7981--7997, 2014, doi:10.1002/2013ja019755
  • Nikolai Pogorelov, et al. "MS-FLUKSS and Its Application to Modeling Flows of Partially Ionized Plasma in the Heliosphere", Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE '14, Atlanta, GA, 2014, doi:10.1145/2616498.2616499
  • 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", ApJ, Vol. 784(1): 73, 2014, doi:10.1088/0004-637x/784/1/73
  • 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", 8th International Conference of Numerical Modeling of Space Plasma Flows (ASTRONUM 2013), Biarritz, France, 2014, url: http://aspbooks.org/custom/publications/paper/488-0167.html
  • S. N. Borovikov, and N. V. Pogorelov. "Voyager 1 Near the Heliopause", ApJ, Vol. 783(1): L16, 2014, doi:10.1088/2041-8205/783/1/l16
  • Xi Luo, Ming Zhang, Hamid K. Rassoul, Nikolai V. Pogorelov, and Jacob Heerikhuisen. "Galactic Cosmic-Ray Modulation in a Realistic Global Magnetohydrodynamic Heliosphere", ApJ, Vol. 764(1): 85, 2013, doi:10.1088/0004-637x/764/1/85
  • Sergey N. Borovikov, Jacob Heerikhuisen, and Nikolai V. Pogorelov. "Hybrid Parallelization of Adaptive MHD-Kinetic Module in Multi-Scale Fluid-Kinetic Simulation Suite", Numerical Modeling of Space Plasma Flows (ASTRONUM2012), ASP Conference Series, San Francisco, CA, 2013, url: http://aspbooks.org/custom/publications/paper/474-0219.html
  • N. V. Pogorelov, et al. "Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite", Numerical Modeling of Space Plasma Flows (ASTRONUM2012), ASP Conference Series, San Francisco, CA, 2013, url: http://aspbooks.org/custom/publications/paper/474-0165.html
  • H. Kucharek, et al. "The Solar Wind as a Possible Source of Fast Temporal Variations of the Heliospheric Ribbon", ApJ, Vol. 776(2): 109, 2013, doi:10.1088/0004-637x/776/2/109
  • N. V. Pogorelov, et al. "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", ApJ, Vol. 772(1): 2, 2013, doi:10.1088/0004-637x/772/1/2
  • T. K. Kim, N. V. Pogorelov, G. P. Zank, H. A. Elliott, and D. J. McComas. "Modeling Solar Wind at the New Horizons Spacecraft", submitted to Astrophys. J. Lett., 2016, submitted

Quinn

  • Harshitha Menon, et al. "Adaptive Techniques for Clustered N-Body Cosmological Simulations", Comput. Astrophys., Vol. 2(1), 2015, doi:10.1186/s40668-015-0007-9
  • F. Governato, et al. "Faint Dwarfs as a Test of DM Models: WDM Versus CDM", Monthly Notices of the Royal Astronomical Society, Vol. 448(1): 792--803, 2015, doi:10.1093/mnras/stu2720
  • 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, Vol. 451(2): 1868--1874, 2015, doi:10.1093/mnras/stv1060
  • Sarah Loebman, et al. "Big-Data Management Use-Case", Proceedings of Workshop on Data analytics in the Cloud - DanaC'14, 2014, doi:10.1145/2627770.2627774
  • Thomas Quinn. "ChaNGa: a Charm++ N-body Treecode (2014)", 11th Ann. Charm++ Wksp., Urbana, IL, 2014
  • Thomas Quinn. "Presentation: The Cosmological Context of Star Formation", 2014, url: http://www.phas.ubc.ca/cosmological-context-star-formation
  • Lukasz Wesolowski, et al. "TRAM: Optimizing Fine-Grained Communication with Topological Routing and Aggregation of Messages", 2014 43rd International Conference on Parallel Processing, 2014, doi:10.1109/icpp.2014.30
  • Thomas Quinn. "ChaNGa: a Charm++ N-body Treecode", 11th Ann. Charm++ Wksp., Urbana, IL, 2013
  • Thomas Quinn. "Pathways to Exascale N-body Simulations", Exascale Computing in Astrophysics Conference, Ascona, Switzerland, 2013, url: https://www.youtube.com/watch?v=XP2yOMB9H8M

Rani

  • R. Dhariwal, Sarma L. Rani, and D. L. Koch. "Analysis and Comparison with DNS of a Stochastic Model for the Relative Motion of High-Stokes-Number Particles in Isotropic Turbulence", 68th Ann. Mtg. APS DFD, Boston, MA, 2015, url: https://meetings.aps.org/Meeting/DFD15/Session/M4.2
  • R. Dhariwal, Sarma L. Rani, and D. L. Koch. "Stochastic Theory and Direct Numerical Simulations of the Relative Motion of High-Inertia Particle Pairs in Isotropic Turbulenc", under review with the Journal of Fluid Mechanics, 2016, submitted

Rauber

  • Colin M. Zarzycki, et al. "Impact of Surface Coupling Grids on Tropical Cyclone Extremes in High-Resolution Atmospheric Simulations", Geoscientific Model Development, Vol. 9(2): 779--788, 2016, doi:10.5194/gmd-9-779-2016
  • Z. Zobel, J. Wang, D. J. Wuebbles, and V. R. Kotamarthi. "Evaluations of High-Resolution Dynamically Downscaled Ensembles over the Contiguous United States", Submitted to Climate Dynamics, 2016, submitted
  • J. T. Bacmeister, et al. "Projected Changes in Tropical Cyclone Activity Under Future Warming Scenarios Using a High-Resolution Climate Model", Submitted to Climatic Change, 2016, submitted

Reed

  • N. W. Chaney, J. D. Herman, P. M. Reed, and E. F. Wood. "Flood and Drought Hydrologic Monitoring: The Role of Model Parameter Uncertainty", Hydrol. Earth Syst. Sci., Vol. 19(7): 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, Vol. 51(1): 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", Environ. Res. Lett., Vol. 10(2): 024010, 2015, doi:10.1088/1748-9326/10/2/024010
  • Matthew Ferringer, Marc DiPrinzio, Timothy Thompson, Kyle Hanifen, and Patrick Reed. "A Framework for the Discovery of Passive-Control, Minimum Energy Satellite Constellations", AIAA/AAS Astrodynamics Specialist Conference, San Diego, CA, 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, Vol. 50(10): 8367--8373, 2014, doi:10.1002/2014wr015976
  • Matthew J. Woodruff, Patrick M. Reed, and Timothy W. Simpson. "Many Objective Visual Analytics: Rethinking the Design of Complex Engineered Systems", Struct Multidisc Optim, Vol. 48(1): 201--219, 2013, doi:10.1007/s00158-013-0891-z

Schulten

  • John E. Stone, et al. "Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing", Parallel Computing, Vol. 55, 2016, doi:10.1016/j.parco.2015.10.015
  • Chuang Liu, et al. "Cyclophilin a Stabilizes the HIV-1 Capsid Through a Novel Non-Canonical Binding Site", Nature Communications, Vol. 7, 2016, doi:10.1038/ncomms10714
  • Boon Chong Goh, et al. "Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis", Structure, Vol. 23(8): 1414--1425, 2015, doi:10.1016/j.str.2015.05.017
  • Juan R. Perilla, Boon Chong Goh, John Stone, and Klaus Schulten. "Chemical Visualization of Human Pathogens: the Retroviral Capsids", Proceedings of the 2015 ACM/IEEE Conference on Supercomputing, Austin, TX, 2015, url: http://sc15.supercomputing.org/sites/all/themes/SC15images/sci_vis/sci_vis_pages/svs112.html
  • C Keith Cassidy, et al. "CryoEM and Computer Simulations Reveal a Novel Kinase Conformational Switch in Bacterial Chemotaxis Signaling", eLife, Vol. 4, 2015, doi:10.7554/elife.08419
  • 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, Vol. 1850(5): 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", J. Am. Chem. Soc., Vol. 137(8): 3031--3040, 2015, doi:10.1021/ja512605w
  • Juan R Perilla, et al. "Molecular Dynamics Simulations of Large Macromolecular Complexes", Current Opinion in Structural Biology, Vol. 31, 2015, doi:10.1016/j.sbi.2015.03.007
  • David J. Hardy, et al. "Multilevel Summation Method for Electrostatic Force Evaluation", J. Chem. Theory Comput., Vol. 11(2): 766--779, 2015, doi:10.1021/ct5009075
  • Ramya Gamini, Wei Han, John E. Stone, and Klaus Schulten. "Assembly of Nsp1 Nucleoporins Provides Insight Into Nuclear Pore Complex Gating", PLoS Comput Biol, Vol. 10(3): e1003488, 2014, doi:10.1371/journal.pcbi.1003488
  • Milana Fraiberg, et al. "CheY's Acetylation Sites Responsible for Generating Clockwise Flagellar Rotation in E Scherichia Coli", Molecular Microbiology, Vol. 95(2): 231--244, 2014, doi:10.1111/mmi.12858
  • Wei Jiang, et al. "Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD", Computer Physics Communications, Vol. 185(3): 908--916, 2014, doi:10.1016/j.cpc.2013.12.014
  • 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 Discuss., Vol. 169, 2014, doi:10.1039/c4fd00005f
  • Michaël L. Cartron, et al. "Integration of Energy and Electron Transfer Processes in the Photosynthetic Membrane of Rhodobacter Sphaeroides", Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1837(10): 1769--1780, 2014, doi:10.1016/j.bbabio.2014.02.003
  • Danielle E. Chandler, Johan Strümpfer, Melih Sener, Simon Scheuring, and Klaus Schulten. "Light Harvesting by Lamellar Chromatophores in Rhodospirillum Photometricum", Biophysical Journal, Vol. 106(11): 2503--2510, 2014, doi:10.1016/j.bpj.2014.04.030
  • Shanmugapriya Sothiselvam, et al. "Macrolide Antibiotics Allosterically Predispose the Ribosome for Translation Arrest", Proceedings of the National Academy of Sciences, Vol. 111(27): 9804--9809, 2014, doi:10.1073/pnas.1403586111
  • 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", SC14: International Conference for High Performance Computing, Networking, Storage and Analysis, New Orleans, LA, 2014, doi:10.1109/sc.2014.12
  • James C. Phillips, et al. "Petascale Tcl with NAMD, VMD, and Swift/T", 2014 First Workshop for High Performance Technical Computing in Dynamic Languages, 2014, doi:10.1109/hptcdl.2014.7
  • Zhe Wu, and Klaus Schulten. "Synaptotagmin's Role in Neurotransmitter Release Likely Involves Ca2+-induced Conformational Transition", Biophysical Journal, Vol. 107(5): 1156--1166, 2014, doi:10.1016/j.bpj.2014.07.041
  • Mark D. Klein, and John E. Stone. "Unlocking the Full Potential of the Cray XK7 Accelerator", Cray User Group Conference, Lugano Switzerland, 2014, url: https://cug.org/proceedings/cug2014_proceedings/includes/files/pap110.pdf
  • Melih Sener, et al. "Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail", SC'14 Visualization and Data Analytics Showcase, New Orleans, LA, 2014, url: http://sc14.supercomputing.org/sites/all/themes/sc14/files/archive/sci_vis/sci_vis_pages/svs115.html
  • Xue Wang, et al. "Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography", PLoS Pathog, Vol. 9(1): e1003132, 2013, doi:10.1371/journal.ppat.1003132
  • John E. Stone, Barry Isralewitz, and Klaus Schulten. "Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters", 2013 Extreme Scaling Workshop (xsw 2013), Boulder, CO, 2013, doi:10.1109/xsw.2013.10
  • John E. Stone. "Fighting HIV with GPU-Accelerated Petascale Computing", SC13 Exhibition, Denver, CO, 2013, url: http://www.ks.uiuc.edu/Research/gpu/files/sc2013nvidia_stone.pdf
  • John E. Stone, Kirby L. Vandivort, and Klaus Schulten. "GPU-Accelerated Molecular Visualization on Petascale Supercomputing Platforms", Proceedings of the 8th International Workshop on Ultrascale Visualization - UltraVis '13, 2013, doi:10.1145/2535571.2535595
  • John E. Stone. "Interactive molecular visualization and analysis with GPU computing", ACS National Meeting, San Diego, CA, 2013, url: http://on-demand.gputechconf.com/gtc/2014/presentations/S4410-visualization-analysis-petascale-moledular-sims.pdf
  • John E. Stone. "Interactive molecular visualization and analysis with GPU computing (GPU Computing Symp.)", GPU Computing Symp., Indianapolis, IN, 2013, url: http://on-demand.gputechconf.com/gtc/2014/presentations/S4410-visualization-analysis-petascale-moledular-sims.pdf
  • Gongpu Zhao, et al. "Mature HIV-1 Capsid Structure by Cryo-Electron Microscopy and All-Atom Molecular Dynamics", Nature, Vol. 497(7451): 643--646, 2013, doi:10.1038/nature12162
  • John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten. "High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL", 2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), 2016, submitted
  • John E. Stone, William R. Sherman, and Klaus Schulten. "Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering", 2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), 2016, submitted

Simpson

  • 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", Antennas Wirel. Propag. Lett., 2016, doi:10.1109/lawp.2016.2545526
  • A. Samimi, M. Rodriguez, N. Dupree, R. Moore, and J. J. Simpso. "The Application of Global 3-D FDTD Earth-ionosphere Models to VLF Propagation: Comparison with LWP", IEEE AP-S International Symposium and USNC/URSI National Radio Science Meeting, Puerto Rico, 2016

Srinivasan

  • C. D. Sudheer, and Ashok Srinivasan. "Efficient Barrier Implementation on the POWER8 Processor", 2015 IEEE 22nd International Conference on High Performance Computing (HiPC), 2015, doi:10.1109/hipc.2015.51

Stan

Stein

  • Unknown. "Flux Emergence and Active Region Formation", NORDITA invited talk, Stockholm, Sweden, 2015
  • Granules. "Flux Emergence and Subsurface Structure of Sunspots", Max Planck Institute for Solar System Research Colloquium, Göttingen, Germany, 2015
  • Kaori Nagashima, et al. "Interpreting the Helioseismic and Magnetic Imager (HMI) Multi-Height Velocity Measurements", Solar Physics, Vol. 289(9): 3457--3481, 2014, doi:10.1007/s11207-014-0543-5
  • R. Stein, and A. Nordlund. "Simulations of Magnetic Flux Emergence", 40th COSPAR Scientific Assembly, Moscow, Russia, 2014, url: http://adsabs.harvard.edu/abs/2014cosp...40E3196S

Sugar

  • Daniel R. Bolton, Raúl A. Briceño, and David J. Wilson. "Connecting Physical Resonant Amplitudes and Lattice QCD", Physics Letters B, Vol. 757, 2016, doi:10.1016/j.physletb.2016.03.043
  • A. Bazavov, et al. "Gradient Flow and Scale Setting on MILC HISQ Ensembles", Physical Review D, Vol. 93(9), 2016, doi:10.1103/physrevd.93.094510
  • David J. Wilson, Raúl A. Briceño, Jozef J. Dudek, Robert G. Edwards, and Christopher E. Thomas. "Coupled ππ , KK Scattering in P-Wave and the ρ Resonance from Lattice QCD", Physical Review D, Vol. 92(9), 2015, doi:10.1103/physrevd.92.094502
  • David J. Wilson, Jozef J. Dudek, Robert G. Edwards, and Christopher E. Thomas. "Resonances in Coupled πK, ηK Scattering from Lattice QCD", Physical Review D, Vol. 91(5), 2015, doi:10.1103/physrevd.91.054008
  • Raúl A. Briceño, et al. "Resonant π+γ→π+π0 Amplitude from Quantum Chromodynamics", Phys. Rev. Lett., Vol. 115(24), 2015, doi:10.1103/physrevlett.115.242001
  • F.T. Winter, M.A. Clark, R.G. Edwards, and B. Joo. "A Framework for Lattice QCD Calculations on GPUs", 2014 IEEE 28th International Parallel and Distributed Processing Symposium, Phoenix, AZ, 2014, doi:10.1109/ipdps.2014.112
  • A. Bazavov, et al. "Charmed and Light Pseudoscalar Meson Decay Constants from Four-Flavor Lattice QCD with Physical Light Quarks", Physical Review D, Vol. 90(7), 2014, doi:10.1103/physrevd.90.074509
  • Bazavov, et al. "Charmed and Light Pseudoscalar Meson Decay Constants from HISQ Simulations", Proceedings of the 32nd International Symposium on Lattice Field Theory, Columbia University, New York, 2014, url: https://arxiv.org/pdf/1411.2667v1
  • A. Bazavov, et al. "Determination of |Vus| from a Lattice QCD Calculation of the K→πℓν Semileptonic Form Factor with Physical Quark Masses", Phys. Rev. Lett., Vol. 112(11), 2014, doi:10.1103/physrevlett.112.112001
  • A. Bazavov, et al. "Gradient Flow Analysis on MILC HISQ Ensembles", Proceedings of the 32nd International Symposium on Lattice Field Theory, Columbia University, New York, 2014, url: http://arxiv.org/abs/1411.0068
  • Thomas Primer, Doug Toussaint, Aida El-Khadra, Elvira Gámiz, James Simone. "Kaon and D Meson Semileptonic Form Factors from Lattice QCD", Proceedings of the 32nd International Symposium on Lattice Field Theory, Columbia University, New York, 2014, url: http://arxiv.org/abs/1411.1651
  • Daniel Mohler, et al. "Low Lying Charmonium States at the Physical Point", Proceedings of the 32nd International Symposium on Lattice Field Theory, Columbia University, New York, 2014, url: https://arxiv.org/abs/1412.1057
  • Jozef J. Dudek, Robert G. Edwards, Christopher E. Thomas, and David J. Wilson. "Resonances in Coupled πK-ηK Scattering from Quantum Chromodynamics", Phys. Rev. Lett., Vol. 113(18), 2014, doi:10.1103/physrevlett.113.182001
  • A. Bazavov, et al. "Charmed and Strange Pseudoscalar Meson Decay Constants from HISQ Simulations", Proceedings of 31st International Symposium on Lattice Field Theory LATTICE 2013, Mainz, Germany, 2013, url: https://arxiv.org/abs/1312.0149
  • E. Gámiz, et al. "K Semileptonic Form Factor with HISQ Fermions at the Physical Point", Proceedings of 31st International Symposium on Lattice Field Theory LATTICE 2013, 2013, url: http://arxiv.org/abs/1311.7264
  • A. Bazavov, et al. "Lattice QCD Ensembles with Four Flavors of Highly Improved Staggered Quarks", Physical Review D, Vol. 87(5), 2013, doi:10.1103/physrevd.87.054505
  • A. Bazavov, et al. "Leptonic-Decay-Constant Ratio fK+/fπ+ from Lattice QCD with Physical Light Quarks", Phys. Rev. Lett., Vol. 110(17), 2013, doi:10.1103/physrevlett.110.172003
  • A. Bazavov, et al. "Symanzik Flow on HISQ Ensembles", Proceedings of 31st International Symposium on Lattice Field Theory LATTICE 2013, Mainz, Germany, 2013, url: https://arxiv.org/abs/1311.1474
  • A. Bazavov, et al. "The Ds, D+, Bs and B decay constants from 2+1 flavor lattice QCD", Proceedings of 31st International Symposium on Lattice Field Theory LATTICE 2013, Mainz, Germany, 2013, url: http://lss.fnal.gov/archive/2013/conf/fermilab-conf-13-585-t.pdf
  • A. Bazavov, et al. "Update on the 2+1+1 Flavor QCD Equation of State with HISQ", Proceedings of 31st International Symposium on Lattice Field Theory LATTICE 2013, Mainz, Germany, 2013, url: http://arxiv.org/abs/1312.5011
  • Thomas Primer, et al. "D-meson Semileptonic Form Factors at Zero Momentum Transfer in (2+1+1)-Flavor Lattice QCD", to be published in Proceedings of Science (Lattice 2015), 2015, submitted
  • A. Bazavov et al. "Decay Constants fB and fBs from HISQ Simulations", to be published in Proceedings of Science (Lattice 2015), 2015, submitted

Tagkopoulos

  • Andreas Pavlogiannis, Vadim Mozhayskiy, and Ilias Tagkopoulos. "A Flood-Based Information Flow Analysis and Network Minimization Method for Gene Regulatory Networks", BMC Bioinformatics, Vol. 14(1): 137, 2013, doi:10.1186/1471-2105-14-137
  • Vadim Mozhayskiy, and Ilias Tagkopoulos. "Microbial Evolution in Vivo and in Silico: Methods and Applications", Integr. Biol., Vol. 5(2): 262--277, 2013, doi:10.1039/c2ib20095c

Voth

  • John M. A. Grime, et al. "Coarse-Grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly", Nature Communications, Vol. 7, 2016, doi:10.1038/ncomms11568
  • John. M. A. Grime, and Gregory A. Voth. "Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations", J. Chem. Theory Comput., Vol. 10(1): 423--431, 2014, doi:10.1021/ct400727q
  • James F. Dama, et al. "The Theory of Ultra-Coarse-Graining. 1. General Principles", J. Chem. Theory Comput., Vol. 9(5): 2466--2480, 2013, doi:10.1021/ct4000444

Wang

  • 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", Procedia Computer Science, Vol. 18, 2013, doi:10.1016/j.procs.2013.05.222
  • 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, Vol. 26(6): 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, Vol. 51, 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, Vol. 61, 2013, doi:10.1016/j.cageo.2013.08.013

Wilhelmson

  • Leigh Orf, Robert Wilhelmson, and Louis Wicker. "Visualization of a Simulated Long-Track EF5 Tornado Embedded Within a Supercell Thunderstorm", Parallel Computing, 2015, doi:10.1016/j.parco.2015.10.014

Woodward

  • Pei-Hung Lin, and Paul R. Woodward. "Transforming the Multifluid PPM Algorithm to Run on GPUs", Journal of Parallel and Distributed Computing, Vol. 93-94, 2016, doi:10.1016/j.jpdc.2016.04.005
  • Ted Wetherbee, Elizabeth Jones, Michael Knox, Stou Sandalski, and Paul Woodward. "In-Core Volume Rendering for Cartesian Grid Fluid Dynamics Simulations", Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15, St. Louis, Mo, 2015, doi:10.1145/2792745.2792780
  • Falk Herwig, Paul R. Woodward, Pei-Hung Lin, Mike Knox, and Chris Fryer. "Global Non-Spherical Oscillations in 3-D 4π Simulations of the H-Ingestion Flash", Astrophysical Journal Letters, Vol. 792(1): L3, 2014, doi:10.1088/2041-8205/792/1/l3
  • Falk Herwig, Paul R. Woodward, Pei-Hung Lin, Mike Knox, and Chris Fryer. "Global Non-Spherical Oscillations in 3-D 4π Simulations of the H-Ingestion Flash", ApJ, Vol. 792(1): L3, 2014, doi:10.1088/2041-8205/792/1/l3
  • Paul R. Woodward, Falk Herwig, and Pei-Hung Lin. "Hydrodynamic Simulations of H Entrainment at the Top of He-Shell Flash Convection", Astrophysical Journal, Vol. 798(1): 49, 2014, doi:10.1088/0004-637x/798/1/49
  • Paul R. Woodward, Falk Herwig, and Pei-Hung Lin. "Hydrodynamic Simulations of H Entrainment at the Top of He-Shell Flash Convection", ApJ, Vol. 798(1): 49, 2014, doi:10.1088/0004-637x/798/1/49
  • Paul R. Woodward, et al. "Scaling the Multifluid PPM Code on Blue Waters and Intel MIC", 2013 Extreme Scaling Workshop (xsw 2013), Boulder, CO, 2013, doi:10.1109/xsw.2013.13

Woosley

  • Max P. Katz, et al. "White Dwarf Mergers on Adaptive Meshes I. Methodology and Code Verification", ApJ, Vol. 819(2): 94, 2016, doi:10.3847/0004-637x/819/2/94
  • 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", ApJ, Vol. 807(1): 60, 2015, doi:10.1088/0004-637x/807/1/60
  • C. M. Malone, et al. "The Deflagration Stage of Chandrasekhar Mass Models for Type Ia Supernovae. I. Early Evolution", ApJ, Vol. 782(1): 11, 2014, doi:10.1088/0004-637x/782/1/11
  • C.M. Malone, et al. "From Convection to Ignition and Beyond: A (Computational) Story of MCh SNIa", Bulletin of the American Astronomical Society, 43, 2013, url: http://adsabs.harvard.edu/abs/2013AAS...22144402M
  • 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", accepted in ApJ, 2016, submitted

Wuebbles

  • D. Wuebbles, W. Washington, G. Meehl, and T. Bettge. "High-Resolution Earth System Global and Regional Modeling for Climate Assessment and Policymaking Require Advanced Computing Infrastructure", NRC Meeting on Computations for Science and Technology, Dallas, TX, 2015
  • K. A. Reed, et al. "Impact of the Dynamical Core on the Direct Simulation of Tropical Cyclones in a High-Resolution Global Model", Geophys. Res. Lett., Vol. 42(9): 3603--3608, 2015, doi:10.1002/2015gl063974
  • D. Wuebbles. "Modeling the Earth's Climate System: from Petascale to Exascale. (Video)", University of Illinois CSE Annual Meeting, Urbana, IL, 2013, url: https://www.youtube.com/watch?v=kTq_uiD-1Ys

Yeung

  • P.K Yeung. "High-Reynolds-Number Turbulence in a Petascale Computational Laboratory", Invited keynote lecture, EuHiT Turbulence Conference, Gottingen, Germany, 2016, url: https://www.euhit.org/events/euhit-turbulence-conference
  • 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, Vol. 27(10): 105101, 2015, doi:10.1063/1.4931602
  • P. K. Yeung, X. M. Zhai, and Katepalli R. Sreenivasan. "Extreme Events in Computational Turbulence", Proceedings of the National Academy of Sciences, Vol. 112(41): 12633--12638, 2015, doi:10.1073/pnas.1517368112
  • P. K. Yeung, D. Buaria, and B.L. Sawford. "Forward and Backward Relative Dispersion at High Reynolds Number", Int. Workshop on Cloud Turbulence, Nagoya, Japan, 2015
  • Kartik P. Iyer, Katepalli R. Sreenivasan, and P. K. Yeung. "Refined Similarity Hypothesis Using Three-Dimensional Local Averages", Physical Review E, Vol. 92(6), 2015, doi:10.1103/physreve.92.063024
  • D. Buaria, and P. K. Yeung. "Challenges in Particle Tracking in Turbulence on a Massive Scale", Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE '14, Atlanta, GA, 2014, doi:10.1145/2616498.2616526
  • 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, Vol. 26(1): 015107, 2014, doi:10.1063/1.4861070
  • Dhawal Buaria, Pui-Kuen Yeung, and Brian Sawford. "Direct Numerical Simulations of the Dispersion of Molecules in Isotropic Turbulence", Proceedings of the 19th Australasian Fluid Mechanics Conference, Melbourne, Australia, 2014, url: http://people.eng.unimelb.edu.au/imarusic/proceedings/19/485.pdf
  • P. K. Yeung. "Early Results from High Reynolds Number DNS at 8,192^3 Resolution", Second Int. Conf. on Mathem. Theory Turbulence via Harmonic Analysis and Comput. Fluid Dyn., Nara, Japan, 2014
  • 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, Vol. 26(8): 085107, 2014, doi:10.1063/1.4892581
  • K. P. Iyer. "Studies of Turbulence Structure and Turbulent Mixing Using Petascale Computing", PhD thesis, 2014, url: https://smartech.gatech.edu/bitstream/handle/1853/52260/KESHAVAIYER-DISSERTATION-2014.pdf
  • P.K Yeung, X. M. Zhai, and K. R. Sreenivasan. "Turbulence at High Resolution: Intense Events in Dissipation, Enstrophy and Acceleration", 67th Annual Meeting of the APS Division of Fluid Dynamics, San Francisco, CA, 2014, url: http://meetings.aps.org/Meeting/DFD14/Session/H27.1
  • P.K Yeung. "Extreme Events and Acceleration Statistics at High Reynolds Number", Invited speakerin "Turbulence" Thematic Session, International Congress on Theoretical and Applied Mechanics, Montreal, Canada, 2016, submitted

Zhang

  • Huihuo Zheng, and Lucas K. Wagner. "Computation of the Correlated Metal-Insulator Transition in Vanadium Dioxide from First Principles", Phys. Rev. Lett., Vol. 114(17), 2015, doi:10.1103/physrevlett.114.176401
  • H. Zheng, and L. K. Wagner. "Ab initio Study of Metal-Insulator Transition in VO2", American Physical Society, APS March Meeting 2013, Baltimore, MD, 2013, url: http://meetings.aps.org/Meeting/MAR13/Event/182788
  • L. K. Wagner, and P. Abbamonte. "Anomalous Spin and Lattice Coupling in La2CuO4 Calculated by First-Principles Quantum Monte Carlo", Superconductivity Gordon Research Conference, Les Diablerets, Switzerland, 2013, url: https://www.orau.gov/scidac3pi2013/presentations/posters/Poster54.pdf
  • F. Ma, S. Zhang, H. Krakauer, and W. Purwanto. "Auxiliary-Field Quantum Monte Carlo Calculations in Solids", ES2013: 25th Annual Workshop on Recent Developments in Electronic Structure Methods, Williamsburg, VA, 2013
  • S. Zhang. "Auxiliary-Field Quantum Monte Carlo for Correlated Electron Systems", Emergent Phenomena in Correlated Matter: Modeling and Simulation, ISBN 978-3-89336-884-6, 2013, url: http://www.cond-mat.de/events/correl13/manuscripts/zhang.pdf
  • L. K. Wagner. "Can We Understand the High-Tc Superconducting Cuprates from First Principles?", The 8th Quantum Monte Carlo in the Apuan Alps International Workshop, Vallico Sotto, Italy, 2013, url: http://www.tcm.phy.cam.ac.uk/~mdt26/tti_talks/qmcitaa_13/wagner_tti2013.pdf
  • S. Zhang. "Computing Electron Correlation Effects: an Auxiliary-Field Perspective", New Frontiers in Electron Correlation, Telluride, CO, 2013
  • Fengjie Ma, Shiwei Zhang, and Henry Krakauer. "Excited State Calculations in Solids by Auxiliary-Field Quantum Monte Carlo", New Journal of Physics, Vol. 15(9): 093017, 2013, doi:10.1088/1367-2630/15/9/093017
  • Wirawan Purwanto, Shiwei Zhang, and Henry Krakauer. "Frozen-Orbital and Downfolding Calculations with Auxiliary-Field Quantum Monte Carlo", J. Chem. Theory Comput., Vol. 9(11): 4825--4833, 2013, doi:10.1021/ct4006486
  • Hao Shi, and Shiwei Zhang. "Symmetry in Auxiliary-Field Quantum Monte Carlo Calculations", Phys. Rev. B, Vol. 88(12), 2013, doi:10.1103/physrevb.88.125132

Illinois Allocation Teams

Aksimentiev

  • Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev. "De Novo Reconstruction of DNA Origami Structures Through Atomistic Molecular Dynamics Simulation", Nucleic Acids Res, Vol. 44(7): 3013--3019, 2016, doi:10.1093/nar/gkw155
  • Yue-xiao Shen, et al. "Highly Permeable Artificial Water Channels That Can Self-Assemble Into Two-Dimensional Arrays", Proceedings of the National Academy of Sciences, Vol. 112(32): 9810--9815, 2015, doi:10.1073/pnas.1508575112
  • Chen-Yu Li, et al. "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field", ACS Nano, Vol. 9(2): 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", J. Phys. Chem. Lett., Vol. 6(23): 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, Vol. 9(11): 10598--10611, 2015, doi:10.1021/acsnano.5b04173
  • C. Maffeo, J. Yoo, and A. Aksimentiev. "Poster: De Novo Prediction of DNA Origami Structure Through Atomistic Molecular Dynamics Simulation", DNA21: 21st Interna-tional Conference on DNA Computing and Molecular Programming, Boston, MA, 2015
  • A. Aksimentiev. "Presentation: DNA Ion Channels", Telluride Science Workshop on Ion Channel Biophysics, Telluride, CO, 2015
  • C.-Y. Li. "Presentation: Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field", FNANO2015, Snowbird, Utah, 2015
  • A. Aksimentiev. "Presentation: Molecular Dynamics of DNA Origami (2015)", NCSA Blue Waters Symposium for Petascale Science and Beyond, Sunriver, Oregon, 2015
  • A. Aksimentiev. "Presentation: Nanopore Sequencing: State of the Art and Future Directions", 5th Annual Next Generation Sequencing Asia Congress, Singapore, 2015
  • C.-Y. Li. "Presentation:Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field", Student–Postdoc Biophysics Symposium, Urbana, IL, 2015
  • C Maffeo, et al. "Close Encounters with DNA", Journal of Physics: Condensed Matter, Vol. 26(41): 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, Vol. 5, 2014, doi:10.1038/ncomms6171
  • Maxim Belkin, Shu-Han Chao, Gino Giannetti, and Aleksei Aksimentiev. "Modeling Thermophoretic Effects in Solid-State Nanopores", J Comput Electron, Vol. 13(4): 826--838, 2014, doi:10.1007/s10825-014-0594-8
  • C.-Y. Li, J. Yoo, and A. Aksimentiev. "Poster: Ion Conductivity, Structural Dynamics and the Effective Force in DNA Origami Nanopores", 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, 2014
  • A. Aksimentiev. "Presentation: Engineering DNA Origami Through Microscopic Sim-ulations", Workshop on Origami Engineering, Urbana, IL, 2014
  • A. Aksimentiev. "Presentation: Meeting Materials Challenges in Nanopore Sequencing of DNA", CECAM workshop "Simulations of biomolecular interactions with inorganic and organic surfaces as a challenge for future nanotechnologies", Toulouse, France, 2014
  • A. Aksimentiev. "Presentation: Modeling Nanopores for Sequencing DNA", Gordon Research Conference on Biointerface Science, Lucca, Italy, 2014
  • A. Aksimentiev. "Presentation: Molecular Dynamics of DNA Origami", Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO14), Snowbird, Utah, 2014
  • A. Aksimentiev. "Presentation: New Approaches to Sequencing DNA Using a Nanopore", 2014 Pioneer workshop on nanopore and nanofluidics "Physics and application as Biodevices", Osaka, Japan, 2014
  • A. Aksimentiev. "Presentation: Reinventing a DNA Sequence Reader", Distinguished Lecture Series "Nanotechnologies through Materials Innovation", Boston, MA, 2014
  • Shouvik Banerjee, et al. "Slowing DNA Transport Using Graphene-DNA Interactions", Adv. Funct. Mater., Vol. 25(6): 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, Vol. 107(10): 2381--2393, 2014, doi:10.1016/j.bpj.2014.10.017
  • M. Belkin and A. Aksimentiev. "Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores", submitted
  • S. Slone, J. Yoo, C.-Y. Li, and A. Aksimentiev. "Molecular Mechanics of DNA Bricks: In Situ Structure, Mechanical Properties and Ionic Conductivity", submitted

Althaus

  • Boris Capitanu, et al. "Extracted Feature Dataset from 4.8 Million HathiTrust Digital Library Public Domain Volumes", 2015, doi:10.13012/j8td9v7m

Aluru

  • A. Barati Farimani, M. Heiranian, and N. R. Aluru. "Electromechanical Signatures for DNA Sequencing Through a Mechanosensitive Nanopore", J. Phys. Chem. Lett., Vol. 6(4): 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", The Journal of Chemical Physics, Vol. 142(23): 234702, 2015, doi:10.1063/1.4922491
  • Amir Barati Farimani, Kyoungmin Min, and Narayana R. Aluru. "DNA Base Detection Using a Single-Layer MoS 2", ACS Nano, Vol. 8(8): 7914--7922, 2014, doi:10.1021/nn5029295

Bodony

Buchta

  • David Buchta, Aaron Anderson, and Jonathan B. Freund. "Near-Field Shocks Radiated by High-Speed Free-Shear-Flow Turbulence", 20th AIAA/CEAS Aeroacoustics Conference, 2014, doi:10.2514/6.2014-3201

Cann

  • 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, Vol. 1850(5): 872--877, 2015, doi:10.1016/j.bbagen.2014.10.019
  • Constantin Schoeler, et al. "Ultrastable Cellulosome-Adhesion Complex Tightens Under Load", Nature Communications, Vol. 5, 2014, doi:10.1038/ncomms6635

Ceperley

  • 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, Vol. 113(18): 4953--4957, 2016, doi:10.1073/pnas.1603853113

Chew

  • Haoran Wang, and Huck Beng Chew. "Molecular Dynamics Simulations of Plasticity and Cracking in Lithiated Silicon Electrodes", Extreme Mechanics Letters, 2016, doi:10.1016/j.eml.2016.02.020
  • Abhilash Harpale, Marco Panesi, and Huck Beng Chew. "Plasma-Graphene Interaction and Its Effects on Nanoscale Patterning", Phys. Rev. B, Vol. 93(3), 2016, doi:10.1103/physrevb.93.035416
  • 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, Vol. 15(3): 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", The Journal of Chemical Physics, Vol. 143(10): 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, Vol. 95(25): 2747--2763, 2015, doi:10.1080/14786435.2015.1077283
  • 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", The Journal of Chemical Physics, Vol. 142(6): 061101, 2015, doi:10.1063/1.4907716
  • Ruizhi Li, and Huck Beng Chew. "Planar-to-Wavy Transition of Cu-Ag Nanolayered Metals: A Precursor Mechanism to Twinning", Philosophical Magazine, Vol. 95(10): 1029--1048, 2015, doi:10.1080/14786435.2015.1006290

Cho

Clark

  • Xiao Chen, Xiongjie Yu, Gil Young Cho, Bryan K. Clark, and Eduardo Fradkin. "Many-Body Localization Transition in Rokhsar-Kivelson-Type Wave Functions", Phys. Rev. B, Vol. 92(21), 2015, doi:10.1103/physrevb.92.214204
  • Bryan Clark. "Presentation: A Variational Approach to Strongly Correlated Systems", Invited talk. Summer School on Emergent Phenomena in Quantum Materials, Cornell University, 2015, url: https://www.youtube.com/watch?v=Gv377Ismdo0
  • Bryan Clark. "Presentation: From Ab‐Initio to Model Systems: Tales of Unusual Conductivity in Electronic Systems at High Temperatures", Invited talk. ES15, Seattle, WA, 2015, url: http://feffproject.org/ES2015/InvitedAbstract/ClarkBryan.pdf
  • Bryan Clark. "Poster: From Variational Ansatz to 'Exact' Results: A Numerical Exploration of Models of Strongly Correlated Systems", Invited talk. EPIQS conference, Intertwined Orders in Strongly Correlated Systems
  • Bryan Clark. "Presentation: Many‐Body Localization: Quantum Mechanics at Infinite Temperature", Invited talk. Condensed Matter Seminar at University of Indianapolis, Bloomington, In
  • Bryan Clark. "Presentation: MBL and Tensor Networks", Invited talk. KITP Many Body Localization
  • Xiongjie Yu, David J. Luitz, and Bryan K. Clark. "Bimodal Entanglement Entropy Distribution in the Many-Body Localization Transition", 2016, submitted
  • Xiongjie Yu, David Pekker, and Bryan K. Clark. "Finding Matrix Product State Representations of Highly-Excited Eigenstates of Many-Body Localized Hamiltonians", 2015, submitted

Cox

Di Girolamo

  • A. L. Jones. "Development of an Accurate 3D Monte Carlo Broadband Atmospheric Radiative Transfer Model", Ph.D. Dissertation, University of Illinois, Urbana, IL, 2016
  • Guangyu Zhao, et al. "Regional Changes in Earth's Color and Texture as Observed from Space Over a 15-Year Period", IEEE Trans. Geosci. Remote Sensing, Vol. 54(7): 4240--4249, 2016, doi:10.1109/tgrs.2016.2538723
  • L. Di Girolamo, L. Liang, and W. Sun. "Bias in MODIS Cloud Drop Effective Radius for Oceanic Water Clouds as Deduced From Measured Cloud Optical Thickness Variability Across Scattering Angles", Joint Assembly of the AGU-GAC-MAC-CGU, Montreal, Canada, 2015
  • L. Di Girolamo, L. Liang, and W. Sun. "Bias in MODIS Cloud Drop Effective Radius for Oceanic Water Clouds as Deduced From Measured Cloud Optical Thickness Variability Across Scattering Angles (MD)", MODIS Science Team Meeting, Silver Spring, MD, 2015
  • 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, Vol. 120(15): 7661--7681, 2015, doi:10.1002/2015jd023256
  • A. L. Jones. "Development of a Highly Accurate 3D Radiative Transfer Model", University of Illinois Atmospheric Sciences Colloquia Series, Urbana, IL, 2015, url: http://illinois.edu/calendar/detail/3491?eventId=32381175&calMin=201504&cal=20150401&skinId=4709
  • A Jones, and L.Di Girolamo. "High Accuracy 3D Radiative Transfer in Cloudy Atmospheres", Blue Waters Symposium, Sunriver, OR, 2015
  • Alexandra Jones, and Larry Di Girolamo. "A New Spectrally Integrating 3D Monte Carlo Radiative Transfer Model", 14th Conference on Atmospheric Radiation, Boston, MA, 2014, url: https://ams.confex.com/ams/14CLOUD14ATRAD/webprogram/Paper249363.html
  • L. Di Girolamo. "Blue Waters Applications of 3D Monte Carlo Atmospheric Radiative Transfer", Blue Waters Symposium, Urbana, IL, 2014

Ertekin

  • Joshua A. Schiller, Lucas K. Wagner, and Elif Ertekin. "Phase Stability and Properties of Manganese Oxide Polymorphs: Assessment and Insights from Diffusion Monte Carlo", Phys. Rev. B, Vol. 92(23), 2015, doi:10.1103/physrevb.92.235209
  • Taishan Zhu, and Elif Ertekin. "Resolving Anomalous Strain Effects on Two-Dimensional Phonon Flows: The Cases of Graphene, Boron Nitride, and Planar Superlattices", Phys. Rev. B, Vol. 91(20), 2015, doi:10.1103/physrevb.91.205429
  • 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", The Journal of Chemical Physics, Vol. 143(22): 224707, 2015, doi:10.1063/1.4937421
  • Taishan Zhu, and Elif Ertekin. "Phonon Transport on Two-Dimensional Graphene/boron Nitride Superlattices", Phys. Rev. B, Vol. 90(19), 2014, doi:10.1103/physrevb.90.195209
  • Jaehyung Yu, Lucas K. Wagner, and Elif Ertekin. "Quantum Monte Carlo Simulations of Nitrogen Defects in Zinc Oxide", submitted

Gregg

  • Y. Zhan, and P. M. Gregg. "Data Assimilation Strategies for Volcano Geodesy", Journal of Volcanology and Geothermal Research, 2016, submitted

Gropp

Hammes-Schiffer

  • 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", The Journal of Physical Chemistry B, Vol. 120(9): 2407--2417, 2016, doi:10.1021/acs.jpcb.5b12015
  • Puja Goyal, Christine A. Schwerdtfeger, Alexander V. Soudackov, and Sharon Hammes-Schiffer. "Nonadiabatic Dynamics of Photoinduced Proton-Coupled Electron Transfer in a Solvated Phenol-Amine Complex", The Journal of Physical Chemistry B, Vol. 119(6): 2758--2768, 2015, doi:10.1021/jp5126969
  • 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", The Journal of Chemical Physics, Vol. 142(21): 214108, 2015, doi:10.1063/1.4921304
  • Andrew Sirjoosingh, Michael V. Pak, Kurt R. Brorsen, and Sharon Hammes-Schiffer. "Quantum Treatment of Protons with the Reduced Explicitly Correlated Hartree-Fock Approach", The Journal of Chemical Physics, Vol. 142(21): 214107, 2015, doi:10.1063/1.4921303
  • Andrew Sirjoosingh and Sharon Hammes-Schiffer. "Development of Non-Born-Oppenheimer Electronic Structure Methods for the Quantum Treatment of Protons", Poster. American Conference on Theoretical Chemistry, 2014
  • Sharon Hammes-Schiffer. "Presentation: Nonadiabatic Dynamics of Photoinduced Proton-Coupled Electron Transfer Processes", Invited talk: American Chemical Society National Meeting, San Francisco, CA, 2014
  • Sharon Hammes-Schiffer. "Presentation: Proton-Coupled Electron Transfer in Catalysis and Energy Conversion", Invited talk: Distinguished Lecture in Theoretical and Computational Chemistry, University of California at San Diego, San Diego, CA, 2014
  • Sharon Hammes-Schiffer. "Presentation: Proton-Coupled Electron Transfer in Catalysis and Energy Conversion (Illinois)", Colloquium, Northwestern University, Evanston, IL, 2014
  • Sharon Hammes-Schiffer. "Presentation: Proton-Coupled Electron Transfer in Catalysis and Energy Conversion (Oslo)", Plenary talk: Promoting Female Excellence in Theoretical and Computational Chemistry II, Oslo, Norway, 2014
  • Sharon Hammes-Schiffer. "Presentation: Proton-Coupled Electron Transfer in Catalysis and Energy Conversion (Rochester)", Invited talk: Colloquium, University of Rochester, 2014
  • Sharon Hammes-Schiffer. "Presentation: Proton-Coupled Electron Transfer in Energy Conversion Processes", Invited talk: Haines Lecture, University of South Dakota, 2014
  • Sharon Hammes-Schiffer. "Presentation: Theoretical Perspectives of Proton-Coupled Electron Transfer and Applications to Catalysis", Invited talk: PCET 2014: Second International Conference on Proton-Coupled Electron Transfer, Uppsala, Sweden, 2014
  • Sharon Hammes-Schiffer. "Presentation: Theoretical Perspectives of Proton-Coupled Electron Transfer and Applications to Catalysis (Colorado)", Invited talk: American Conference of Theoretical Chemistry, Telluride, CO, 2014
  • Sharon Hammes-Schiffer. "Presentation: Theoretical Perspectives of Proton-Coupled Electron Transfer and Applications to Catalysis (Rome)", Invited talk: International Conference on Hydrogen Atom Transfer, Rome, Italy, 2014
  • Sharon Hammes-Schiffer. "Theoretical Perspectives on Proton-Coupled Electron Transfer and Applications to Catalysis", Invited Talk. Poster. American Conference on Theoretical Chemistry, 2014
  • T. Culpitt, K. R. Brorsen, M. V. Pak, and S. Hammes-Schiffer. "Multicomponent Density Functional Theory Embedding Formulation", submitted

Hirata

  • Michael A. Salim, Soohaeng Yoo Willow, and So Hirata. "Ice Ih Anomalies: Thermal Contraction, Anomalous Volume Isotope Effect, and Pressure-Induced Amorphization", The Journal of Chemical Physics, Vol. 144(20): 204503, 2016, doi:10.1063/1.4951687
  • 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?", J. Phys. Chem. Lett., Vol. 7(4): 680--684, 2016, doi:10.1021/acs.jpclett.5b02430
  • 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", Sci. Rep., Vol. 5, 2015, doi:10.1038/srep14358
  • S. Hirata. "A Few Potentially Controversial Issues in Many-Body Theory", Low-scaling and Unconventional Electronic Structure Techniques Conf., Telluride, CO, 2014
  • S. Hirata. "Ab Initio Solid-State Chemistry", Am. Conf. Theor. Chem., Telluride, CO, 2014
  • 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", J. Chem. Theory Comput., Vol. 9(10): 4396--4402, 2013, doi:10.1021/ct400557z
  • S. Hirata, et al. "Ab Initio Ice, Dry Ice, and Liquid Water", A chapter (under review) in Fragmentation: Toward Accurate Calculations on Complex Molecular Systems edited by Mark S. Gordon, 2016, submitted

Iyer

  • Phuong Cao, Eric C. Badger, Zbigniew T. Kalbarczyk, and Ravishankar K. Iyer. "A Framework for Generation, Replay, and Analysis of Real-World Attack Variants", Proceedings of the Symposium and Bootcamp on the Science of Security - HotSos '16, 2016, doi:10.1145/2898375.2898392
  • Subho S. Banerjee, et al. "Efficient and Scalable Workflows for Genomic Analyses", Proceedings of the ACM International Workshop on Data-Intensive Distributed Computing - DIDC '16, 2016, doi:10.1145/2912152.2912156
  • S. S. Banerjee, et al. "Sequences to Systems", Coordinated Science Laboratory Technical ReportUILU-ENG-16-2201, 2016
  • Jha, S., et al. "Understanding Gemini Interconnect Failovers on Blue Waters", Proceedings of the Cray User's Group (CUG), London, England, 2016, url: https://cug.org/conference-proceedings
  • Catello Di Martino, Saurabh Jha, William Kramer, Zbigniew Kalbarczyk, and Ravishankar K. Iyer. "LogDiver", Proceedings of the 5th Workshop on Fault Tolerance for HPC at eXtreme Scale - FTXS '15, 2015, doi:10.1145/2751504.2751511

Jakobsson

  • Amir Barati Farimani, Narayana R. Aluru, Emad Tajkhorshid, and Eric Jakobsson. "Computational Approach to Designing Antibody for Ebola Virus", Biophysical Journal, Vol. 110(3): 537a, 2016, doi:10.1016/j.bpj.2015.11.2877
  • B. Farimani, N. R. Aluru, and Eric Jakobsson. "Effect of Confinement on Protein Dynamic and Structure", Biophysical Society Meetin 2015, Baltimore, MD, 2015

Jasiuk

  • Seid Koric, Fereshteh A Sabet, Ouli Jin, and Iwona M. Jasiuk. "Direct numerical Simulation of Bone Plasticity and Strength", International Symposium on Plasticity and Its Current Applications, Keauhou, Hawaii, 2016, url: https://www.researchgate.net/publication/289976562_DIRECT_NUMERICAL_SIMULATION_OF_BONE_PLASTICITY_AND_STRENGTH
  • S. Koric, F.A. Sabet, and I. Jasiuk. "Influence of Tissue Level Plasticity on Apparent Response of Trabecular Bone", International Symposium on Plasticity, 2017, submitted
  • F.A. Sabet, et al. "Hierarchical Modeling of Plasticity and Strength of Trabecular Bone", XXIV ICTAM, Montreal, Canada, 2016, submitted
  • F. A. Sabet, O. Jin, S. Koric, and I. Jasiuk. "Nonlinear Micro-CT FE Modeling of Trabecular Bone – Sensitivity of Apparent Response to Tissue Constitutive Law", Journal of the Mechanical Behavior of Biomedical Materials, 2016, submitted

Kemball

  • Yashar D. Hezaveh, et al. "Detection of Lensing Substructure Using Alma Observations of the Dusty Galaxy SDP.81", ApJ, Vol. 823(1): 37, 2016, doi:10.3847/0004-637x/823/1/37
  • E. Seidel, et al. "Computing and Data Challenges for Multi-Messenger Astronomy", Exascale Radio Astronomy, (AAS Topical Conference Series Vol. 2., Bulletin of the American Astronomical Society), Monterey, CA, 2014, url: http://adsabs.harvard.edu/abs/2014era..conf20001S

Le Chenadec

  • Unknown. "A Survey of Momentum-Conserving Methods for High-Reynolds Incompressible Two-Phase Flows", ILASS-Americas proceedings, submitted
  • Unknown. "Realizable and Symmetric Transport of Geometric Moments and Application to the Moment-of-Fluid Method", Journal of Computational Physics, submitted

Levin

  • Saurabh S. Sawant, Burak Korkut, Ozgur Tumuklu, and Deborah A. Levin. "Development of an AMR Octree DSMC Approach for Shock Dominated Flows", 53rd AIAA Aerospace Sciences Meeting, 2015, doi:10.2514/6.2015-0070

Liu

  • Lijun Liu, and Quan Zhou. "Deep Recycling of Oceanic Asthenosphere Material During Subduction", Geophys. Res. Lett., Vol. 42(7): 2204--2211, 2015, doi:10.1002/2015gl063633
  • Lijun Liu. "Rejuvenation of Appalachian Topography Caused by Subsidence-Induced Differential Erosion", Nature Geoscience, Vol. 7(7): 518--523, 2014, doi:10.1038/ngeo2187

Luitz

  • David J. Luitz. "Long Tail Distributions Near the Many-Body Localization Transition", Phys. Rev. B, Vol. 93(13), 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", 2016, submitted

Luthey-Schulten

  • Tyler M. Earnest, et al. "Ribosome Biogenesis in Replicating Cells: Integration of Experiment and Theory", Biopolymers, 2016, doi:10.1002/bip.22892
  • Tyler M. Earnest, et al. "Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly", Biophysical Journal, Vol. 109(6): 1117--1135, 2015, doi:10.1016/j.bpj.2015.07.030

Makri

  • P. L. Walters, and N. Makri. "Quantum-Classical Path Integral Simulations of Ferrocene-Ferrocenium Charge Transfer in Solution", 251th ACS National Meeting & Exposition, San Diego, CA, 2016
  • Peter L. Walters, and Nancy Makri. "Quantum-Classical Path Integral Simulation of Ferrocene-Ferrocenium Charge Transfer in Liquid Hexane", J. Phys. Chem. Lett., Vol. 6(24): 4959--4965, 2015, doi:10.1021/acs.jpclett.5b02265

Masud

  • 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, Vol. 10(4): e0124575, 2015, doi:10.1371/journal.pone.0124575
  • J. Kwack, S. Kang, G. Bhatt, and A. Masud,. "Outflow Boundary Conditions for Non-Newtonian Models for Blood", Modeling and Simulation in Science, Engineering and Technology Book Series, 2015, url: http://www.springer.com.proxy2.library.illinois.edu/series/4960
  • 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, Vol. 53(4): 751--776, 2013, doi:10.1007/s00466-013-0928-6
  • J. Kwack, A. Masud, and K.R. Rajagopal,. "Stabilized Mixed Three-field Formulation for a Generalized Incompressible Oldroyd-B Model", International Journal for Numerical Methods in Fluids, 2016, submitted

McFarquhar

  • J. Um, and G. M. McFarquhar. "Formation of Atmospheric Halos by Hexagonal Ice Crystals", 14th Conference on Atmospheric Radiation, Boston, MA, 2014, url: https://ams.confex.com/ams/14CLOUD14ATRAD/webprogram/Paper250064.html
  • G. M. McFarquhar, and J. Um. "The Impact of Natural Variations of Ice Crystal Aspect Ratios on Single-Scattering Properties", 14th Conference on Atmospheric Radiation, Boston, MA, 2014, url: https://ams.confex.com/ams/14CLOUD14ATRAD/webprogram/Paper249221.html
  • J. Um, and G. M. McFarquhar. "Efficient Numerical Orientation Average for Calculations of Single-Scattering Properties of Small Atmospheric Ice Crystals", Proc. ASR Science Team Meeting, U.S. Department of Energy, Potomac, MD, 2013
  • 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, Vol. 127, 2013, doi:10.1016/j.jqsrt.2013.05.020

Nagi

  • Ketan Date, and Rakesh Nagi. "GPU-Accelerated Hungarian Algorithms for the Linear Assignment Problem", Parallel Computing, Vol. 57, 2016, doi:10.1016/j.parco.2016.05.012

Olson

  • A. Bienz, R. Falgout, W. Gropp, L. Olson, and J. Schroder. "Reducing Parallel Communication in Algebraic Multigrid Through Sparsification", SIAM Journal on Scientific Computin, 2015, submitted

Ostoja-Starzewski

  • Sohan Kale, Ankit Saharan, Seid Koric, and Martin Ostoja-Starzewski. "Scaling and Bounds in Thermal Conductivity of Planar Gaussian Correlated Microstructures", J. Appl. Phys., Vol. 117(10): 104301, 2015, doi:10.1063/1.4914128
  • Sohan Kale, Seid Koric, and Martin Ostoja-Starzewski. "Stochastic Continuum Damage Mechanics Using Spring Lattice Models", AMM, Vol. 784, 2015, doi:10.4028/www.scientific.net/amm.784.350

Schleife

  • Joel B Varley, and André Schleife. "Bethe-Salpeter Calculation of Optical-Absorption Spectra of In2O3 and Ga2O3", Semiconductor Science and Technology, Vol. 30(2): 024010, 2015, doi:10.1088/0268-1242/30/2/024010
  • 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", Comput. Sci. Eng., Vol. 16(5): 54--60, 2014, doi:10.1109/mcse.2014.55

Schulten

  • 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", The Journal of Physical Chemistry B, 2016, doi:10.1021/acs.jpcb.6b01327
  • Andreas Schweitzer, et al. "Structure of the Human 26S Proteasome at a Resolution of 3.9 Å", Proceedings of the National Academy of Sciences, 2016, doi:10.1073/pnas.1608050113

Shapiro

  • Milton Ruiz, Ryan N. Lang, Vasileios Paschalidis, and Stuart L. Shapiro. "Binary Neutron Star Mergers: A Jet Engine for Short Gamma-Ray Burst", ApJ, Vol. 824(1): L6, 2016, doi:10.3847/2041-8205/824/1/l6
  • Vasileios Paschalidis, Milton Ruiz, and Stuart L. Shapiro. "Relativistic Simulations of Black Hole-Neutron Star Coalescence: The Jet Emerges", ApJ, Vol. 806(1): L14, 2015, doi:10.1088/2041-8205/806/1/l14
  • 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, Vol. 89(6), 2014, doi:10.1103/physrevd.89.064060
  • Roman Gold, et al. "Accretion Disks Around Binary Black Holes of Unequal Mass: General Relativistic MHD Simulations of Postdecoupling and Merger", Physical Review D, Vol. 90(10), 2014, doi:10.1103/physrevd.90.104030
  • 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, Vol. 90(6), 2014, doi:10.1103/physrevd.90.064032
  • Milton Ruiz, Vasileios Paschalidis, and Stuart L. Shapiro. "Pulsar Spin-Down Luminosity: Simulations in General Relativity", Physical Review D, Vol. 89(8), 2014, doi:10.1103/physrevd.89.084045

Shukla

  • Diwakar Shukla, Ariana Peck, and Vijay S. Pande. "Conformational Heterogeneity of the Calmodulin Binding Interface", Nature Communications, Vol. 7, 2016, doi:10.1038/ncomms10910
  • Shukla et al. "Application of Hidden Markov Models in Biomolecular Simulations", Methods in Molecular Biology, 2016, submitted
  • K. Bender Moffett, S.C. Huber, and D. Shukla. "Conformational Engineering of αC Helix for Regulating the Activity of Plant Kinases", 2016, submitted
  • Moffett et al. "Guiding Functional Dynamics and Dimerization of Proteins Using Evolutionary Couplings", Journal of Chemical Theory and Computation, 2015, submitted

Sriver

  • 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", J. Geophys. Res. Oceans, Vol. 121(1): 586--601, 2016, doi:10.1002/2015jc011226
  • L. Hui, and R. L. Sriver. "Modeled Sensitivity of the Upper-Ocean Response to Tropical Cyclones in the Northwestern Pacific Using a Fully-coupled Climate Model with Varying Ocean Resolution", American Geophysical Union, Fall Meeting 2014, San Francisco, CA, 2014, url: http://adsabs.harvard.edu/abs/2014AGUFM.A33L3380L
  • H. Li, and R. Sriver. "Effect of Ocean Grid Resolution on Tropical Cyclone-Induced Upper Ocean Responses Using a Global Ocean General Circulation Model", Journal of Geophysical Research - Oceans, under review, 2016, submitted

Sutton

Tajkhorshid

  • Mahmoud Moradi, Giray Enkavi, and Emad Tajkhorshid. "Atomic-Level Characterization of Transport Cycle Thermodynamics in the Glycerol-3-Phosphate:phosphate Antiporter", Nature Communications, Vol. 6, 2015, doi:10.1038/ncomms9393
  • 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, Vol. 31, 2015, doi:10.1016/j.sbi.2015.04.001
  • Mahmoud Moradi, and Emad Tajkhorshid. "Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems", J. Chem. Theory Comput., Vol. 10(7): 2866--2880, 2014, doi:10.1021/ct5002285
  • M. Moradi, and E. Tajkhorshid. "Mechanistic Picture for Conformational Transition of a Membrane Transporter at Atomic Resolution", Proceedings of the National Academy of Sciences, Vol. 110(47): 18916--18921, 2013, doi:10.1073/pnas.1313202110

Thomas

  • 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", CFD Modeling and Simulation in Materials Processing 2016, 2016, doi:10.1002/9781119274681.ch20
  • Kai Jin, Brian G. Thomas, and Xiaoming Ruan. "Modeling and Measurements of Multiphase Flow and Bubble Entrapment in Steel Continuous Casting", Metall and Materi Trans B, Vol. 47(1): 548--565, 2015, doi:10.1007/s11663-015-0525-5
  • 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, Vol. 137(7): 071104, 2015, doi:10.1115/1.4029731
  • L. C. Hibbeler, B. G. Thomas, R. C. Schimmel, and H. H. Visser. "Simulation and Online Measurement of Narrow Face Mold Distortion in Thin-slab Casting", Proc. of the 8th European Continuous Casting Conference, Graz, Austria, 2014, url: https://www.semanticscholar.org/paper/Simulation-and-Online-Measurement-of-Narrow-Face-Hibbeler-Thomas/936445b426c8a12d63af0880bead82f00815ebb7
  • S-M. Cho, B G. Thomas, and S-H. 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, 2016, accepted, 2016, submitted
  • Jin K., 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", Journal of Fluids Engineering, submitted, submitted
  • Jin K., 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, submitted, submitted

Trapp

  • Robert J. Trapp, and Kimberly A. Hoogewind. "The Realization of Extreme Tornadic Storm Events Under Future Anthropogenic Climate Change", Journal of Climate, 2016, doi:10.1175/jcli-d-15-0623.1

Um

  • G. M. McFarquhar, and J. Um. "Light Scattering By Atmospheric Hexagonal Ice Crystals for Determination of Applicability of Geometric Optics and Formation of Atmospheric Circumscribed Halos", International Symposium on Radiation, Auckland, New Zealand, 2016
  • J. Um, and G. M. McFarquhar. "Light Scattering by Atmospheric Ice Crystals: Application to Forward Scattering Probes", International Symposium on Radiation, Auckland, New Zealand, 2016
  • J. Um, and G. M. McFarquhar. "A Lower Limit of Applicability of the Conventional Geometric Optics Method: A Comparison with the Discrete Dipole Approximation for the Scattering Properties of Atmospheric Ice Crystals.", 4th XSEDE Annual Conference, St. Louis, MO, 2015
  • J. Um, and G. M. McFarquhar. "Applicability of Geometric Optics Method for Calculations of Single-Scattering Properties of Atmospheric Ice Crystals", Blue Waters Symposium, Sunriver, OR, 2015
  • 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, Vol. 165, 2015, doi:10.1016/j.jqsrt.2015.07.001
  • J. Um. "Calculations of Microphysical and Radiative Properties of Ice Clouds", National Institute of Meteorological Research, KMA, Jeju, Republic of Korea, 2014
  • Junshik Um, and Greg M. McFarquhar. "Formation of Atmospheric Halos by Hexagonal Ice Crystals", 14th Conference on Atmospheric Radiation, Boston, MA, 2014, url: https://ams.confex.com/ams/14CLOUD14ATRAD/webprogram/Paper250064.html
  • J. Um, and G. M. McFarquhar. "Scattering Calculations of Atmospheric Ice Crystals: Studies on Orientation Average and Atmospheric Halo", Blue Waters Symposium, Champaign, IL, 2014, url: https://bluewaters.ncsa.illinois.edu/c/document_library/get_file?uuid=3d153134-ada7-4884-96ae-9e7351eaba01&groupId=10157
  • G.M. McFarquhar, and J. Um. "The Impact of Natural Variations of Ice Crystal Aspect Ratios on Single-Scattering Radiative Properties", 14th Conference on Atmospheric Radiation, AMS, Boston, MA, 2014, url: https://ams.confex.com/ams/14CLOUD14ATRAD/webprogram/Paper249221.html
  • 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, Vol. 127, 2013, doi:10.1016/j.jqsrt.2013.05.020

Valocchi

  • 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, Vol. 73, 2014, doi:10.1016/j.advwatres.2014.07.010

Wagner

Wang

Warnow

  • 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, Vol. 2, 2016, doi:10.1038/npjbiofilms.2016.4
  • P. Vachaspati and T. Warnow. "FastRFS: Fast and Accurate Robinson-Foulds Supertrees using Constrained Exact Optimization", Submitted for publication, submitted
  • N. Nguyen, M. Nute, S. Mirarab, and T. Warnow. "HIPPI: Highly Accurate Protein Family Classification with Ensembles of HMMs", Submitted for publication, submitted

West

  • Jeffrey Curtis, Nicole Riemer, and Matthew West. "Poster: A 3D Particle-resolved Model to Quantify the Importance of Aerosol Mixing State for CCN Activity", Atmospheric Radiation Measurement/Atmospheric System Research (ARM/ASR) PI Meeting, Department of Energy, 2016, url: http://asr.science.energy.gov/meetings/stm/posters/view?id=1541

Wilhelmson

GLCPC Teams

Ackerman

Balsara

  • 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, Vol. 318, 2016, doi:10.1016/j.jcp.2016.05.006
  • Blakesley Burkhart, A. Lazarian, D. Balsara, C. Meyer, and J. Cho. "Alfvénic Turbulence Beyond the Ambipolar Diffusion Scale", ApJ, Vol. 805(2): 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, Vol. 297, 2015, doi:10.1016/j.jcp.2015.05.020
  • 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, Vol. 439(3): 2197--2210, 2014, doi:10.1093/mnras/stt1893

Draayer

  • Kristina D. Launey, Tomas Dytrych, and Jerry P. Draayer. "Symmetry-Guided Large-Scale Shell-Model Theory", Progress in Particle and Nuclear Physics, Vol. 89, 2016, doi:10.1016/j.ppnp.2016.02.001
  • 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", Int. J. Mod. Phys. E, Vol. 24(05): 1530005, 2015, doi:10.1142/s0218301315300052
  • 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", J. Phys.: Conf. Ser., Vol. 578, 2015, doi:10.1088/1742-6596/578/1/012010
  • T. Dytrych, et al. "Electron-Scattering Form Factors for Li-6 in the Ab Initio Symmetry-Guided Framework", Phys. Rev. C, Vol. 91(2), 2015, doi:10.1103/physrevc.91.024326
  • T Dytrych, et al. "Emergence of Simple Patterns in Complex Atomic Nuclei from First Principles", J. Phys.: Conf. Ser., Vol. 639, 2015, doi:10.1088/1742-6596/639/1/012008
  • K D Launey, A C Dreyfuss, R B Baker, J P Draayer, and T Dytrych. "Emergent Symmetries in Atomic Nuclei from First Principles", J. Phys.: Conf. Ser., Vol. 597, 2015, doi:10.1088/1742-6596/597/1/012054
  • J. P. Draayer, K. D. Launey, and T. Dytrych. "Fuel of the Cosmos", International Innovation, Vol. 160, 2015, url: https://issuu.com/internationalinnovation/docs/160_composite
  • 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", J. Phys.: Conf. Ser., Vol. 580, 2015, doi:10.1088/1742-6596/580/1/012044
  • Daniel Langr, Pavel Tvrdík, Tomáš Dytrych, and Jerry P. Draayer. "Algorithm 947", ACM Transactions on Mathematical Software, Vol. 41(1): 1--26, 2014, doi:10.1145/2669372
  • 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", J. Phys.: Conf. Ser., Vol. 569, 2014, doi:10.1088/1742-6596/569/1/012061
  • T. Dytrych, et al. "Emergence of Simple Patterns in Complex Atomic Nuclei from First Principles.", Proc. Int. Conf. Nuclear Theory in the Supercomputing Era 2014, Khabarovsk, Russia, 2014, url: http://ntse.khb.ru/files/uploads/2014/abstracts/50_abs_Dytrych.pdf
  • 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, Vol. 185(1): 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 Yearbook of Science & Technology, 2014, doi:10.1036/1097-8542.YB140314
  • G. K. Tobin, et al. "Symplectic No-Core Shell-Model Approach to Intermediate-Mass Nuclei", Phys. Rev. C, Vol. 89(3), 2014, doi:10.1103/physrevc.89.034312
  • T. Dytrych, et al. "Collective Modes in Light Nuclei from First Principles", Phys. Rev. Lett., Vol. 111(25), 2013, doi:10.1103/physrevlett.111.252501
  • 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, Vol. 727(4-5): 511--515, 2013, doi:10.1016/j.physletb.2013.10.048
  • K D Launey, et al. "Symmetry-Adapted Ab Initio No-Core Shell Model Calculations for 12 C", J. Phys.: Conf. Ser., Vol. 436, 2013, doi:10.1088/1742-6596/436/1/012023
  • K. D. Launey, et al. "Symmetry-Adapted No-Core Shell Model for Light Nuclei", Fission and Properties of Neutron-Rich Nuclei, Proceedings of the Fifth International Conference on ICFN5, Sanibel Island, Florida, 2013, doi:10.1142/9789814525435_0003
  • Jerry P. Draayer, et al. "Unraveling Mysteries of the Strong Interaction - 'Top Down' Versus 'Bottom Up' Considerations", Proceedings, International Conference on Nuclear Theory in the Supercomputing Era (NTSE-2013), 2013, url: http://www.ntse-2013.khb.ru/Proc/Draayer.pdf
  • T. Dytrych, et al. "Utilizing Symmetry Coupling Schemes in Ab Initio Nuclear Structure Calculations", Proceedings, International Conference on Nuclear Theory in the Supercomputing Era (NTSE-2013), 2013, url: http://www.ntse-2013.khb.ru/Proc/Dytrych.pdf

Glotzer

  • 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", Adv. Mater., Vol. 27(26): 3947--3952, 2015, doi:10.1002/adma.201501329
  • Jens Glaser, et al. "Strong Scaling of General-Purpose Molecular Dynamics Simulations on GPUs", Computer Physics Communications, Vol. 192, 2015, doi:10.1016/j.cpc.2015.02.028
  • Jens Glaser, Pavani Medapuram, Thomas M. Beardsley, Mark W. Matsen, and David C. Morse. "Universality of Block Copolymer Melts", Phys. Rev. Lett., Vol. 113(6), 2014, doi:10.1103/physrevlett.113.068302

Hansen

  • Yongyang Cai, Timothy M. Lenton, and Thomas S. Lontzek. "Risk of Multiple Interacting Tipping Points Should Encourage Rapid CO2 Emission Reduction", Nature Climate Change, Vol. 6(5): 520--525, 2016, doi:10.1038/nclimate2964
  • Yongyang Cai, Kenneth Judd, and Jevgenijs Steinbuks. "A Nonlinear Certainty Equivalent Approximation Method for Dynamic Stochastic Problems", NBER Working Paper No. 21590, 2015, doi:10.3386/w21590
  • 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, Vol. 112(15): 4606--4611, 2015, doi:10.1073/pnas.1503890112
  • 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, Vol. 5(5): 441--444, 2015, doi:10.1038/nclimate2570
  • 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 Policy Research Working Paper 7009, 2014, url: http://documents.worldbank.org/curated/en/2014/08/20128369/effect-climate-technological-uncertainty-crop-yields-optimal-path-global-land-use
  • S. Yeltekin, Y. Cai, and K.L. Judd. "Computing Equilibria of Dynamic Games", Operations Research, 2015, submitted
  • Y. Cai, K.L. Judd, and T.S. Lontzek. "Numerical Dynamic Programming with Error Control: An Application to Climate Policy", Operations Research, 2015, submitted
  • Yongyang Cai, Kenneth L. Judd, and Thomas S. Lontzek. "The Social Cost of Carbon with Economic and Climate Risks", Journal of Political Economy, 2015, submitted

Khalili-Araghi

  • Poya Yasaei, et al. "Bimodal Phonon Scattering in Graphene Grain Boundaries", Nano Letters, Vol. 15(7): 4532--4540, 2015, doi:10.1021/acs.nanolett.5b01100

Makwana

  • 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, Vol. 22(4): 042902, 2015, doi:10.1063/1.4916492

Mankin

  • Shanmugapriya Sothiselvam, et al. "Macrolide Antibiotics Allosterically Predispose the Ribosome for Translation Arrest", Proceedings of the National Academy of Sciences, Vol. 111(27): 9804--9809, 2014, doi:10.1073/pnas.1403586111


Sharma

  • A Sharma, et al. "Green and Cool Roofs to Mitigate Urban Heat Island Effects in the Chicago Metropolitan Area: Evaluation with a Regional Climate Model", Environ. Res. Lett., Vol. 11(6): 064004, 2016, doi:10.1088/1748-9326/11/6/064004
  • A. Sharma, et al. "Green and Cool Roofs to Mitigate Urban Heating: An Analysis with a Regional Climate Model", 96th American Meteorological Society Annual Meeting, New Orleans, LA, 2016, url: https://ams.confex.com/ams/96Annual/webprogram/Paper289180.html
  • Ashish Sharma, et al. "Urban Meteorological Modeling Using WRF: A Sensitivity Study", International Journal of Climatology, 2016, doi:10.1002/joc.4819
  • Patrick Conry, et al. "Chicago's Heat Island and Climate Change: Bridging the Scales via Dynamical Downscaling", J. Appl. Meteor. Climatol., Vol. 54(7): 1430--1448, 2015, doi:10.1175/jamc-d-14-0241.1
  • A. Sharma, et al. "Sensitivity of WRF Model to Landuse, with Applications to Chicago Metropolitan Urban Heat Island and Lake Breeze", In AGU Fall Meeting Abstracts, San Francisco, CA, 2015, url: https://agu.confex.com/agu/fm15/webprogram/Paper74591.html
  • Mohammad Zaved Kaiser Khan, Rajeshwar Mehrotra, Ashish Sharma, and A. Sankarasubramanian. "Global Sea Surface Temperature Forecasts Using an Improved Multimodel Approach", Journal of Climate, Vol. 27(10): 3505--3515, 2014, doi:10.1175/jcli-d-13-00486.1

Subramaniam

  • B. Sun. "Modeling Heat and Mass Transfer in Reacting Gas-solid Flow Using Particle-resolved Direct Numerical Simulation", PhD thesis, Iowa State University, 2016

Wentzcovitch

  • Ryan J. Wu, et al. "Atomic and Electronic Structure of Exfoliated Black Phosphorus", Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, Vol. 33(6): 060604, 2015, doi:10.1116/1.4926753
  • Michel L. Marcondes, and Renata M. Wentzcovitch. "Hybrid Ab-Initio/experimental High Temperature Equations of State: Application to the NaCl Pressure Scale", J. Appl. Phys., Vol. 117(21): 215902, 2015, doi:10.1063/1.4921904
  • Gaurav Shukla, et al. "Thermoelasticity of Fe 2+ -Bearing Bridgmanite", Geophys. Res. Lett., Vol. 42(6): 1741--1749, 2015, doi:10.1002/2014gl062888

Wilde

  • Scott J. Krieder, et al. "Design and Evaluation of the Gemtc Framework for GPU-Enabled Many-Task Computing", Proceedings of the 23rd international symposium on High-performance parallel and distributed computing - HPDC '14, Vancouver, Canada, 2014, doi:10.1145/2600212.2600228

Graduate Fellows

Bedford

  • M. C. Bedford, I. Kryukov, and N. V. Pogorelov. "Poster: A Multi-ion Model of the Heliosphere with Secondary Charge Exchange", American Geophysical Union, Fall Meeting 2014, San Francisco, CA, 2014, url: http://adsabs.harvard.edu/abs/2014AGUFMSH11B4054B

Brooks

  • M. T. Brooks, V. J. Coles, R. R. Hood, and J. F. R. Gower. "Linking Satellite Observations with Coupled Bio-physical Models of Sargassum", AGU/ASLO/TOS Ocean Sciences Meeting, New Orleans, LA, 2016

Calhoun

  • J. Calhoun, L. Olson, M. Snir, and W.D. Gropp. "Towards a More Fault Resilient Multigrid Solver", In Proceedings of the High Performance Computing Symposium, HPC '15, Alexandria, VA, 2015, url: http://dl.acm.org/citation.cfm?id=2872599.2872600
  • Jon Calhoun, Luke Olson, and Marc Snir. "FlipIt: An LLVM Based Fault Injector for HPC", Lecture Notes in Computer Science, 2014, doi:10.1007/978-3-319-14325-5_47
  • Kris Beckwith, et al. "Fully-Implicit Ultrascale Physics Solvers and Application to Ion Source Modelling", 2014 IEEE 41st International Conference on Plasma Sciences (ICOPS) held with 2014 IEEE International Conference on High-Power Particle Beams (BEAMS), 2014, doi:10.1109/plasma.2014.7012726
  • Jon Calhoun, Franck Cappello, Luke Olson, and Marc Snir. "Lossy Checkpointing PDE Simulations: Mathematical Guidance for Compression Error Setting", 2016, submitted

Drake

  • J.A. Drake, and B.M. Pettitt. "Poster: The Protein Backbone: How Structural and Thermodynamic Properties Scale with Length", 251st American Chemical Society National Meeting and Exposition, 2016
  • J.A. Drake, and B.M. Pettitt. "The Protein Backbone: How Structural and Thermodynamic Properties Scale with Length", Poster at Sealy Center for Structural Biology and Molecular Biophysics 21st Annual Structural Biology Symposium, 2016
  • J.A. Drake, and B.M. Pettitt. "Poster: Protein Backbone Thermodynamics: Towards Estimating Conformational Entropy", Sealy Center for Structural Biology and Molecular Biophysics 21st Annual Structural Biology Symposium, 2015
  • J.A. Drake, and B.M. Pettitt. "Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility: Implication for Aggregation and Collapse", 2016, submitted

Jones

  • A. L. Jones. "Development of an Accurate 3D Monte Carlo Broadband Atmospheric Radiative Transfer Model", Doctoral dissertation, University of Illinois, 2016

Kokkila

  • Sara I. L. Kokkila Schumacher, Edward G. Hohenstein, Robert M. Parrish, Lee-Ping Wang, and Todd J. Martínez. "Tensor Hypercontraction Second-Order Møller-Plesset Perturbation Theory: Grid Optimization and Reaction Energies", J. Chem. Theory Comput., Vol. 11(7): 3042--3052, 2015, doi:10.1021/acs.jctc.5b00272

Mathews

  • Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper. "LES of an Aero-Optical Turret Flow at High Reynolds Number", 54th AIAA Aerospace Sciences Meeting, 2016, doi:10.2514/6.2016-1461
  • E. Mathews, K. Wang, M. Wang, and E. J. Jumper. "LES Prediction and Analysis of the Aero-optical Environment Around a 3-D Turret", 68th Annual Meeting of the APS Division of Fluid Dynamics, Boston, MA, 2015, url: http://adsabs.harvard.edu/abs/2015APS..DFDD20010M
  • 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", 46th AIAA Plasmadynamics and Lasers Conference, 2015, doi:10.2514/6.2015-3248

Méndez

  • Joshua S. Méndez Harper, and Josef Dufek. "The Effects of Granular Dynamics on the Triboelectric Charging of Volcanic ash: Experiments and Numerical Simulations", Proceedings of the 2016 Meeting of the Electrostatics Society of America, Purdue University, 2016, url: http://www.electrostatics.org/images/M1.pdf

Minot

Reames

  • L.J. Reames. "Diurnal Variations in Severe Weather Forecast Parameters of Rapid Update Cycle-2 Tornado Proximity Environments", Weather and Forecasting, 2016, submitted

Slota

  • George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri. "High-Performance Graph Analytics on Manycore Processors", 2015 IEEE International Parallel and Distributed Processing Symposium, 2015, doi:10.1109/ipdps.2015.54
  • George M. Slota, and Kamesh Madduri. "Parallel Color-Coding", Parallel Computing, Vol. 47, 2015, doi:10.1016/j.parco.2015.02.004
  • G.M. Slota, K. Madduri, and S. Rajamanickam. "Poster: Parallel Graph Algorithms on Modern System", PhD Forum Poster at the 29th IEEE International Parallel and Distributed Processing Symposium (IPDPS15), 2015
  • George M. Slota, Kamesh Madduri, and Sivasankaran Rajamanickam. "Distributed Graph Layout for Scalable Small-world Network Analysis", 2015, submitted
  • George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri. "Supercomputing for Web Graph Analytics", 2015, submitted

Totorica

  • Samuel R. Totorica, Tom Abel, and Frederico Fiuza. "Nonthermal Electron Energization from Magnetic Reconnection in Laser-Driven Plasmas", Phys. Rev. Lett., Vol. 116(9), 2016, doi:10.1103/physrevlett.116.095003

Zemskova

  • Varvara E. Zemskova, Brian L. White, and Alberto Scotti. "Available Potential Energy and the General Circulation: Partitioning Wind, Buoyancy Forcing, and Diapycnal Mixing", J. Phys. Oceanogr., Vol. 45(6): 1510--1531, 2015, doi:10.1175/jpo-d-14-0043.1

Industry

Koric

Innovation

 

  • G. M. Laskowski, J. Kopriva, V. Michelassi, S. Shankaran, U. Paliath, R. Bhaskaran, Q. Wang, C. Talnikar, Z. J. Wang, F. Jia,  Future directions of high-fidelity CFD for aero-thermal turbomachinery research, analysis and design, 46th AIAA Fluid Dynamics Conference, AIAA Aviation, 2016.
  • S. Jha, V. Formicola, C. Di Martino, Z. Kalbarczyk, W. Kramer, R. Iyer, Analysis of Gemini Interconnect Recovery Mechanisms: Methods and Observations, Cray Users Group Meeting (CUG 2016), London, UK, 2016.

NCSA Staff

  • F. Cappello, A. Geist, W. Gropp, L. Kale, W. Kramer, M. Snir. Toward Exascale Resilience. Int. Journal of High Performance Computing Applications, 23(4), pp. 374-388, 2009. http://hpc.sagepub.com/content/23/4.toc
  • J. Dongarra et al., The International Exascale Software Project Roadmap.Int. Journal of High Performance Computing Applications, 25(1), pp. 3-60, 2011.
  • D. Guo, W. Gropp, Optimizing Sparse Data Structures for Sparse Matrix-Vector Multiply, The International Journal of High Performance Computing Applications, Volume 25(1), pp. 115-131, February 2011.
  • Gainaru, F. Cappello, J. Fullop, S. Trausan-Matu, W. Kramer, Adaptive Event Prediction Strategy with Dynamic Time Window for Large-Scale HPC Systems, Managing Large-Scale Systems via the Analysis of System Logs and the Application of Machine Learning Techniques, 23nd ACM SIGOPS, Cascais, Portugal, 2011.
  • Gainaru, F. Cappello, W. Kramer, Event log mining tool for large scale HPC systems, Proceedings of Europar, August 29-September 2, Bordeaux, France, 2011.
  • E. M. Heien, D. Kondo, A. Gainaru, D. Lapine, W. Kramer, F. Cappello, Modeling and Tolerating Heterogeneous Failures in Large Parallel Systems,  Supercomputing'11, Seattle, WA, 2011.
  • W. Kramer, How to Measure Useful, Sustained Performance, Supercomputing'11, Seattle, WA, 2011.
  • W. Kramer, Blue Waters - A Super System for Super Challenges, Cray User Group Meeting (CUG 2012), Stuttgart, Germany, 2012.
  • 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, Cray User Group Meeting (CUG 2012), Stuttgart, Germany, 2012.
  • Gainaru, F. Cappello, W. Kramer, Taming of the Shrew: Modeling the Normal and Faulty Behavior of Large-scale HPC Systems, Proceedings of IPDPS, Shanghai, China, May 2012.
  • W. Kramer, Top500 versus Sustained Performance – Or the Top Ten Problems with the TOP500 List – And What to Do About Them, 21ST International Conference On Parallel , Architectures And Compilation Techniques (PACT12), Minneapolis, MN, September 2012.
  • Gainaru, F. Cappello, M. Snir, W. Kramer, Fault prediction under the microscope: A closer look into HPC systems, Supercomputing'2012,Salt Lake City, UT, 2012.
  • R. Sisneros, C. Malone, A. Nonaka, S. Woosley, Investigation of Turbulence in the Early Stages of a High Resolution Supernova Simulation, Scientific Visualization Showcase, High Performance Computing, Networking, Storage and Analysis (SCC), 2012 SC Companion, 2012, 1557-1558.
  • O'Shea, M. Norman, B. Smith, M. Turk, M. Kuhlen, J. Wise, D. Reynolds, R. Harkness, M. Gajbe, D. Semeraro, Cosmology on the Blue Waters Early Science System, Scientific Visualization Showcase, High Performance Computing, Networking, Storage and Analysis (SCC), 2012 SC Companion, 2012, 1557-1558, ISBN: 978-0-7695-4956-9 (SC 2012)
  • K. Nagamine, L. Oser, J. P. Ostriker, M. Gajbe, G. Bryan, R. Cen, T. Naab, Weak Scaling Results from the GADGET-3 Cosmological Smoothed Particle Hydrodynamics Simulations, XSEDE 2012.
  • K. Chadalavada, M. Gajbe, Understanding the effects of process placement on application performance on an AMD Interlagos processor. Cray User Group Meeting (CUG 2012), Stuttgart, Germany, 2012
  • Canning, J. Shalf, N. J. Wright S. Anderson, M. Gajbe, A Hybrid MPI/OpenMP 3d FFT for Plane Wave First-principles Materials Science Codes. 9th International Conference on Scientific Computing (CSC' 12), 2012.
  • Y. Sun, G. Zheng, C. Mei, E. Bohm, J. Phillips, T. Jones and L. Kale, Optimizing Fine-grained Communication in a Biomolecular Simulation Application on Cray XK6, Proceedings of SC'12, Salt Lake City, UT, USA, 2012.
  • Guo, W. Gropp, Adaptive thread distributions for SpMV on a GPU, XSEDE Extreme Scale Workshop, 2012.
  • J. Muggli, B. Bode, T. Hoefler, W. Kramer, C. Mendes, Blue Waters Testing Environment, Cray User Group Meeting (CUG2012), Stuttgart, Germany, 2012.
  • W. Kramer, Measuring Sustained Performance on Blue Waters with the SPP Metric, Cray User Group Meeting (CUG2013), Napa, California, 2013.
  • Gainaru, F. Cappello, M. Snir and W. Kramer, Failure prediction for HPC systems and applications: Current situation and open issues - International Journal of High Performance Computing Applications, Volume 27, pp.273-282, 2013, doi:10.1177/1094342013488258.
  • P. Johnsen, M. Straka, M. Shapiro, A. Norton, T. Galarneau, Petascale WRF simulation of Hurricane Sandy - Deployment of NCSA's Cray XE6 Blue Waters. The International Conference for High Performance Computing, Networking, Storage, and Analysis, Denver, CO, 2013.
  • K. Chadalavada, R. Sisneros, Analysis of the Blue Waters File System Architecture for Application I/O Performance, Cray User Group Meeting (CUG 2013), Napa, CA, May, 2013.
  • M. Dorier, R. Sisneros, T. Peterka, G. Antoniu, D. Semeraro, Damaris/Viz: a Nonintrusive, Adaptable and User-Friendly In Situ Visualization Framework.  In Large-Scale Data Analysis and Visualization (LDAV), 2013 IEEE Symposium on, pp. 67-75, IEEE, 2013.  
  • L. Oser, K. Nagamine, J. Ostriker, M. Gajbe, G. Bryan, R. Cen and T. Naab, Alleviating the scaling problems of cosmological hydrodynamic simulations with HECA. XSEDE 2013.
  • R. Sisneros, L. Orf, G. Bryan, Ultra-high Resolution Simulation of a Downburst-producing Thunderstorm, Scientific Visualization Showcase, High Performance Computing, Networking, Storage and Analysis (SCC), 2013 SC Companion, 2013.
  • Mendes, B. Bode, G. Bauer, J. Muggli, C. Beldica, W. Kramer, Blue Waters Acceptance: Challenges and Accomplishments. Cray User Group Meeting (CUG2013), Napa, CA, 2013.
  • L. Kale, G. Zheng, Parallel Science and Engineering Applications: The Charm++ Approach: Chapter 1: The Charm++ Programming Model (book chapter), CRC Press, 2013.
  • Di Martino, F. Baccanico, W. Kramer, J.  Fullop, J. Z. Kalbarczyk, R. Iyer, Lessons Learned From the Analysis of System Failures at Petascale: The Case of Blue Waters, The 44th Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN 2014), Atlanta, GA, 2014.
  • F. Cappello, A. Geist, W. Gropp, S. Kale, W. Kramer, M. Snir, Toward Exascale Resilience: 2014 update, Supercomputing Frontiers and Innovations, Jack Dongarra and Vladimir Voevodin editors, June 2014.
  • V. Anisimov, G. Bauer, K. Chadalavada, R. Olson, J. Glenski, W. Kramer, E. Aprà, K. Kowalski, Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures, Journal of Chemical Theory and Computation, Volume 10(10), pp. 4307-4316, 2014, doi:10.1021/ct500404c.
  • Guo, W. Gropp, Applications of the Streamed formats for Sparse Matrix Operations, The International Journal of High Performance Computing Applications,Volume 28(1),pp. 3-12, February 2014.
  • Schleife, E. Draeger, V. Anisimov, A. Correa,  Y. Kanai, Quantum Dynamics Simulation of Electrons in Materials on High-Performance Computers, Computing in Science and Engineering, Special Issue: Advances in Leadership Computing, Volume 16(5), pp. 54-60, 2014.
  • L. Mendes, G. H. Bauer, W. T. Kramer, R. A. Fiedler, Expanding Blue Waters with Improved Acceleration Capability, Cray User Group Meeting (CUG2014), Lugano, Switzerland, May 2014.
  • L. Mendes, B. Bode, G. H. Bauer, J. Enos, C. Beldica, W. T. Kramer, Deploying a Large Petascale System: the Blue Waters Experience, Proceedings of the 14th International Conference of Computational Science (ICCS'2014), Cairns, Australia, 2014.
  • Loftus, A. Parga, Clearing the Obstacles to Backup PiB-Size Filesystems, Cray User Group Meeting (CUG2014), Lugano, Switzerland, 2014.
  • L. Fazenda, C. L. Mendes, L. V. Kale, J. Panetta, E. R. Rodrigues, Dynamic Load Balancing in GPU-Based Systems for a MPI Program, Proceedings of the 2014 International Conference on High Performance Computing & Simulation (HPCS'2014), Bologna, Italy, July 2014.
  • J. Fullop, R. Sisneros, A Diagnostic Utility For Analyzing Periods Of Degraded Job Performance, Cray User Group Meeting (CUG2014), Lugano, Switzerland, May, 2014.
  • R. Sisneros, K. Chadalavada, Toward Understanding Congestion Protection Events on Blue Waters Via Visual Analytics, Cray User Group Meeting (CUG2014), Lugano, Switzerland, 2014.
  • R. Sisneros, J. Fullop, B. D. Semeraro, G. Bauer, Ribbons: Enabling the Effective Use of HPC Utilization Data for System Support Staff, EuroVis Workshop on Visual Analytics, pp. 13-17, The Eurographics Association, Wales, UK, 2014.
  • D. Semeraro, R. Sisneros, J. Fullop, G. H. Bauer, It Takes a Village: Monitoring the Blue Waters Supercomputer, IEEE Cluster Workshop on Monitoring and Analysis for High Performance Computing Systems Plus Applications, 2014.
  • M. Klein, J. Stone, Unlocking the Full Potential of the Cray XK7 Accelerator, Cray User Group Meeting (CUG2014), Lugano, Switzerland, 2014.
  • J. Enos, G. Bauer, R. Brunner, S. Islam, M. Steed, D. Jackson, R. Fiedler, Topology-Aware Job Scheduling Strategies for Torus Networks, Cray User Group Meeting (CUG2014), Lugano, Switzerland, May 2014.
  • N. W. Chaney, J. Herman, P. Reed, E. F. Wood, T. Cortese, Drought and Flood Prediction: The Role of HPC and Big Data, poster at Supercomputing'14, New Orleans, 2014.
  • Agelastos, B. Allan, J. Brandt, P. Cassella, J. Enos, J. Fullop, A. Gentile, S. Monk, N. Naksinehaboon, J. Ogden, M. Rajan, M. Showerman, J. Stevenson, N. Taerat, T. Tucker, Lightweight Distributed Metric Service: A Scalable Infrastructure for Continuous Monitoring of Large Scale Computing Systems and Applications, Proceedings of Supercomputing'14, New Orleans, 2014.
  • M. S. Breitenfeld, K. Chadalavada, R. Sisneros, S. Byna, Recent Progress in Tuning Performance of Large-scale I/O with Parallel HDF5, Proceedings of 9th Parallel Data Storage Workshop at SC'2014, New Orleans, 2014.
  • S. Byna, R. Sisneros, K. Chadalavada, Q. Koziol, Tuning Parallel I/O on Blue Waters for Writing 10 Trillion Particles, Whitepaper, 2014.
  • (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.720.2066&rep=rep1&type=pdf)
  • W. Kramer, M. Butler, G. Bauer, K. Chadalavada, C. Mendes, Blue Waters Parallel I/O Storage Sub-system, High Performance Parallel I/O, Prabhat and Quincey Koziol editors, CRC Publications, Taylor and Francis Group, Boca Raton, FL, 2015, Hardback Print ISBN 13:978-1-4665-8234-7
  • Di Martino, Z. Kalbarczyk, W. Kramer, R. Iyer, Measuring and understanding extreme-scale resilience: A field study of 5,000,000 HPC application runs, 45th IEEE/IFIP International Conference on Dependable Systems and Networks (DSN 2015), pp. 25–36, 22–25, Rio de Janeiro, Brazil, June 2015. URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7266835
  • M. Gajbe, K. Chadalavada, G. Bauer, W. Kramer, Benchmarking and Performance Studies of Mapreduce, Hadoop Framework on Blue Waters Supercomputer, WorldComp 15 - ABDA'15 International Conference on Advances in Big Data Analytics, July 2015.
  • URL: http://worldcomp-proceedings.com/proc/p2015/ABD3392.pdf
  • Di Martino, S. Jha, Z. Kalbarczyk, W. Kramer, R. Iyer, LogDiver: A Tool for Measuring Resilience of Extreme-Scale Systems and Applications,  Proceeding of the 5th Workshop on Fault Tolerance for HPC at eXtreme Scale (FTXS'15), Pages 11-18, ACM New York, NY, 2015, ISBN: 978-1-4503-3569-0 doi:10.1145/2751504.2751511
  • H. Menon, L. Wesolowski, G. Zheng, P. Jetley, L. Kale, T. Quinn and F. Governato, Adaptive techniques for clustered N-body cosmological simulations, Computational Astrophysics and Cosmology, Volume 2(1), pp.1-16, 2015.
  • Guo, W. Gropp, L. Olson, A Hybrid Format for Better Performance of  Sparse Matrix-Vector Multiplication on a GPU, The International Journal of High Performance Computing Applications, Published online, July 2015, doi: 10.1177/1094342015593156.
  • Meneses, X. Ni, G. Zheng, C. L. Mendes, L. V. Kale, Using Migratable Objects to Enhance Fault Tolerance Schemes in Supercomputers, IEEE Transactions on Parallel and Distributed Systems, Volume 26, pp. 2061-2074, 2015, doi: 10.1109/TPDS.2014.2342228.
  • Y. Feng, M. Straka, T. Di Matteo, R. Croft, MP-sort: Sorting at Scale on BlueWaters, Cray User Group Meeting (CUG2015), Chicago, 2015.
  • R. Sisneros, Visualizing the Big (and Large) Data from an HPC Resource, Astronomical Society of the Pacific Conference Series, Volume 498, 2015.
  • R. Sisneros,  A Feature-first Approach to Clustering for Highlighting Regions of Interest in Scientific Data, Proceedings of International Conference on Computational Science (ICCS), Procedia Computer Science, 51C, pp. 2207-2216, 2015.
  • C. L. Mendes, B. Bode, G. H. Bauer, J. Enos, C. Beldica, W. T. Kramer, Deployment and testing of the sustained petascale Blue Waters system, Journal of Computational Science, Volume 10, pp. 327-337, 2015.
  • M. Dorier, G. Antoniu, F. Cappello, M. Snir, R. Sisneros, O. Yildiz, S. Ibrahim, T. Peterka, and L. Orf, Damaris: Addressing Performance Variability in Data Management for Post-Petascale Simulations, Preprint submitted to Journal of Parallel and Distributed Computing, 2015.
  • Bock, L. Orf, R. Sisneros, Visualization of a Tornado-producing Thunderstorm: A Study of Visual Representation, Scientific Visualization Showcase, High Performance Computing, Networking, Storage and Analysis (SC), SC Companion, 2015.
  • 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, J. Vienne, Solving the Klein-Gordon equation using Fourier spectral methods: A benchmark test for computer performance, Proceedings of The Spring Simulation Multi-Conference (SpringSim'15), Alexandria, VA, USA, 2015.
  • P. Forai, G. Peretti-Pezzi, B. Bode, K. Hoste, Making Scientific Software Installation Reproducible on Cray Systems Using EasyBuild, Cray User Group Meeting (CUG2016), London, England, 2016.
  • N. Sultana, A. Calvert, J. Overbey, G. Arnold, From OpenACC to OpenMP4: Toward Automatic Translation, XSEDE 2016.
  • L. Rahmani, M. Dorier, L. Bougé, G. Antoniu, R. Sisneros, T. Peterka, Towards Smart Visualization Framework for Climate Simulations, Whitepaper, 2016.
  • (https://hal.inria.fr/hal-01290268/document)
  • J. E. Stone, P. Messmer, R. Sisneros, K. Schulten, High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL, Workshop on High Performance Data Analysis and Visualization (HPDAV), International Parallel and Distributed Processing Symposium (IPDPS), 2016.
  • R. Sisneros, D. Pugmire, Tuned to Terrible: A Study of Parallel Particle Advection State of the Practice, Workshop on High Performance Data Analysis and Visualization (HPDAV), International Parallel and Distributed Processing Symposium (IPDPS), 2016.
  • Xu, S. Byna, V. Venkatesan, R. Sisneros, O. Kulkarni, M. Chaarawi, K. Chadalavada, LIOProf: Exposing Lustre File System Behavior for I/O Middleware, Cray User Group Meeting (CUG2016), London, UK, 2016.
  • R. Sisneros, A Classification of Parallel I/O Toward Demystifying HPC I/O Best Practices, Cray User Group Meeting (CUG2016), London, UK, 2016.
  • M. Dorier, R. Sisneros, L. Bautista-Gomez, T. Peterka, L. Orf, R. Ross, L. Rahmani, G. Antoniu, L. Bougé, Performance-Constrained In Situ Visualization of Atmospheric Simulations, IEEE Cluster, Taipei, Taiwan, 2016

Technical Reports

  • Matthew D. Jones, Joseph P. White, Martins Innus, Robert L. DeLeon, Nikolay Simakov, Jeffrey T. Palmer, Steven M. Gallo, and Thomas R. Furlani, Michael Showerman, Robert Brunner, Andry Kot, Gregory Bauer, Brett Bode, Jeremy Enos, and William Kramer, "Workload Analysis of Blue Waters". 01/13/2017.  arXiv:1703.00924 [cs.DC]

Publications current as of June 30, 2016