Publication Information

2009

M. Ryan Joung, Renyue Cen, and Greg L. Bryan: "Galaxy Size Problem at z=3: Simulated Galaxies Are Too Small", ApJ, IOP Publishing, Vol 692, Num 1, pp L1--L4, 2009, doi:10.1088/0004-637x/692/1/l1

Tomasz Kuś, Victor F. Lotrich, and Rodney J. Bartlett: "Parallel Implementation of the Equation-of-Motion Coupled-Cluster Singles and Doubles Method and Application for Radical Adducts of Cytosine", The Journal of Chemical Physics, AIP Publishing, Vol 130, Num 12, pp 124122, 2009, doi:10.1063/1.3091293

Paul R. Woodward, Jagan Jayaraj, Pei-Hung Lin, and William Dai: "First Experience of Compressible Gas Dynamics Simulation on the Los Alamos Roadrunner Machine", Concurrency and Computation: Practice and Experience, Wiley-Blackwell, Vol 21, Num 17, pp 2160--2175, 2009, doi:10.1002/cpe.1494

Franck Cappello, Al Geist, Bill Gropp, Laxmikant Kale, Bill Kramer, and Marc Snir: "Toward Exascale Resilience", The International Journal of High Performance Computing Applications, SAGE Publications, Vol 23, Num 4, pp 374--388, 2009, doi:10.1177/1094342009347767

2010

Hidenobu Yajima, Jun-Hwan Choi, and Kentaro Nagamine: "Escape Fraction of Ionizing Photons from High-Redshift Galaxies in Cosmological SPH Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 412, Num 1, pp 411--422, 2010, doi:10.1111/j.1365-2966.2010.17920.x

Jeremiah P. Ostriker, Ena Choi, Luca Ciotti, Gregory S. Novak, and Daniel Proga: "Momentum Driving: Which Physical Processes Dominate Active Galactic Nucleus Feedback?", ApJ, IOP Publishing, Vol 722, Num 1, pp 642--652, 2010, doi:10.1088/0004-637x/722/1/642

Jun-Hwan Choi, and Kentaro Nagamine: "Effects of Cosmological Parameters and Star Formation Models on the Cosmic Star Formation History in ΛCDM Cosmological Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 407, Num 3, pp 1464--1476, 2010, doi:10.1111/j.1365-2966.2010.17029.x

Jun-Hwan Choi, and Kentaro Nagamine: "Multicomponent and Variable Velocity Galactic Outflow in Cosmological Hydrodynamic Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 410, Num 4, pp 2579--2592, 2010, doi:10.1111/j.1365-2966.2010.17632.x

Kentaro Nagamine, Jun-Hwan Choi, and Hidenobu Yajima: "Effects of Ultraviolet Background and Local Stellar Radiation on the H I Column Density Distribution", ApJ, IOP Publishing, Vol 725, Num 2, pp L219--L222, 2010, doi:10.1088/2041-8205/725/2/l219

Luca Ciotti, Jeremiah P. Ostriker, and Daniel Proga: "Feedback from Central Black Holes in Elliptical Galaxies. III: Models with Both Radiative and Mechanical Feedback", ApJ, IOP Publishing, Vol 717, Num 2, pp 708--723, 2010, doi:10.1088/0004-637x/717/2/708

Ludwig Oser, Jeremiah P. Ostriker, Thorsten Naab, Peter H. Johansson, and Andreas Burkert: "The Two Phases of Galaxy Formation", ApJ, IOP Publishing, Vol 725, Num 2, pp 2312--2323, 2010, doi:10.1088/0004-637x/725/2/2312

Min-Su Shin, Jeremiah P. Ostriker, and Luca Ciotti: "Feedback from Central Black Holes in Elliptical Galaxies. II: Can Purely Mechanical Energy Feedback Models Work?", ApJ, IOP Publishing, Vol 711, Num 1, pp 268--283, 2010, doi:10.1088/0004-637x/711/1/268

Beverly A. Sanders, Rod Bartlett, Erik Deumens, Victor Lotrich, and Mark Ponton: "A Block-Oriented Language and Runtime System for Tensor Algebra with Very Large Arrays", Institute of Electrical & Electronics Engineers (IEEE), 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, New Orleans, LA, 2010, doi:10.1109/sc.2010.3

Dmitry I. Lyakh, and Rodney J. Bartlett: "An Adaptive Coupled-Cluster Theory: @CC Approach", The Journal of Chemical Physics, AIP Publishing, Vol 133, Num 24, pp 244112, 2010, doi:10.1063/1.3515476

V.F. Lotrich, J.M. Ponton, A.S. Perera, E. Deumens, R.J. Bartlett, and B.A. Sanders: "Super Instruction Architecture of Petascale Electronic Structure Software: The Story", Molecular Physics, Informa UK Limited, Vol 108, Num 21-23, pp 3323--3330, 2010, doi:10.1080/00268976.2010.512566

J. Jayaraj, P.-H. Lin, and P. R. Woodward: "Interactive Supercomputing Enabled by Cell Processor Accelerators", presented at 2010 Symposium on Application Accelerators in High-Performance Computing, Knoxville, Tennessee, U.S.A., 2010

P. R. Woodward, D. H. Porter, W. Dai, T. Fuchs, T. Nowatzki, M. Knox, G. Dimonte, F. Herwig, and C. Freyer: "The Piecewise-Parabolic Boltzmann Advection Scheme (PPB) Applied to Multifluid Hydrodynamics", United States Department of Energy (Los Alamos National Laboratory), Los Alamos National Laboratory report LA-UR-10-01823, 2010

P. R. Woodward, J. Jayaraj, P.-H. Lin, G. M. Rockefeller, C. L. Fryer, G. Dimonte, W. Dai, and R. J. Kares: "Simulating Rayleigh-Taylor (RT) Instability Using PPM Hydrodynamics at Scale on Roadrunner", Los Alamos National Laboratory, 2010 Nuclear Explosive Code Development Conference (NECDC 2010), LA-UR-11-00061, Los Alamos, New Mexico, U.S.A., 2010

P.-H. Lin, J. Jayaraj, and P. R. Woodward: "A Strategy for Automatically Generating High Performance CUDA Code for a GPU Accelerator from a Specialized Fortran Code Expression", presented at the 2010 Symposium on Application Accelerators in High Performance Computing (SAAHPC 2010), Knoxville, Tennessee, U.S.A., 2010

Paul R. Woodward, Jagan Jayaraj, Pei-Hung Lin, Pen-Chung Yew, Michael Knox, Jim Greensky, Anthony Nowatski, and Karl Stoffels: "Boosting the Performance of Computational Fluid Dynamics Codes for Interactive Supercomputing", Procedia Computer Science, Elsevier BV, Vol 1, Num 1, pp 2055--2064, 2010, doi:10.1016/j.procs.2010.04.230

Cristiana Stan, Marat Khairoutdinov, Charlotte A. DeMott, V. Krishnamurthy, David M. Straus, David A. Randall, James L. Kinter, and J. Shukla: "An Ocean-Atmosphere Climate Simulation with an Embedded Cloud Resolving Model", Geophys. Res. Lett., Wiley-Blackwell, Vol 37, Num 1, 2010, doi:10.1029/2009gl040822

C. Reisswig: "Binary Black Hole Mergers and Novel Approaches to Gravitational Wave Extraction in Numerical Relativity", PhD thesis, Leibniz Universität Hannover, 2010

J. Nordhaus, T. D. Brandt, A. Burrows, E. Livne, and C. D. Ott: "Theoretical Support for the Hydrodynamic Mechanism of Pulsar Kicks", Physical Review D, American Physical Society (APS), Vol 82, Num 10, 2010, doi:10.1103/physrevd.82.103016

Leonid Oliker, Jonathan Carter, Vincent Beckner, John Bell, Harvey Wasserman, Mark Adams, Stéphane Ethier, and Erik Schnetter: "Large-Scale Numerical Simulations on High-End Computational Platforms", Informa UK Limited, Chapman & Hall/CRC Computational Science, pp 123--150, 2010, doi:10.1201/b10509-7

O. Korobkin: "Non-axisymmetric Instabilities in Self-Gravitating Tori around Black Holes, and Solving Einstein Constraints with Superconvergent Finite Element Methods", PhD thesis, Louisiana State University, 2010

Carlos O. Lousto, Hiroyuki Nakano, Yosef Zlochower, and Manuela Campanelli: "Intermediate-Mass-Ratio Black Hole Binaries: Intertwining Numerical and Perturbative Techniques", Physical Review D, American Physical Society (APS), Vol 82, Num 10, 2010, doi:10.1103/physrevd.82.104057

Carlos O. Lousto, Hiroyuki Nakano, Yosef Zlochower, and Manuela Campanelli: "Intermediate-Mass-Ratio Black-Hole Binaries: Numerical Relativity Meets Perturbation Theory", Phys. Rev. Lett., American Physical Society (APS), Vol 104, Num 21, 2010, doi:10.1103/physrevlett.104.211101

Carlos O. Lousto, Hiroyuki Nakano, Yosef Zlochower, and Manuela Campanelli: "Statistical Studies of Spinning Black-Hole Binaries", Physical Review D, American Physical Society (APS), Vol 81, Num 8, 2010, doi:10.1103/physrevd.81.084023

Steven Gottlieb, Guochun Shi, Aaron Torok, and Volodymyr Kindratenko: "QUDA Programming for Staggered Quarks", Proceedings of Science, Proceedings, 28th International Symposium on Lattice field theory (Lattice 2010), pp 026, Villasimius, Italy, 2010

Matthew J. Turk, Britton D. Smith, Jeffrey S. Oishi, Stephen Skory, Samuel W. Skillman, Tom Abel, and Michael L. Norman: "Yt: A Multi-Code Analysis Toolkit for Astrophysical Simulation Data", ApJS, IOP Publishing, Vol 192, Num 1, pp 9, 2010, doi:10.1088/0067-0049/192/1/9

D. Guo, and W. Gropp: "Optimizing Sparse Data Structures for Matrix-Vector Multiply", The International Journal of High Performance Computing Applications, SAGE Publications, Vol 25, Num 1, pp 115--131, 2010, doi:10.1177/1094342010374847

H. Karimabadi, B. Loring, H. X. Vu, Y. Omelchenko, M. Tatineni, A. Majumdar, U. Ayachit and B. Geveci: "Petascale Global Kinetic Simulations of The Magnetosphere and Visualization Strategies for Analysis of Very Large Multi-Variate Data Sets", Astronomical Society of the Pacific, ASP Conference Series: 5th international conference of numerical modeling of space plasma flows (ASTRONUM 2010), Vol 444, pp 281, San Diego, California, USA, 2010

2011

D. C. Hambrick, J. P. Ostriker, P. H. Johansson, and T. Naab: "The Effects of X-Ray and UV Background Radiation on the Low-Mass Slope of the Galaxy Mass Function", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 413, Num 4, pp 2421--2428, 2011, doi:10.1111/j.1365-2966.2011.18312.x

D. Clay Hambrick, Jeremiah P. Ostriker, Thorsten Naab, and Peter H. Johansson: "The Effects of X-Ray Feedback from Active Galactic Nuclei on Host Galaxy Evolution", ApJ, IOP Publishing, Vol 738, Num 1, pp 16, 2011, doi:10.1088/0004-637x/738/1/16

Gregory S. Novak, Jeremiah P. Ostriker, and Luca Ciotti: "Feedback from Central Black Holes in Elliptical Galaxies: Two-Dimensional Models Compared to One-Dimensional Models", ApJ, IOP Publishing, Vol 737, Num 1, pp 26, 2011, doi:10.1088/0004-637x/737/1/26

Paramita Barai, Daniel Proga, and Kentaro Nagamine: "Smoothed Particle Hydrodynamics Simulations of Black Hole Accretion: A Step to Model Black Hole Feedback in Galaxies", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 418, Num 1, pp 591--611, 2011, doi:10.1111/j.1365-2966.2011.19508.x

Renyue Cen, and Nora Elisa Chisari: "Star Formation Feedback and Metal Enrichment History of the Intergalactic Medium", ApJ, IOP Publishing, Vol 731, Num 1, pp 11, 2011, doi:10.1088/0004-637x/731/1/11

Stephanie Tonnesen, and Greg L. Bryan: "The Tail of the Stripped Gas That Cooled: HI, Halpha and X-Ray Observational Signatures of Ram Pressure Stripping", ApJ, IOP Publishing, Vol 727, Num 2, pp 133, 2011, doi:10.1088/0004-637x/727/2/133

Stephanie Tonnesen, Greg L. Bryan, and Rena Chen: "How to Light It Up: Simulating Ram-Pressure Stripped X-Ray Bright Tails", ApJ, IOP Publishing, Vol 731, Num 2, pp 98, 2011, doi:10.1088/0004-637x/731/2/98

Dmitry I. Lyakh, Victor F. Lotrich, and Rodney J. Bartlett: "The `Tailored' CCSD(T) Description of the Automerization of Cyclobutadiene", Chemical Physics Letters, Elsevier BV, Vol 501, Num 4-6, pp 166--171, 2011, doi:10.1016/j.cplett.2010.11.058

Erik Deumens, Victor F. Lotrich, Ajith Perera, Mark J. Ponton, Beverly A. Sanders, and Rodney J. Bartlett: "Software Design of ACES III with the Super Instruction Architecture", Wiley Interdisciplinary Reviews: Computational Molecular Science, Wiley-Blackwell, Vol 1, Num 6, pp 895--901, 2011, doi:10.1002/wcms.77

Erik Deumens, Victor F. Lotrich, Ajith S. Perera, Rodney J. Bartlett, Nakul Jindal, and Beverly A. Sanders: "The Super Instruction Architecture", Elsevier BV, Annual Reports in Computational Chemistry, pp 179--191, 2011, doi:10.1016/b978-0-444-53835-2.00008-0

Monika Musiał‚, Ajith Perera, and Rodney J. Bartlett: "Multireference Coupled-Cluster Theory: The Easy Way", The Journal of Chemical Physics, AIP Publishing, Vol 134, Num 11, pp 114108, 2011, doi:10.1063/1.3567115

Monika Musiał‚, and Rodney J. Bartlett: "Charge-Transfer Separability and Size-Extensivity in the Equation-of-Motion Coupled Cluster Method: EOM-CCx", The Journal of Chemical Physics, AIP Publishing, Vol 134, Num 3, pp 034106, 2011, doi:10.1063/1.3511783

Monika Musiał‚, and Rodney J. Bartlett: "Multi-Reference Fock Space Coupled-Cluster Method in the Intermediate Hamiltonian Formulation for Potential Energy Surfaces", The Journal of Chemical Physics, AIP Publishing, Vol 135, Num 4, pp 044121, 2011, doi:10.1063/1.3615500

Musiał, Monika and Kucharski, Stanisław A. and Bartlett, Rodney J.: "Multireference Double Electron Attached Coupled Cluster Method with Full Inclusion of the Connected Triple Excitations: MR-DA-CCSDT", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 7, Num 10, pp 3088--3096, 2011, doi:10.1021/ct200195q

Robert W. Molt, Thomas Watson, Victor F. Lotrich, and Rodney J. Bartlett: "RDX Geometries, Excited States, and Revised Energy Ordering of Conformers via MP2 and CCSD(T) Methodologies: Insights Into Decomposition Mechanism", J. Phys. Chem. A, American Chemical Society (ACS), Vol 115, Num 5, pp 884--890, 2011, doi:10.1021/jp109695v

V. Lotrich, and Rodney J. Bartlett: "External Coupled-Cluster Perturbation Theory: Description and Application to Weakly Interaction Dimers. Corrections to the Random Phase Approximation", The Journal of Chemical Physics, AIP Publishing, Vol 134, Num 18, pp 184108, 2011, doi:10.1063/1.3570573

Falk Herwig, Marco Pignatari, Paul R. Woodward, David H. Porter, Gabriel Rockefeller, Chris L. Fryer, Michael Bennett, and Raphael Hirschi: "Convective-Reactive Proton-C12 Combustion in Sakurai's Object (V4334 Sagittarii) and Implications for the Evolution and Yields from the First Generations of Stars", ApJ, IOP Publishing, Vol 727, Num 2, pp 89, 2011, doi:10.1088/0004-637x/727/2/89

Pei-Hung Lin, Jagan Jayaraj, and Paul R. Woodward: "A Study of the Performance of Multifluid PPM Gas Dynamics on CPUs and GPUs", Institute of Electrical & Electronics Engineers (IEEE), 2011 Symposium on Application Accelerators in High-Performance Computing, pp 42-51, Knoxville, Tennessee, U.S.A., 2011, doi:10.1109/saahpc.2011.27

Vadim Mozhayskiy, and Ilias Tagkopoulos: "In Silico Evolution of Multi-Scale Microbial Systems in the Presence of Mobile Genetic Elements and Horizontal Gene Transfer", Springer Science + Business Media, Bioinformatics Research and Applications, pp 262--273, 2011, doi:10.1007/978-3-642-21260-4_26

Vadim Mozhayskiy, Bob Miller, Kwan-Liu Ma, and Ilias Tagkopoulos: "A Scalable Multi-Scale Framework for Parallel Simulation and Visualization of Microbial Evolution", Association for Computing Machinery (ACM), Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery - TG '11, Salt Lake City, UT, 2011, doi:10.1145/2016741.2016749

Alex B. Nielsen, Michael Jasiulek, Badri Krishnan, and Erik Schnetter: "Slicing Dependence of Nonspherically Symmetric Quasilocal Horizons in Vaidya Spacetimes", Physical Review D, American Physical Society (APS), Vol 83, Num 12, 2011, doi:10.1103/physrevd.83.124022

C. D. Ott, C. Reisswig, E. Schnetter, E. O'Connor, U. Sperhake, F. Löffler,, P. Diener, E. Abdikamalov, I. Hawke, and A. Burrows: "Dynamics and Gravitational Wave Signature of Collapsar Formation", Phys. Rev. Lett., American Physical Society (APS), Vol 106, Num 16, pp 161103, 2011, doi:10.1103/physrevlett.106.161103

C. Reisswig, C. D. Ott, U. Sperhake, and E. Schnetter: "Gravitational Wave Extraction in Simulations of Rotating Stellar Core Collapse", Physical Review D, American Physical Society (APS), Vol 83, Num 6, 2011, doi:10.1103/physrevd.83.064008

Evan O'Connor, and Christian D. Ott: "Black Hole Formation in Failing Core-Collapse Supernovae", ApJ, IOP Publishing, Vol 730, Num 2, pp 70, 2011, doi:10.1088/0004-637x/730/2/70

Ian Vega, Barry Wardell, and Peter Diener: "Effective Source Approach to Self-Force Calculations", Class. Quantum Grav., IOP Publishing, Vol 28, Num 13, pp 134010, 2011, doi:10.1088/0264-9381/28/13/134010

Oleg Korobkin, Ernazar B. Abdikamalov, Erik Schnetter, Nikolaos Stergioulas, and Burkhard Zink: "Stability of General-Relativistic Accretion Disks", Physical Review D, American Physical Society (APS), Vol 83, Num 4, 2011, doi:10.1103/physrevd.83.043007

Timothy D. Brandt, Adam Burrows, Christian D. Ott, and Eli Livne: "Results from Core-Collapse Simulations with Multi-Dimensional, Multi-Angle Neutrino Transport", ApJ, IOP Publishing, Vol 728, Num 1, pp 8, 2011, doi:10.1088/0004-637x/728/1/8

Bruno C Mundim, Bernard J Kelly, Yosef Zlochower, Hiroyuki Nakano, and Manuela Campanelli: "Hybrid Black-Hole Binary Initial Data", Class. Quantum Grav., IOP Publishing, Vol 28, Num 13, pp 134003, 2011, doi:10.1088/0264-9381/28/13/134003

Carlos O. Lousto, and Yosef Zlochower: "Hangup Kicks: Still Larger Recoils by Partial Spin-Orbit Alignment of Black-Hole Binaries", Phys. Rev. Lett., American Physical Society (APS), Vol 107, Num 23, 2011, doi:10.1103/physrevlett.107.231102

Carlos O. Lousto, and Yosef Zlochower: "Modeling Maximum Astrophysical Gravitational Recoil Velocities", Physical Review D, American Physical Society (APS), Vol 83, Num 2, 2011, doi:10.1103/physrevd.83.024003

Carlos O. Lousto, and Yosef Zlochower: "Orbital Evolution of Extreme-Mass-Ratio Black-Hole Binaries with Numerical Relativity", Phys. Rev. Lett., American Physical Society (APS), Vol 106, Num 4, 2011, doi:10.1103/physrevlett.106.041101

Hiroyuki Nakano, Manuela Campanelli, Carlos O Lousto, and Yosef Zlochower: "Perturbative Effects of Spinning Black Holes in the Extreme Mass-Ratio Limit", Class. Quantum Grav., IOP Publishing, Vol 28, Num 13, pp 134005, 2011, doi:10.1088/0264-9381/28/13/134005

Hiroyuki Nakano, Yosef Zlochower, Carlos O. Lousto, and Manuela Campanelli: "Intermediate-Mass-Ratio Black Hole Binaries. II. Modeling Trajectories and Gravitational Waveforms", Physical Review D, American Physical Society (APS), Vol 84, Num 12, 2011, doi:10.1103/physrevd.84.124006

M C Babiuc, J Winicour, and Y Zlochower: "Binary Black Hole Waveform Extraction at Null Infinity", Class. Quantum Grav., IOP Publishing, Vol 28, Num 13, pp 134006, 2011, doi:10.1088/0264-9381/28/13/134006

Marcelo Ponce, Carlos Lousto, and Yosef Zlochower: "Seeking for Toroidal Event Horizons from Initially Stationary BH Configurations", Class. Quantum Grav., IOP Publishing, Vol 28, Num 14, pp 145027, 2011, doi:10.1088/0264-9381/28/14/145027

Marcelo Ponce, Joshua A. Faber, and James C. Lombardi: "Accretion Disks Around Kicked Black Holes: Post-Kick Dynamics", ApJ, IOP Publishing, Vol 745, Num 1, pp 71, 2011, doi:10.1088/0004-637x/745/1/71

Yosef Zlochower, Manuela Campanelli, and Carlos O Lousto: "Modeling Gravitational Recoil from Black-Hole Binaries Using Numerical Relativity", Class. Quantum Grav., IOP Publishing, Vol 28, Num 11, pp 114015, 2011, doi:10.1088/0264-9381/28/11/114015

En-Jui Lee, Po Chen, Thomas H. Jordan, and Liqiang Wang: "Rapid Full-Wave Centroid Moment Tensor (CMT) Inversion in a Three-Dimensional Earth Structure Model for Earthquakes in Southern California", Geophysical Journal International, Oxford University Press (OUP), Vol 186, Num 1, pp 311--330, 2011, doi:10.1111/j.1365-246x.2011.05031.x

Mikhail Smelyanskiy, Karthikeyan Vaidyanathan, Jee Choi, Bálint Joó, Jatin Chhugani, Michael A. Clark, and Pradeep Dubey: "High-Performance Lattice QCD for Multi-Core Based Parallel Systems Using a Cache-Friendly Hybrid Threaded-MPI Approach", Association for Computing Machinery (ACM), Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis (SC '11), pp 69:1--69:11, Seattle, Washington, U.S.A., 2011, doi:10.1145/2063384.2063477

R. Babich, M. A. Clark, B. Joó, G. Shi, R. C. Brower, and S. Gottlieb: "Scaling Lattice QCD Beyond 100 GPUs", Association for Computing Machinery (ACM), Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '11, 2011, doi:10.1145/2063384.2063478

H. Karimabadi, J. Dorelli, H. X. Vu, B. Loring, Y. Omelchenko, Dimitris Vassiliadis, Shing F. Fung, Xi Shao, Ioannis A. Daglis, and Joseph D. Huba: "Is Quadrupole Structure of Out-of-Plane Magnetic Field Evidence for Hall Reconnection?", AIP Publishing, AIP Conference Proceedings 1320, 137 (2011), Sani Resort, Halkidiki, Greece, 2011, doi:10.1063/1.3544318

H. Karimabadi, J. Dorelli, V. Roytershteyn, W. Daughton, and L. Chacón: "Flux Pileup in Collisionless Magnetic Reconnection: Bursty Interaction of Large Flux Ropes", Phys. Rev. Lett., American Physical Society (APS), Vol 107, Num 2, pp 025002, 2011, doi:10.1103/physrevlett.107.025002

H. Karimabadi, V. Roytershteyn, C.G. Mouikis, L.M. Kistler, and W. Daughton: "Flushing Effect in Reconnection: Effects of Minority Species of Oxygen Ions", Planetary and Space Science, Elsevier BV, Vol 59, Num 7, pp 526--536, 2011, doi:10.1016/j.pss.2010.07.014

William Kramer: "How to Measure Useful, Sustained Performance", ACM Press, State of the Practice Reports (SC '11), pp 2:1-2:18, Seattle, Washington, U.S.A., 2011, doi:10.1145/2063348.2063351

Eric Heien, Derrick Kondo, Ana Gainaru, Dan LaPine, Bill Kramer, and Franck Cappello: "Modeling and Tolerating Heterogeneous Failures in Large Parallel Systems", ACM Press, Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis (SC '11), pp 45:1-45:11, Seattle, Washington, U.S.A., 2011, doi:10.1145/2063384.2063444

Ana Gainaru, Franck Cappello, Joshi Fullop, Stefan Trausan-Matu, and William Kramer: "Adaptive Event Prediction Strategy with Dynamic Time Window for Large-Scale HPC Systems", ACM Press, Managing Large-scale Systems via the Analysis of System Logs and the Application of Machine Learning Techniques (SLAML '11), pp 4:1-4:8, Cascais, Portugal, 2011, doi:10.1145/2038633.2038637

Jack Dongarra, Pete Beckman, Terry Moore, Patrick Aerts, Giovanni Aloisio, Jean-Claude Andre, David Barkai, Jean-Yves Berthou, Taisuke Boku, Bertrand Braunschweig, Franck Cappello, Barbara Chapman, Xuebin Chi, Alok Choudhary, Sudip Dosanjh, Thom Dunning, Sandro Fiore, Al Geist, Bill Gropp, Robert Harrison, Mark Hereld, Michael Heroux, Adolfy Hoisie, Koh Hotta, Zhong Jin, Yutaka Ishikawa, Fred Johnson, Sanjay Kale, Richard Kenway, David Keyes, Bill Kramer, Jesus Labarta, Alain Lichnewsky, Thomas Lippert, Bob Lucas, Barney Maccabe, Satoshi Matsuoka, Paul Messina, Peter Michielse, Bernd Mohr, Matthias S. Mueller, Wolfgang E. Nagel, Hiroshi Nakashima, Michael E Papka, Dan Reed, Mitsuhisa Sato, Ed Seidel, John Shalf, David Skinner, Marc Snir, Thomas Sterling, Rick Stevens, Fred Streitz, Bob Sugar, Shinji Sumimoto, William Tang, John Taylor, Rajeev Thakur, Anne Trefethen, Mateo Valero, Aad van der Steen, Jeffrey Vetter, Peg Williams, Robert Wisniewski, and Kathy Yelick: "The International Exascale Software Project Roadmap", The International Journal of High Performance Computing Applications, SAGE Publications, Vol 25, Num 1, pp 3--60, 2011, doi:10.1177/1094342010391989

Ron Babich, Richard Brower, Mike Clark, Steven Gottlieb, Balint Joo, and Guochun Shi: "Progress on the QUDA Code Suite", 29th International Symposium on Lattice field theory (Lattice 2011), Proceedings of Science, pp 033, Lake Tahoe, California, U.S.A., 2011

M. C. Babiuc, B. Szilágyi, J. Winicour, and Y. Zlochower: "Characteristic Extraction Tool for Gravitational Waveforms", Physical Review D, American Physical Society (APS), Vol 84, Num 4, pp 044057, 2011, doi:10.1103/physrevd.84.044057

Ana Gainaru, Franck Cappello, Stefan Trausan-Matu, and Bill Kramer: "Event Log Mining Tool for Large Scale HPC Systems", Springer Berlin Heidelberg, Euro-Par 2011 Parallel Processing, pp 52--64, Bordeaux, France, 2011, doi:10.1007/978-3-642-23400-2_6

2012

P. R. Woodward, J. Jayaraj, P.-H. Lin, M. Knox, D. H. Porter, C. L. Fryer, G. Dimonte, C. Joggerst, G.M. Rockefeller, W. Dai, R. J. Kares, and V. A. Thomas: "Simulating Turbulent Mixing from Richtmyer-Meshkov and Rayleigh-Taylor Instabilities in Converging Geometries Using Moving Cartesian Grids", Los Alamos National Laboratory, 2012 Nuclear Explosive Code Development Conference (NECDC 2012), LA-UR-13-20949, Livermore, California, U.S.A., 2012

Jeongnim Kim, Kenneth P Esler, Jeremy McMinis, Miguel A Morales, Bryan K Clark, Luke Shulenburger, and David M Ceperley: "Hybrid Algorithms in Quantum Monte Carlo", J. Phys.: Conf. Ser., IOP Publishing, Vol 402, pp 012008, 2012, doi:10.1088/1742-6596/402/1/012008

Kenneth Esler, Jeongnim Kim, David Ceperley, and Luke Shulenburger: "Accelerating Quantum Monte Carlo Simulations of Real Materials on GPU Clusters", Comput. Sci. Eng., Institute of Electrical & Electronics Engineers (IEEE), Vol 14, Num 1, pp 40--51, 2012, doi:10.1109/mcse.2010.122

Pei-Hung Lin, Jagan Jayaraj, Paul Woodward, and Pen-Chung Yew: "A Study of Performance Portability Using Piecewise-Parabolic Method (PPM) Gas Dynamics Applications", Procedia Computer Science, Elsevier BV, Vol 9, Num Supplement C, pp 1988-1991, 2012, doi:10.1016/j.procs.2012.04.217

Vadim Mozhayskiy, and Ilias Tagkopoulos: "Guided Evolution of in Silico Microbial Populations in Complex Environments Accelerates Evolutionary Rates Through a Step-Wise Adaptation", BMC Bioinformatics, Springer Nature, Vol 13, Num Suppl 10, pp S10, 2012, doi:10.1186/1471-2105-13-s10-s10

Vadim Mozhayskiy, and Ilias Tagkopoulos: "Horizontal Gene Transfer Dynamics and Distribution of Fitness Effects During Microbial in Silico Evolution", BMC Bioinformatics, Springer Nature, Vol 13, Num Suppl 10, pp S13, 2012, doi:10.1186/1471-2105-13-s10-s13

Graham D. Fletcher, Dmitri G. Fedorov, Spencer R. Pruitt, Theresa L. Windus, and Mark S. Gordon: "Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 8, Num 1, pp 75--79, 2012, doi:10.1021/ct200548v

Humayun Arafat, P. Sadayappan, James Dinan, Sriram Krishnamoorthy, and Theresa L. Windus: "Load Balancing of Dynamical Nucleation Theory Monte Carlo Simulations Through Resource Sharing Barriers", Institute of Electrical & Electronics Engineers (IEEE), 2012 IEEE 26th International Parallel and Distributed Processing Symposium, Shanghai, China, 2012, doi:10.1109/ipdps.2012.35

D. Roten, K. B. Olsen, and J. C. Pechmann: "3D Simulations of M 7 Earthquakes on the Wasatch Fault, Utah, Part II: Broadband (0-10 Hz) Ground Motions and Nonlinear Soil Behavior", Bulletin of the Seismological Society of America, Seismological Society of America (SSA), Vol 102, Num 5, pp 2008--2030, 2012, doi:10.1785/0120110286

Y. Cui, K.B. Olsen, J. Zhou, P. Small, A. Chourasia, S.M. Day, P.J. Maechling, and T.H. Jordan: "Development and Optimizations of a SCEC Community Anelastic Wave Propagation Platform for Multicore Systems and GPU-Based Accelerators", Seismological Research Letters, Seismological Society of America (SSA), Vol 83, Num 2, pp 396, 2012, doi:10.1785/gssrl.83.2.316

A. Zebrowski, F. Löffler, and E. Schnetter: "The BL-Octree: An Efficient Data Structure for Discretized Block-Based Adaptive Mesh Refinement", Advances in Parallel Computing, IOS Press, Vol 22, pp 81-88, 2012, doi:10.3233/978-1-61499-041-3-81

Carlos O. Lousto, Hiroyuki Nakano, Yosef Zlochower, Bruno C. Mundim, and Manuela Campanelli: "Study of Conformally Flat Initial Data for Highly Spinning Black Holes and Their Early Evolutions", Physical Review D, American Physical Society (APS), Vol 85, Num 12, 2012, doi:10.1103/physrevd.85.124013

Carlos O. Lousto, Yosef Zlochower, Massimo Dotti, and Marta Volonteri: "Gravitational Recoil from Accretion-Aligned Black-Hole Binaries", Physical Review D, American Physical Society (APS), Vol 85, Num 8, 2012, doi:10.1103/physrevd.85.084015

Frank Löffler, Joshua Faber, Eloisa Bentivegna, Tanja Bode, Peter Diener, Roland Haas, Ian Hinder, Bruno C Mundim, Christian D Ott, Erik Schnetter, Gabrielle Allen, Manuela Campanelli, and Pablo Laguna: "The Einstein Toolkit: A Community Computational Infrastructure for Relativistic Astrophysics", Class. Quantum Grav., IOP Publishing, Vol 29, Num 11, pp 115001, 2012, doi:10.1088/0264-9381/29/11/115001

Joshua A. Faber, and Frederic A. Rasio: "Binary Neutron Star Mergers", Living Reviews in Relativity, Springer Science + Business Media, Vol 15, 2012, doi:10.12942/lrr-2012-8

Scott C. Noble, Bruno C. Mundim, Hiroyuki Nakano, Julian H. Krolik, Manuela Campanelli, Yosef Zlochower, and Nicolás Yunes: "Circumbinary Magnetohydrodynamic Accretion into Inspiraling Binary Black Holes", ApJ, IOP Publishing, Vol 755, Num 1, pp 51, 2012, doi:10.1088/0004-637x/755/1/51

Yosef Zlochower, Marcelo Ponce, and Carlos O. Lousto: "Accuracy Issues for Numerical Waveforms", Physical Review D, American Physical Society (APS), Vol 86, Num 10, 2012, doi:10.1103/physrevd.86.104056

R. Sisneros, C. Malone, A. Nonaka, and S. Woosley: "Investigation of Turbulence in the Early Stages of a High Resolution Supernova Simulation", Institute of Electrical & Electronics Engineers (IEEE), 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, 2012, doi:10.1109/sc.companion.2012.325

G. P. Zank, J. Heerikhuisen, B. E. Wood, N. V. Pogorelov, E. Zirnstein, and D. J. McComas: "Heliospheric Structure: The Bow Wave and the Hydrogen Wall", ApJ, IOP Publishing, Vol 763, Num 1, pp 20, 2012, doi:10.1088/0004-637x/763/1/20

James Bordner, Michael L. Norman, and Brian W. O'Shea: "Enzo-P/Cello: Extreme Adaptive Mesh Refinement for Astrophysics and Cosmology", University of Illinois at Urbana-Champaign, Proceedings of the Extreme Scaling Workshop (XSEDE '12), pp 4:1--4:11, Champaign, Illinois, U.S.A., 2012

Vitor Cardoso and Leonardo Gualtieri and Carlos Herdeiro and Ulrich Sperhake (editors) and Paul M Chesler and LuisLehner and Seong Chan Park and Harvey S Reall and Carlos F Sopuerta (section coordinators) and Daniela Alic and Oscar JC Dias and Roberto Emparan and Valeria Ferrari and Steven B Giddings and Mahdi Godazgar and Ruth Gregory and Veronika EHubeny and Akihiro Ishibashi and Greg Landsberg and Carlos O Lousto and David Mateos and Vicki Moeller and HirotadaOkawa and Paolo Pani and M Andy Parker and Frans Pretorius and Masaru Shibata and Hajime Sotani and Toby Wiseman and HelviWitek and Nicolas Yunes and Miguel Zilhão: "NR/HEP: Roadmap for the Future", Class. Quantum Grav., IOP Publishing, Vol 29, Num 24, pp 244001, 2012, doi:10.1088/0264-9381/29/24/244001

P. F. Hopkins: "A General Class of Lagrangian Smoothed Particle Hydrodynamics Methods and Implications for Fluid Mixing Problems", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 428, Num 4, pp 2840--2856, 2012, doi:10.1093/mnras/sts210

Aaron Anderson, and Jonathan Freund: "Source Mechanisms of Jet Crackle", American Institute of Aeronautics and Astronautics (AIAA), 18th AIAA/CEAS Aeroacoustics Conference (33rd AIAA Aeroacoustics Conference), 2012, doi:10.2514/6.2012-2251

Joseph Muggli, Brett Bode, Torsten Hoefler, William Kramer and Celso L. Mendes: "Blue Waters Testing Environment", presented at CUG 2012, Stuttgart, Germany, 2012

Guo, Dahai and Gropp, William: "Adaptive Thread Distributions for SpMV on a GPU", University of Illinois at Urbana-Champaign, Proceedings of the Extreme Scaling Workshop, BW-XSEDE '12, pp 2:1-2:5, Chicago, Illinois, U.S.A., 2012

Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, James C. Phillips, Laximant V. Kale, and Terry R. Jones: "Optimizing Fine-Grained Communication in a Biomolecular Simulation Application on Cray XK6", IEEE, 2012 International Conference for High Performance Computing, Networking, Storage and Analysis, pp 1-11, 2012, doi:10.1109/sc.2012.87

K. Chadalavada, M. Gajbe: "Understanding the effects of process placement on application performance on an AMD Interlagos processor", presented at CUG 2012, Stuttgart, Germany, 2012

B. O'Shea and M. Norman and B. Smith and M. Turk and M. Kuhlen and J. Wise and D. Reynolds and R. Harkness and M. Gajbe and D. Semeraro: "Cosmology on the Blue Waters Early Science System", IEEE, 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, pp 1578-1578, 2012, doi:10.1109/SC.Companion.2012.370

Gainaru, Ana and Cappello, Franck and Snir, Marc and Kramer, William: "Fault Prediction Under the Microscope: A Closer Look into HPC Systems", IEEE Computer Society Press, Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC '12), pp 77:1-77:11, Salt Lake City, Utah, U.S.A., 2012

W. Kramer: "Top500 versus sustained performance - the top problems with the TOP500 list - and what to do about them", IEEE, 2012 21st International Conference on Parallel Architectures and Compilation Techniques (PACT), pp 223-230, Minneapolis, Minnesota, U.S.A., 2012

Ana Gainaru, Franck Cappello, and William Kramer: "Taming of the Shrew: Modeling the Normal and Faulty Behaviour of Large-Scale HPC Systems", IEEE, 2012 IEEE 26th International Parallel and Distributed Processing Symposium, pp 1168-1179, Shanghai, China, 2012, doi:10.1109/ipdps.2012.107

G. H. Bauer, T. Hoefler, W. T. Kramer, R. A. Fiedler: "Analyses and Modeling of Applications Used to Demonstrate Sustained Petascale Performance on Blue Waters", presented at CUG 2012, Stuttgart, Germany, 2012

Carleton DeTar, A.S. Kronfeld, Song-Haeng Lee, L. Levkova, D. Mohler, J.N. Simone: "Charmonium Mass Splittings at the Physical Point", Proceedings of Science, Proceedings, 30th International Symposium on Lattice Field Theory (Lattice 2012), pp 257, Cairns, Australia, 2012

Marek Blazewicz, Steven R. Brandt, Peter Diener, David M. Koppelman, Krzysztof Kurowski, Frank Löffler, Erik Schnetter, and Jian Tao: "A Massive Data Parallel Computational Framework for Petascale/Exascale Hybrid Computer Systems", presented at the International Conference on Parallel Computing (ParCo 2011), Ghent, Belgium, 2012

Marek Blazewicz, Steven R. Brandt, Peter Diener, David M. Koppelman, Krzysztof Kurowski, Frank Löffler, Erik Schnetter, and Jian Tao: "A Massive Data Parallel Computational Framework for Petascale/Exascale Hybrid Computer Systems", Advances in Parallel Computing, IOS Press, Applications, Tools and Techniques on the Road to Exascale Computing, Vol 22, pp 351–358, Amsterdam, The Netherlands, 2012, doi:10.3233/978-1-61499-041-3-351

P Ajith and Michael Boyle and Duncan A Brown and Bernd Brügmann and Luisa T Buchman and Laura Cadonati and ManuelaCampanelli and Tony Chu and Zachariah B Etienne and Stephen Fairhurst and Mark Hannam and James Healy and Ian Hinder and SaschaHusa and Lawrence E Kidder and Badri Krishnan and Pablo Laguna and Yuk Tung Liu and Lionel London and Carlos OLousto and Geoffrey Lovelace and Ilana MacDonald and Pedro Marronetti and Satya Mohapatra and Philipp Mösta and DoreenMüller and Bruno C Mundim and Hiroyuki Nakano and Frank Ohme and Vasileios Paschalidis and Larne Pekowsky and DenisPollney and Harald P Pfeiffer and Marcelo Ponce and Michael Pürrer and George Reifenberger and Christian Reisswig and LucíaSantamaría and Mark A Scheel and Stuart L Shapiro and Deirdre Shoemaker and Carlos F Sopuerta and Ulrich Sperhake and BélaSzilágyi and Nicholas W Taylor and Wolfgang Tichy and Petr Tsatsin and Yosef Zlochower: "The NINJA-2 Catalog of Hybrid Post-Newtonian/numerical-Relativity Waveforms for Non-Precessing Black-Hole Binaries", Class. Quantum Grav., IOP Publishing, Vol 29, Num 12, pp 124001, 2012, doi:10.1088/0264-9381/29/12/124001

2013

Paul R. Woodward, Jagan Jayaraj, Pei-Hung Lin, Michael Knox, Simon D. Hammond, James Greensky, and Sarah E. Anderson: "Scaling the Multifluid PPM Code on Blue Waters and Intel MIC", Institute of Electrical & Electronics Engineers (IEEE), 2013 Extreme Scaling Workshop (xsw 2013), Boulder, Colorado, U.S.A., 2013, doi:10.1109/xsw.2013.13

Ludwig Oser, Manisha Gajbe, Kentaro Nagamine, Greg Bryan, Jeremiah P. Ostriker, and Renyue Cen: "Alleviating the Scaling Problem of Cosmological Hydrodynamic Simulations with HECA", Association for Computing Machinery (ACM), Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13, pp 9:1-9:4, San Diego, CA, 2013, doi:10.1145/2484762.2484776

M. Hirschmann, T. Naab, R. Dave, B. D. Oppenheimer, J. P. Ostriker, R. S. Somerville, L. Oser, R. Genzel, L. J. Tacconi, N. M. Forster-Schreiber, A. Burkert, and S. Genel: "The Effect of Metal Enrichment and Galactic Winds on Galaxy Formation in Cosmological Zoom Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 436, Num 4, pp 2929--2949, 2013, doi:10.1093/mnras/stt1770

Renyue Cen, and Zheng Zheng: "The Nature of Lyα Blobs: Powered by Extreme Starbursts", ApJ, IOP Publishing, Vol 775, Num 2, pp 112, 2013, doi:10.1088/0004-637x/775/2/112

Taysun Kimm, and Renyue Cen: "Heavy Dust Obscuration of Z=7 Galaxies in a Cosmological Hydrodynamic Simulation", ApJ, IOP Publishing, Vol 776, Num 1, pp 35, 2013, doi:10.1088/0004-637x/776/1/35

Nakul Jindal, Victor Lotrich, Erik Deumens, and Beverly A. Sanders: "SIPMaP: A Tool for Modeling Irregular Parallel Computations in the Super Instruction Architecture", Institute of Electrical & Electronics Engineers (IEEE), 2013 IEEE 27th International Symposium on Parallel and Distributed Processing, Boston, MA, 2013, doi:10.1109/ipdps.2013.35

F. Ma, S. Zhang, H. Krakauer, and W. Purwanto: "Auxiliary-Field Quantum Monte Carlo Calculations in Solids", presented at the 25th Annual Workshop on Recent Developments in Electronic Structure Methods (ES2013), Williamsburg, Virginia, U.S.A., 2013

Fengjie Ma, Shiwei Zhang, and Henry Krakauer: "Excited State Calculations in Solids by Auxiliary-Field Quantum Monte Carlo", New Journal of Physics, IOP Publishing, Vol 15, Num 9, pp 093017, 2013, doi:10.1088/1367-2630/15/9/093017

Hao Shi, and Shiwei Zhang: "Symmetry in Auxiliary-Field Quantum Monte Carlo Calculations", Phys. Rev. B, American Physical Society (APS), Vol 88, Num 12, 2013, doi:10.1103/physrevb.88.125132

L. K. Wagner: "Can We Understand the High-Tc Superconducting Cuprates from First Principles?", presented at the 8th Quantum Monte Carlo in the Apuan Alps International Workshop, Vallico Sotto, Italy, 2013

S. Zhang: "Auxiliary-Field Quantum Monte Carlo for Correlated Electron Systems", Verlag des Forschungszentrum Jülich, Emergent Phenomena in Correlated Matter Modeling and Simulation, Vol. 3 (Lecture notes of the Autumn School on Correlated Electrons 2013), 2013

Wirawan Purwanto, Shiwei Zhang, and Henry Krakauer: "Frozen-Orbital and Downfolding Calculations with Auxiliary-Field Quantum Monte Carlo", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 9, Num 11, pp 4825--4833, 2013, doi:10.1021/ct4006486

Andreas Pavlogiannis, Vadim Mozhayskiy, and Ilias Tagkopoulos: "A Flood-Based Information Flow Analysis and Network Minimization Method for Gene Regulatory Networks", BMC Bioinformatics, Springer Nature, Vol 14, Num 1, pp 137, 2013, doi:10.1186/1471-2105-14-137

Vadim Mozhayskiy, and Ilias Tagkopoulos: "Microbial Evolution in Vivo and in Silico: Methods and Applications", Integr. Biol., Royal Society of Chemistry (RSC), Vol 5, Num 2, pp 262--277, 2013, doi:10.1039/c2ib20095c

Jun Zhou, Yifeng Cui, Efecan Poyraz, Dong Ju Choi, and Clark C. Guest: "Multi-GPU Implementation of a 3D Finite Difference Time Domain Earthquake Code on Heterogeneous Supercomputers", Procedia Computer Science, Elsevier BV, Vol 18, pp 1255--1264, 2013, doi:10.1016/j.procs.2013.05.292

Ricardo Taborda, and Jacobo Bielak: "Ground-Motion Simulation and Validation of the 2008 Chino Hills, California, Earthquake", Bulletin of the Seismological Society of America, Seismological Society of America (SSA), Vol 103, Num 1, pp 131--156, 2013, doi:10.1785/0120110325

Y. Cui, A. Chourasia, Z. Shi, S. M. Day, P. J. Maechling, T. H. Jordan, E. Poyraz, K. B. Olsen, J. Zhou, K. Withers, S. Callaghan, J. Larkin, C. Guest, and D. Choi: "Physics-Based Seismic Hazard Analysis on Petascale Heterogeneous Supercomputers", Association for Computing Machinery (ACM), Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '13), Denver, Colorado, U.S.A., 2013, doi:10.1145/2503210.2503300

Y. Cui, E. Poyraz, J. Zhou, S. Callaghan, P. Maechling, T.H. Jordan, L. Shih, and P. Chen: "Accelerating CyberShake Calculations on the XE6/XK7 Platform of Blue Waters", Institute of Electrical & Electronics Engineers (IEEE), 2013 Extreme Scaling Workshop (XSW 2013), Boulder, Colorado, U.S.A., 2013, doi:10.1109/xsw.2013.6

Erik Schnetter: "Performance and Optimization Abstractions for Large Scale Heterogeneous Systems in the Cactus/Chemora Framework", Institute of Electrical & Electronics Engineers (IEEE), 2013 Extreme Scaling Workshop (xsw 2013), Boulder, CO, 2013, doi:10.1109/xsw.2013.9

Carlos O. Lousto, and Yosef Zlochower: "Exploring the Outer Limits of Numerical Relativity", Physical Review D, American Physical Society (APS), Vol 88, Num 2, 2013, doi:10.1103/physrevd.88.024001

Carlos O. Lousto, and Yosef Zlochower: "Nonlinear Gravitational Recoil from the Mergers of Precessing Black-Hole Binaries", Physical Review D, American Physical Society (APS), Vol 87, Num 8, 2013, doi:10.1103/physrevd.87.084027

Miguel Zilhão and Frank Löffler: "An Introduction to the Einstein Toolkit", International Journal of Modern Physics A, World Scientific Pub Co Pte Lt, Vol 28, Num 22n23, pp 1340014, 2013, doi:10.1142/s0217751x13400149

Philipp Mösta, Bruno C Mundim, Joshua A Faber, Roland Haas, Scott C Noble, Tanja Bode, Frank Löffler, Christian D Ott, Christian Reisswig, and Erik Schnetter: "GRHydro: A New Open-Source General-Relativistic Magnetohydrodynamics Code for the Einstein Toolkit", Class. Quantum Grav., IOP Publishing, Vol 31, Num 1, pp 015005, 2013, doi:10.1088/0264-9381/31/1/015005

Dawei Mu, Po Chen, and Liqiang Wang: "Accelerating the Discontinuous Galerkin Method for Seismic Wave Propagation Simulations Using Multiple GPUs with CUDA and MPI", Earthquake Science, Springer Science + Business Media, Vol 26, Num 6, pp 377--393, 2013, doi:10.1007/s11589-013-0047-7

Dawei Mu, Po Chen, and Liqiang Wang: "Accelerating the Discontinuous Galerkin Method for Seismic Wave Propagation Simulations Using the Graphic Processing Unit (GPU)--Single-GPU Implementation", Computers & Geosciences, Elsevier BV, Vol 51, pp 282--292, 2013, doi:10.1016/j.cageo.2012.07.017

En-Jui Lee, He Huang, John M. Dennis, Po Chen, and Liqiang Wang: "An Optimized Parallel LSQR Algorithm for Seismic Tomography", Computers & Geosciences, Elsevier BV, Vol 61, pp 184--197, 2013, doi:10.1016/j.cageo.2013.08.013

He Huang, John M. Dennis, Liqiang Wang, and Po Chen: "A Scalable Parallel LSQR Algorithm for Solving Large-Scale Linear System for Tomographic Problems: A Case Study in Seismic Tomography", Procedia Computer Science, Elsevier BV, Vol 18, pp 581--590, 2013, doi:10.1016/j.procs.2013.05.222

James F. Dama, Anton V. Sinitskiy, Martin McCullagh, Jonathan Weare, Benoît Roux, Aaron R. Dinner, and Gregory A. Voth: "The Theory of Ultra-Coarse-Graining. 1. General Principles", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 9, Num 5, pp 2466--2480, 2013, doi:10.1021/ct4000444

Daniel R. Roe, and Thomas E. Cheatham: "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 9, Num 7, pp 3084--3095, 2013, doi:10.1021/ct400341p

R A Fonseca, J Vieira, F Fiuza, A Davidson, F S Tsung, W B Mori, and L O Silva: "Exploiting Multi-Scale Parallelism for Large Scale Numerical Modelling of Laser Wakefield Accelerators", Plasma Phys. Control. Fusion, IOP Publishing, Vol 55, Num 12, pp 124011, 2013, doi:10.1088/0741-3335/55/12/124011

Kai J. Kohlhoff, Diwakar Shukla, Morgan Lawrenz, Gregory R. Bowman, David E. Konerding, Dan Belov, Russ B. Altman, and Vijay S. Pande: "Cloud-Based Simulations on Google Exacycle Reveal Ligand Modulation of GPCR Activation Pathways", Nature Chemistry, Nature Publishing Group, Vol 6, Num 1, pp 15--21, 2013, doi:10.1038/nchem.1821

J. E. Fonseca, T. Kubis, M. Povolotskyi, B. Novakovic, A. Ajoy, G. Hegde, H. Ilatikhameneh, Z. Jiang, P. Sengupta, Y. Tan, and G. Klimeck: "Efficient and Realistic Device Modeling from Atomic Detail to the Nanoscale", J Comput Electron, Springer Science + Business Media, Vol 12, Num 4, pp 592--600, 2013, doi:10.1007/s10825-013-0509-0

Lang Zeng, Yu He, Michael Povolotskyi, XiaoYan Liu, Gerhard Klimeck, and Tillmann Kubis: "Low Rank Approximation Method for Efficient Green's Function Calculation of Dissipative Quantum Transport", J. Appl. Phys., AIP Publishing, Vol 113, Num 21, pp 213707, 2013, doi:10.1063/1.4809638

Yaohua Tan, Michael Povolotskyi, Tillmann Kubis, Yu He, Zhengping Jiang, Gerhard Klimeck, and Timothy B. Boykin: "Empirical Tight Binding Parameters for GaAs and MgO with Explicit Basis Through DFT Mapping", J Comput Electron, Springer Science + Business Media, Vol 12, Num 1, pp 56--60, 2013, doi:10.1007/s10825-013-0436-0

A. Bazavov, C. Bernard, C. DeTar, J. Foley, W. Freeman, Steven Gottlieb, U. M. Heller, J. E. Hetrick, J. Kim, J. Laiho, L. Levkova, M. Lightman, J. Osborn, S. Qiu, R. L. Sugar, D. Toussaint, R. S. Van de Water, and R. Zhou: "Leptonic-Decay-Constant Ratio fK+/fπ+ from Lattice QCD with Physical Light Quarks", Phys. Rev. Lett., American Physical Society (APS), Vol 110, Num 17, 2013, doi:10.1103/physrevlett.110.172003

A. Bazavov, C. Bernard, J. Komijani, C. DeTar, L. Levkova, W. Freeman, Steven Gottlieb, Ran Zhou, U. M. Heller, J. E. Hetrick, J. Laiho, J. Osborn, R. L. Sugar, D. Toussaint, and R. S. Van de Water: "Lattice QCD Ensembles with Four Flavors of Highly Improved Staggered Quarks", Physical Review D, American Physical Society (APS), Vol 87, Num 5, 2013, doi:10.1103/physrevd.87.054505

E. Gámiz, A. Bazavov, C. Bernard, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, Steven Gottlieb, U.M. Heller, J. Komijani, A.S. Kronfeld, J. Laiho, P.B. Mackenzie, E.T. Neil, T. Primer, J.N. Simone, R. Sugar, D. Toussaint, R.S. Van de Water, Ran Zhou: "K Semileptonic Form Factor with HISQ Fermions at the Physical Point", Proceedings of Science, Proceedings, 31st International Symposium on Lattice Field Theory LATTICE 2013, Mainz, Germany, 2013

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., American Physical Society (APS), Vol 110, Num 26, 2013, doi:10.1103/physrevlett.110.265004

Hao Xu, John H. Wise, and Michael L. Norman: "Population III Stars and Remnants in High-Redshift Galaxies", ApJ, IOP Publishing, Vol 773, Num 2, pp 83, 2013, doi:10.1088/0004-637x/773/2/83

Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang: "Mature HIV-1 Capsid Structure by Cryo-Electron Microscopy and All-Atom Molecular Dynamics", Nature, Nature Publishing Group, Vol 497, Num 7451, pp 643--646, 2013, doi:10.1038/nature12162

John E. Stone, Barry Isralewitz, and Klaus Schulten: "Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters", Institute of Electrical & Electronics Engineers (IEEE), 2013 Extreme Scaling Workshop (xsw 2013), Boulder, CO, 2013, doi:10.1109/xsw.2013.10

John E. Stone, Kirby L. Vandivort, and Klaus Schulten: "GPU-Accelerated Molecular Visualization on Petascale Supercomputing Platforms", Association for Computing Machinery (ACM), Proceedings of the 8th International Workshop on Ultrascale Visualization - UltraVis '13, 2013, doi:10.1145/2535571.2535595

Xue Wang, Fengting Xu, Jiasen Liu, Bingquan Gao, Yanxin Liu, Yujia Zhai, Jun Ma, Kai Zhang, Timothy S. Baker, Klaus Schulten, Dong Zheng, Hai Pang, and Fei Sun: "Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography", PLoS Pathog, Public Library of Science (PLoS), Vol 9, Num 1, pp e1003132, 2013, doi:10.1371/journal.ppat.1003132

Antonio J. Peña, Ralf G. Correa Carvalho, James Dinan, Pavan Balaji, Rajeev Thakur, and William Gropp: "Analysis of Topology-Dependent MPI Performance on Gemini Networks", Association for Computing Machinery (ACM), Proceedings of the 20th European MPI Users' Group Meeting (EuroMPI '13), pp 61-66, Madrid, Spain, 2013, doi:10.1145/2488551.2488564

H. Kucharek, S. A. Fuselier, P. Wurz, N. Pogorelov, S. Borovikov, M. A. Lee, E. Moebius, D. Reisenfeld, H. Funsten, N. Schwadron, and D. McComas: "The Solar Wind as a Possible Source of Fast Temporal Variations of the Heliospheric Ribbon", ApJ, IOP Publishing, Vol 776, Num 2, pp 109, 2013, doi:10.1088/0004-637x/776/2/109

N. V. Pogorelov, S. N. Borovikov, M. C. Bedford, J. Heerikhuisen, T. K. Kim, I. A. Kryukov, and G. P. Zank: "Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite", Astronomical Society of the Pacific, Numerical Modeling of Space Plasma Flows (ASTRONUM2012), Vol 474, pp 165, Big Island, Hawai'i, U.S.A., 2013

N. V. Pogorelov, S. T. Suess, S. N. Borovikov, R. W. Ebert, D. J. McComas, and G. P. Zank: "Three-Dimensional Features of the Outer Heliosphere Due to Coupling Between the Interstellar and Interplanetary Magnetic Fields. Iv. Solar Cycle Model Based on Ulysses Observations", ApJ, IOP Publishing, Vol 772, Num 1, pp 2, 2013, doi:10.1088/0004-637x/772/1/2

Sergey N. Borovikov, Jacob Heerikhuisen, and Nikolai V. Pogorelov: "Hybrid Parallelization of Adaptive MHD-Kinetic Module in Multi-Scale Fluid-Kinetic Simulation Suite", Astronomical Society of the Pacific, Numerical Modeling of Space Plasma Flows (ASTRONUM2012), ASP Conference Series, Vol 474, pp 219-225, Big Island, Hawai'i, U.S.A., 2013

Xi Luo, Ming Zhang, Hamid K. Rassoul, Nikolai V. Pogorelov, and Jacob Heerikhuisen: "Galactic Cosmic-Ray Modulation in a Realistic Global Magnetohydrodynamic Heliosphere", ApJ, IOP Publishing, Vol 764, Num 1, pp 85, 2013, doi:10.1088/0004-637x/764/1/85

Matthew J. Woodruff, Patrick M. Reed, and Timothy W. Simpson: "Many Objective Visual Analytics: Rethinking the Design of Complex Engineered Systems", Struct Multidisc Optim, Springer Science + Business Media, Vol 48, Num 1, pp 201--219, 2013, doi:10.1007/s00158-013-0891-z

Alison C. Dreyfuss, Kristina D. Launey, Tomáš Dytrych, Jerry P. Draayer, and Chairul Bahri: "Hoyle State and Rotational Features in Carbon-12 Within a No-Core Shell-Model Framework", Physics Letters B, Elsevier BV, Vol 727, Num 4-5, pp 511--515, 2013, doi:10.1016/j.physletb.2013.10.048

Jerry P. Draayer, Tomáš Dytrych, Kristina D. Launey, Alison C. Dreyfuss, Mia C. Ferriss, Gregory K. Tobin, Feng Pan, and Xin Guan: "Unraveling Mysteries of the Strong Interaction - 'Top Down' Versus 'Bottom Up' Considerations", Pacific Nat. U., Proceedings, International Conference on Nuclear Theory in the Supercomputing Era (NTSE-2013), pp 47, Ames, Iowa, U.S.A., 2013

K D Launey, A C Dreyfuss, T Dytrych, J P Draayer, D Langr, P Maris, J P Vary, and C Bahri: "Symmetry-Adapted Ab Initio No-Core Shell Model Calculations for 12 C", J. Phys.: Conf. Ser., IOP Publishing, Vol 436, pp 012023, 2013, doi:10.1088/1742-6596/436/1/012023

K. D. Launey, T. Dytrych, J. P. Draayer, G. K. Tobin, M. C. Ferriss, D. Langr, A. C. Dreyfuss, P. Maris, J. P. Vary, and C. Bahri: "Symmetry-Adapted No-Core Shell Model for Light Nuclei", World Scientific Pub Co Pte Lt, Fission and Properties of Neutron-Rich Nuclei, Vol Proceedings of the Fifth International Conference on ICFN5, pp 29-38, Sanibel Island, Florida, U.S.A., 2013, doi:10.1142/9789814525435_0003

T. Dytrych, J. P. Draayer, K. D. Launey, P. Maris, J. P. Vary, and D. Langr: "Utilizing Symmetry Coupling Schemes in Ab Initio Nuclear Structure Calculations", Pacific Nat. U., Proceedings, International Conference on Nuclear Theory in the Supercomputing Era (NTSE-2013), pp 62, Ames, Iowa, U.S.A., 2013

T. Dytrych, K. D. Launey, J. P. Draayer, P. Maris, J. P. Vary, E. Saule, U. Catalyurek, M. Sosonkina, D. Langr, and M. A. Caprio: "Collective Modes in Light Nuclei from First Principles", Phys. Rev. Lett., American Physical Society (APS), Vol 111, Num 25, 2013, doi:10.1103/physrevlett.111.252501

JaeHyuk Kwack, and Arif Masud: "A Stabilized Mixed Finite Element Method for Shear-Rate Dependent Non-Newtonian Fluids: 3D Benchmark Problems and Application to Blood Flow in Bifurcating Arteries", Computational Mechanics, Springer Science + Business Media, Vol 53, Num 4, pp 751--776, 2013, doi:10.1007/s00466-013-0928-6

Junshik Um, and Greg M. McFarquhar: "Optimal Numerical Methods for Determining the Orientation Averages of Single-Scattering Properties of Atmospheric Ice Crystals", Journal of Quantitative Spectroscopy and Radiative Transfer, Elsevier BV, Vol 127, pp 207--223, 2013, doi:10.1016/j.jqsrt.2013.05.020

N. Battaglia, H. Trac, R. Cen, and A. Loeb: "Reionization on Large Scales. I. A Parametric Model Constructed from Radiation-Hydrodynamic Simulations", ApJ, IOP Publishing, Vol 776, Num 2, pp 81, 2013, doi:10.1088/0004-637x/776/2/81

M. Moradi, and E. Tajkhorshid: "Mechanistic Picture for Conformational Transition of a Membrane Transporter at Atomic Resolution", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 110, Num 47, pp 18916--18921, 2013, doi:10.1073/pnas.1313202110

Soohaeng Yoo Willow, Matthew R. Hermes, Kwang S. Kim, and So Hirata: "Convergence Acceleration of Parallel Monte Carlo Second-Order Many-Body Perturbation Calculations Using Redundant Walkers", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 9, Num 10, pp 4396--4402, 2013, doi:10.1021/ct400557z

Zheng, Gengbin and Kale, Laxmikant: "The Charm++ Programming Model", CRC Press, Parallel Science and Engineering Applications, pp 1-16, 2013, doi:10.1201/b16251-2

Matthieu Dorier, Robert Sisneros, Tom Peterka, Gabriel Antoniu, and Dave Semeraro: "Damaris/Viz: A Nonintrusive, Adaptable and User-Friendly in Situ Visualization Framework", IEEE, 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), pp 67-75, 2013, doi:10.1109/ldav.2013.6675160

K. Chadalavada, R. Sisneros: "Analysis of the Blue Waters File System Architecture for Application I/O Performance", presented at CUG 2013, Napa Valley, California, U.S.A., 2013

Peter Johnsen, Mark Straka, Melvyn Shapiro, Alan Norton, and Thomas Galarneau: "Petascale WRF Simulation of Hurricane Sandy Deployment of NCSA's Cray XE6 Blue Waters", ACM Press, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13, pp 1-7, 2013, doi:10.1145/2503210.2503231

Ana Gainaru, Franck Cappello, Marc Snir, and William Kramer: "Failure Prediction for HPC Systems and Applications", The International Journal of High Performance Computing Applications, SAGE Publications, Vol 27, Num 3, pp 273--282, 2013, doi:10.1177/1094342013488258

A. Bazavov, C. Bernard, C. DeTar, J. Foley, S. Gottlieb, U. M. Heller, J. E. Hetrick, J. Laiho, L. Levkova, J. Osborn, R. Sugar, D. Toussaint, R. S. Van de Water, and R. Zhou: "Update on the 2+1+1 Flavor QCD Equation of State with HISQ", Proceedings of Science, Proceedings of 31st International Symposium on Lattice Field Theory LATTICE 2013, Mainz, Germany, 2013

A. Bazavov, C. Bernard, C. Bouchard, C. DeTar, D. Du, A.X. El-Khadra, J. Foley, E.D. Freeland, E. Gámiz, S. Gottlieb, U.M. Heller, J. Kim, J. Komijani, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, D. Mohler, E.T. Neil, M.B. Oktay, S. Qiu, J.N. Si: "The Ds, D+, Bs and B decay constants from 2+1 flavor lattice QCD", Proceedings of Science, Proceedings of 31st International Symposium on Lattice Field Theory, Vol LATTICE 2013, pp 394, Mainz, Germany, 2013

A. Bazavov, C. Bernard, N. Brown, C. DeTar, J. Foley, Steven Gottlieb, U. M. Heller, J. E. Hetrick, J. Laiho, L. Levkova, M. Oktay, R. L. Sugar, D. Toussaint, R. S. Van de Water, R. Zhou: "Symanzik Flow on HISQ Ensembles", Proceedings of Science, Proceedings of 31st International Symposium on Lattice Field Theory, Vol LATTICE 2013, pp 269, Mainz, Germany, 2013

Ian Hinder and Alessandra Buonanno and Michael Boyle and Zachariah B Etienne and James Healy and Nathan KJohnson-McDaniel and Alessandro Nagar and Hiroyuki Nakano and Yi Pan and Harald P Pfeiffer and Michael Pürrer and ChristianReisswig and Mark A Scheel and Erik Schnetter and Ulrich Sperhake and Bela Szilágyi and Wolfgang Tichy and BarryWardell and Anıl Zenginoğlu and Daniela Alic and Sebastiano Bernuzzi and Tanja Bode and Bernd Brügmann and Luisa TBuchman and Manuela Campanelli and Tony Chu and Thibault Damour and Jason D Grigsby and Mark Hannam and Roland Haas and Daniel AHemberger and Sascha Husa and Lawrence E Kidder and Pablo Laguna and Lionel London and Geoffrey Lovelace and Carlos OLousto and Pedro Marronetti and Richard A Matzner and Philipp Mösta and Abdul Mroué and Doreen Müller and Bruno CMundim and Andrea Nerozzi and Vasileios Paschalidis and Denis Pollney and George Reifenberger and LucianoRezzolla and Stuart L Shapiro and Deirdre Shoemaker and Andrea Taracchini and Nicholas W Taylor and Saul ATeukolsky and Marcus Thierfelder and Helvi Witek and Yosef Zlochower: "Error-Analysis and Comparison to Analytical Models of Numerical Waveforms Produced by the NRAR Collaboration", Classical and Quantum Gravity, IOP Publishing, Vol 31, Num 2, pp 025012, 2013, doi:10.1088/0264-9381/31/2/025012

A. Bazavov, C. Bernard, C. Bouchard, C. DeTar, D. Du, A.X. El-Khadra, J. Foley, E.D. Freeland, E. Gamiz, Steven Gottlieb, U.M. Heller, J. Kim, J. Komijani, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussai: "Charmed and Strange Pseudoscalar Meson Decay Constants from HISQ Simulations", Proceedings of Science, Proceedings, 31st International Symposium on Lattice Field Theory (Lattice 2013), pp 405, Mainz, Germany, 2013

H. Zheng, and L. K. Wagner: "Ab initio Study of Metal-Insulator Transition in VO2", presented at the American Physical Society March Meeting 2013, American Physical Society, Vol 58, Num 1, Baltimore, Maryland, U.S.A., 2013

Celso L. Mendes, Brett Bode, Gregory H. Bauer, Joseph R. Muggli, Cristina Beldica and William T. Kramer: "Blue Waters Acceptance: Challenges and Accomplishments", presented at CUG 2013, Napa, California, U.S.A., 2013

Ji-hoon Kim and Tom Abel and Oscar Agertz and Greg L. Bryan and Daniel Ceverino and Charlotte Christensen and Charlie Conroy and Avishai Dekel and Nickolay Y. Gnedin and Nathan J. Goldbaum and Javiera Guedes and Oliver Hahn and Alexander Hobbs and Philip F. Hopkins and Cameron B. Hummels and Francesca Iannuzzi and Dusan Keres and Anatoly Klypin and Andrey V. Kravtsov and Mark R. Krumholz and Michael Kuhlen and Samuel N. Leitner and Piero Madau and Lucio Mayer and Christopher E. Moody and Kentaro Nagamine and Michael L. Norman and Jose Onorbe and Brian W. O'Shea and Annalisa Pillepich and Joel R. Primack and Thomas Quinn and Justin I. Read and Brant E. Robertson and Miguel Rocha and Douglas H. Rudd and Sijing Shen and Britton D. Smith and Alexander S. Szalay and Romain Teyssier and Robert Thompson and Keita Todoroki and Matthew J. Turk and James W. Wadsley and John H. Wise and and Adi Zolotov: "The AGORA High-Resolution Galaxy Simulations Comparison Project", ApJS, IOP Publishing, Vol 210, Num 1, pp 14, 2013, doi:10.1088/0067-0049/210/1/14

Zheqiang Shi, and Steven M. Day: "Rupture Dynamics and Ground Motion from 3-D Rough-Fault Simulations", J. Geophys. Res. Solid Earth, Wiley-Blackwell, Vol 118, Num 3, pp 1122--1141, 2013, doi:10.1002/jgrb.50094

Parijat Sengupta, Tillmann Kubis, Yaohua Tan, Michael Povolotskyi, and Gerhard Klimeck: "Design Principles for HgTe Based Topological Insulator Devices", J. Appl. Phys., AIP Publishing, Vol 114, Num 4, pp 043702, 2013, doi:10.1063/1.4813877

2014

Constantin Schoeler, Klara H. Malinowska, Rafael C. Bernardi, Lukas F. Milles, Markus A. Jobst, Ellis Durner, Wolfgang Ott, Daniel B. Fried, Edward A. Bayer, Klaus Schulten, Hermann E. Gaub, and Michael A. Nash: "Ultrastable Cellulosome-Adhesion Complex Tightens Under Load", Nature Communications, Springer Nature, Vol 5, pp 5635, 2014, doi:10.1038/ncomms6635

T. Dytrych, K. D. Launey, and J. P. Draayer: "Symmetry-Adapted No-Core Shell Model", McGraw-Hill Yearbook of Science & Technology, McGraw-Hill Education, 2014, doi:10.1036/1097-8542.YB140314

M. Litos, E. Adli, W. An, C. I. Clarke, C. E. Clayton, S. Corde, J. P. Delahaye, R. J. England, A. S. Fisher, J. Frederico, S. Gessner, S. Z. Green, M. J. Hogan, C. Joshi, W. Lu, K. A. Marsh, W. B. Mori, P. Muggli, N. Vafaei-Najafabadi, D. Walz, G. White: "High-Efficiency Acceleration of an Electron Beam in a Plasma Wakefield Accelerator", Nature, Nature Publishing Group, Vol 515, Num 7525, pp 92--95, 2014, doi:10.1038/nature13882

M. Tzoufras, F. S. Tsung, W. B. Mori, and A. A. Sahai: "Improving the Self-Guiding of an Ultraintense Laser by Tailoring Its Longitudinal Profile", Phys. Rev. Lett., American Physical Society (APS), Vol 113, Num 24, 2014, doi:10.1103/physrevlett.113.245001

Christina Bergonzo, Niel M. Henriksen, Daniel R. Roe, Jason M. Swails, Adrian E. Roitberg, and Thomas E. Cheatham: "Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 10, Num 1, pp 492--499, 2014, doi:10.1021/ct400862k

Daniel R. Roe, Christina Bergonzo, and Thomas E. Cheatham: "Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics With Hamiltonian Replica Exchange Methods", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 118, Num 13, pp 3543--3552, 2014, doi:10.1021/jp4125099

Falk Herwig, Paul R. Woodward, Pei-Hung Lin, Mike Knox, and Chris Fryer: "Global Non-spherical Oscillations in Three-dimensional 4π Simulations of the H-ingestion Flash", Astrophysical Journal Letters, IOP Publishing, Vol 792, Num 1, pp L3, 2014, doi:10.1088/2041-8205/792/1/l3

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, Proceedings of the National Academy of Sciences, Vol 111, Num 22, pp 7914--7919, 2014, doi:10.1073/pnas.1407300111

Renyue Cen: "Evolution of Cold Streams and Emergence of the Hubble Sequence", ApJ, IOP Publishing, Vol 789, Num 1, pp L21, 2014, doi:10.1088/2041-8205/789/1/l21

Renyue Cen: "Frequent Spin Reorientation of Galaxies Due to Local Interactions", ApJ, IOP Publishing, Vol 785, Num 1, pp L15, 2014, doi:10.1088/2041-8205/785/1/l15

Renyue Cen: "On the Origin of the Hubble Sequence: I. Insights on Galaxy Color Migration from Cosmological Simulations", ApJ, IOP Publishing, Vol 781, Num 1, pp 38, 2014, doi:10.1088/0004-637x/781/1/38

Renyue Cen: "Temporal Self-Organization in Galaxy Formation", ApJ, IOP Publishing, Vol 785, Num 2, pp L21, 2014, doi:10.1088/2041-8205/785/2/l21

Renyue Cen, and Taysun Kimm: "Infrared Properties of Z=7 Galaxies from Cosmological Simulations", ApJ, IOP Publishing, Vol 782, Num 1, pp 32, 2014, doi:10.1088/0004-637x/782/1/32

Stephanie Tonnesen, and Renyue Cen: "On the Reversal of SFR-Density Relation at Z=1: Insights from Simulations", ApJ, IOP Publishing, Vol 788, Num 2, pp 133, 2014, doi:10.1088/0004-637x/788/2/133

Taysun Kimm, and Renyue Cen: "Escape Fraction of Ionizing Photons During Reionization: Effects Due to Supernova Feedback and Runaway OB Stars", ApJ, IOP Publishing, Vol 788, Num 2, pp 121, 2014, doi:10.1088/0004-637x/788/2/121

Nakul Jindal, Victor Lotrich, Erik Deumens, and Beverly A. Sanders: "Exploiting GPUs with the Super Instruction Architecture", Int J Parallel Prog, Springer Science + Business Media, Vol 44, Num 2, pp 309--324, 2014, doi:10.1007/s10766-014-0319-4

Lukasz Wesolowski, Ramprasad Venkataraman, Abhishek Gupta, Jae-Seung Yeom, Keith Bisset, Yanhua Sun, Pritish Jetley, Thomas R. Quinn, and Laxmikant V. Kale: "TRAM: Optimizing Fine-Grained Communication with Topological Routing and Aggregation of Messages", Institute of Electrical & Electronics Engineers (IEEE), 2014 43rd International Conference on Parallel Processing, Minneapolis, MN, 2014, doi:10.1109/icpp.2014.30

D. Buaria, and P. K. Yeung: "Challenges in Particle Tracking in Turbulence on a Massive Scale", Association for Computing Machinery (ACM), Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE '14, Atlanta, Georgia, U.S.A., 2014, doi:10.1145/2616498.2616526

K. P. Iyer, and P. K. Yeung: "Structure Functions and Applicability of Yaglom's Relation in Passive-Scalar Turbulent Mixing at Low Schmidt Numbers with Uniform Mean Gradient", Physics of Fluids, AIP Publishing, Vol 26, Num 8, pp 085107, 2014, doi:10.1063/1.4892581

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

P.K Yeung, X. M. Zhai, and K. R. Sreenivasan: "Turbulence at High Resolution: Intense Events in Dissipation, Enstrophy and Acceleration", presented at the 67th Annual Meeting of the APS Division of Fluid Dynamics, American Physical Society, Vol 59, Num 20, San Francisco, California, U.S.A., 2014

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., Wiley-Blackwell, Vol 41, Num 8, pp 2769--2777, 2014, doi:10.1002/2014gl059411

Doriam Restrepo, and Jacobo Bielak: "Virtual Topography: A Fictitious Domain Approach for Analyzing Free-Surface Irregularities in Large-Scale Earthquake Ground Motion Simulation", International Journal for Numerical Methods in Engineering, Wiley-Blackwell, Vol 100, Num 7, pp 504--533, 2014, doi:10.1002/nme.4756

En-Jui Lee, Po Chen, Thomas H. Jordan, Phillip B. Maechling, Marine A. M. Denolle, and Gregory C. Beroza: "Full-3-D Tomography for Crustal Structure in Southern California Based on the Scattering-Integral and the Adjoint-Wavefield Methods", J. Geophys. Res. Solid Earth, Wiley-Blackwell, Vol 119, Num 8, pp 6421--6451, 2014, doi:10.1002/2014jb011346

F. Wang, and T. H. Jordan: "Comparison of Probabilistic Seismic-Hazard Models Using Averaging-Based Factorization", Bulletin of the Seismological Society of America, Seismological Society of America (SSA), Vol 104, Num 3, pp 1230--1257, 2014, doi:10.1785/0120130263

Heming Xu, Yifeng Cui, James H. Dieterich, Keith Richards-Dinger, Efecan Poyraz, and Dong Ju Choi: "Aftershock Sequence Simulations Using Synthetic Earthquakes and Rate-State Seismicity Formulation", Earthquake Science, Springer Science + Business Media, Vol 27, Num 4, pp 401--410, 2014, doi:10.1007/s11589-014-0087-7

M. Böse, R. W. Graves, D. Gill, S. Callaghan, and P. J. Maechling: "CyberShake-Derived Ground-Motion Prediction Models for the Los Angeles Region with Application to Earthquake Early Warning", Geophysical Journal International, Oxford University Press (OUP), Vol 198, Num 3, pp 1438--1457, 2014, doi:10.1093/gji/ggu198

Philipp Mösta, Sherwood Richers, Christian D. Ott, Roland Haas, Anthony L. Piro, Kristen Boydstun, Ernazar Abdikamalov, Christian Reisswig, and Erik Schnetter: "Magnetorotational Core-Collapse Supernovae in Three Dimensions", ApJ, IOP Publishing, Vol 785, Num 2, pp L29, 2014, doi:10.1088/2041-8205/785/2/l29

Bruno C. Mundim, Hiroyuki Nakano, Nicolás Yunes, Manuela Campanelli, Scott C. Noble, and Yosef Zlochower: "Approximate Black Hole Binary Spacetime via Asymptotic Matching", Physical Review D, American Physical Society (APS), Vol 89, Num 8, pp 084008, 2014, doi:10.1103/physrevd.89.084008

Carlos O. Lousto, and Yosef Zlochower: "Black Hole Binary Remnant Mass and Spin: A New Phenomenological Formula", Physical Review D, American Physical Society (APS), Vol 89, Num 10, 2014, doi:10.1103/physrevd.89.104052

Carlos O. Lousto, and Yosef Zlochower: "Where Angular Momentum Goes in a Precessing Black-Hole Binary", Physical Review D, American Physical Society (APS), Vol 89, Num 2, 2014, doi:10.1103/physrevd.89.021501

John. M. A. Grime, and Gregory A. Voth: "Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 10, Num 1, pp 423--431, 2014, doi:10.1021/ct400727q

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

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., American Chemical Society (ACS), Vol 136, Num 40, pp 13959--13962, 2014, doi:10.1021/ja5032776

Jason M. Swails, Darrin M. York, and Adrian E. Roitberg: "Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 10, Num 3, pp 1341--1352, 2014, doi:10.1021/ct401042b

Julien C Thibault, Daniel R Roe, Julio C Facelli, and Thomas E Cheatham: "Data Model, Dictionaries, and Desiderata for Biomolecular Simulation Data Indexing and Sharing", Journal of Cheminformatics, Springer Nature, Vol 6, Num 1, pp 4, 2014, doi:10.1186/1758-2946-6-4

Julien C. Thibault, Thomas E. Cheatham, and Julio C. Facelli: "iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings", Journal of Chemical Information and Modeling, American Chemical Society (ACS), Vol 54, Num 6, pp 1810--1819, 2014, doi:10.1021/ci500173w

Natali V. Di Russo, Marcelo A. Marti, and Adrian E. Roitberg: "Underlying Thermodynamics of pH-Dependent Allostery", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 118, Num 45, pp 12818--12826, 2014, doi:10.1021/jp507971v

Niel M. Henriksen, Hamed S. Hayatshahi, Darrell R. Davis, and Thomas E. Cheatham: "Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations", Journal of Chemical Information and Modeling, American Chemical Society (ACS), Vol 54, Num 6, pp 1758--1772, 2014, doi:10.1021/ci500132c

T. Dwight McGee, Jesse Edwards, and Adrian E. Roitberg: "pH-REMD Simulations Indicate That the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Monoprotonated State", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 118, Num 44, pp 12577--12585, 2014, doi:10.1021/jp504011c

Viktor K. Decyk, and Tajendra V. Singh: "Particle-in-Cell Algorithms for Emerging Computer Architectures", Computer Physics Communications, Elsevier BV, Vol 185, Num 3, pp 708--719, 2014, doi:10.1016/j.cpc.2013.10.013

Lee-Ping Wang, Alexey Titov, Robert McGibbon, Fang Liu, Vijay S. Pande, and Todd J. Martínez: "Discovering Chemistry with an Ab Initio Nanoreactor", Nature Chemistry, Nature Publishing Group, Vol 6, Num 12, pp 1044--1048, 2014, doi:10.1038/nchem.2099

Ganesh Hegde, Michael Povolotskyi, Tillmann Kubis, James Charles, and Gerhard Klimeck: "An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. II. Application—Effect of quantum confinement and homogeneous strain on Cu conductance", J. Appl. Phys., AIP Publishing, Vol 115, Num 12, pp 123704, 2014, doi:10.1063/1.4868979

Ganesh Hegde, Michael Povolotskyi, Tillmann Kubis, Timothy Boykin, and Gerhard Klimeck: "An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation", J. Appl. Phys., AIP Publishing, Vol 115, Num 12, pp 123703, 2014, doi:10.1063/1.4868977

Pengyu Long, Michael Povolotskyi, Bozidar Novakovic, Tillmann Kubis, Gerhard Klimeck, and Mark J. W. Rodwell: "Design and Simulation of Two-Dimensional Superlattice Steep Transistors", IEEE Electron Device Lett., Institute of Electrical & Electronics Engineers (IEEE), Vol 35, Num 12, pp 1212--1214, 2014, doi:10.1109/led.2014.2364593

A. Bazavov, C. Bernard, C. M. Bouchard, C. DeTar, Daping Du, A. X. El-Khadra, J. Foley, E. D. Freeland, E. Gámiz, Steven Gottlieb, U. M. Heller, Jongjeong Kim, A. S. Kronfeld, J. Laiho, L. Levkova, P. B. Mackenzie, E. T. Neil, M. B. Oktay, Si-Wei Qiu, J.: "Determination of |Vus| from a Lattice QCD Calculation of the K→πℓν Semileptonic Form Factor with Physical Quark Masses", Phys. Rev. Lett., American Physical Society (APS), Vol 112, Num 11, pp 112001, 2014, doi:10.1103/physrevlett.112.112001

A. Bazavov, C. Bernard, J. Komijani, C. M. Bouchard, C. DeTar, J. Foley, L. Levkova, D. Du, J. Laiho, A. X. El-Khadra, E. D. Freeland, E. Gámiz, Steven Gottlieb, U. M. Heller, J. Kim, D. Toussaint, A. S. Kronfeld, P. B. Mackenzie, J. N. Simone, R. S. Van: "Charmed and Light Pseudoscalar Meson Decay Constants from Four-Flavor Lattice QCD with Physical Light Quarks", Physical Review D, American Physical Society (APS), Vol 90, Num 7, pp 074509, 2014, doi:10.1103/physrevd.90.074509

Daniel Mohler, Carleton DeTar, Andreas S. Kronfeld, Song-haeng Lee, Ludmila Levkova, J. N. Simone: "Low Lying Charmonium States at the Physical Point", Proceedings of Science, Proceedings, 32nd International Symposium on Lattice Field Theory (Lattice 2014), pp 085, Brookhaven, New York, U.S.A., 2014

F.T. Winter, M.A. Clark, R.G. Edwards, and B. Joo: "A Framework for Lattice QCD Calculations on GPUs", Institute of Electrical & Electronics Engineers (IEEE), 2014 IEEE 28th International Parallel and Distributed Processing Symposium, Phoenix, AZ, 2014, doi:10.1109/ipdps.2014.112

Jozef J. Dudek, Robert G. Edwards, Christopher E. Thomas, and David J. Wilson: "Resonances in Coupled πK-ηK Scattering From Quantum Chromodynamics", Phys. Rev. Lett., American Physical Society (APS), Vol 113, Num 18, 2014, doi:10.1103/physrevlett.113.182001

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., American Physical Society (APS), Vol 113, Num 15, 2014, doi:10.1103/physrevlett.113.155005

H. Karimabadi, V. Roytershteyn, H. X. Vu, Y. A. Omelchenko, J. Scudder, W. Daughton, A. Dimmock, K. Nykyri, M. Wan, D. Sibeck, M. Tatineni, A. Majumdar, B. Loring, and B. Geveci: "The Link Between Shocks, Turbulence, and Magnetic Reconnection in Collisionless Plasmas", Physics of Plasmas, AIP Publishing, Vol 21, Num 6, pp 062308, 2014, doi:10.1063/1.4882875

J. Jara-Almonte, W. Daughton, and H. Ji: "Debye Scale Turbulence Within the Electron Diffusion Layer During Magnetic Reconnection", Physics of Plasmas, AIP Publishing, Vol 21, Num 3, pp 032114, 2014, doi:10.1063/1.4867868

W. H. Matthaeus, S. Oughton, K. T. Osman, S. Servidio, M. Wan, S. P. Gary, M. A. Shay, F. Valentini, V. Roytershteyn, H. Karimabadi, and S. C. Chapman: "Nonlinear and Linear Timescales Near Kinetic Scales in Solar Wind Turbulence", ApJ, IOP Publishing, Vol 790, Num 2, pp 155, 2014, doi:10.1088/0004-637x/790/2/155

Yi-Hsin Liu, Joachim Birn, William Daughton, Michael Hesse, and Karl Schindler: "Onset of Reconnection in the Near Magnetotail: PIC Simulations", J. Geophys. Res. Space Physics, Wiley-Blackwell, Vol 119, Num 12, pp 9773--9789, 2014, doi:10.1002/2014ja020492

C. M. Malone, A. Nonaka, S. E. Woosley, A. S. Almgren, J. B. Bell, S. Dong, and M. Zingale: "The Deflagration Stage of Chandrasekhar Mass Models for Type Ia Supernovae. I. Early Evolution", ApJ, IOP Publishing, Vol 782, Num 1, pp 11, 2014, doi:10.1088/0004-637x/782/1/11

Hao Xu, Kyungjin Ahn, John H. Wise, Michael L. Norman, and Brian W. O'Shea: "Heating the Intergalactic Medium by X-Rays from Population III Binaries in High-Redshift Galaxies", ApJ, IOP Publishing, Vol 791, Num 2, pp 110, 2014, doi:10.1088/0004-637x/791/2/110

Pengfei Chen, John H. Wise, Michael L. Norman, Hao Xu, and Brian W. O'Shea: "Scaling Relations for Galaxies Prior to Reionization", ApJ, IOP Publishing, Vol 795, Num 2, pp 144, 2014, doi:10.1088/0004-637x/795/2/144

Danielle E. Chandler, Johan Strümpfer, Melih Sener, Simon Scheuring, and Klaus Schulten: "Light Harvesting by Lamellar Chromatophores in Rhodospirillum Photometricum", Biophysical Journal, Elsevier BV, Vol 106, Num 11, pp 2503--2510, 2014, doi:10.1016/j.bpj.2014.04.030

James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten: "Petascale Tcl with NAMD, VMD, and Swift/T", Institute of Electrical & Electronics Engineers (IEEE), 2014 First Workshop for High Performance Technical Computing in Dynamic Languages, 2014, doi:10.1109/hptcdl.2014.7

James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laxmikant V. Kale: "Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation", Institute of Electrical & Electronics Engineers (IEEE), SC14: International Conference for High Performance Computing, Networking, Storage and Analysis, New Orleans, LA, 2014, doi:10.1109/sc.2014.12

John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten: "GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting", Faraday Discuss., Royal Society of Chemistry (RSC), Vol 169, pp 265--283, 2014, doi:10.1039/c4fd00005f

Mark D. Klein and John E. Stone: "Unlocking the Full Potential of the Cray XK7 Accelerator", presented at CUG 2014, Lugano, Switzerland, 2014

Michaël L. Cartron, John D. Olsen, Melih Sener, Philip J. Jackson, Amanda A. Brindley, Pu Qian, Mark J. Dickman, Graham J. Leggett, Klaus Schulten, and C. Neil Hunter: "Integration of Energy and Electron Transfer Processes in the Photosynthetic Membrane of Rhodobacter Sphaeroides", Biochimica et Biophysica Acta (BBA) - Bioenergetics, Elsevier BV, Vol 1837, Num 10, pp 1769--1780, 2014, doi:10.1016/j.bbabio.2014.02.003

Milana Fraiberg, Oshri Afanzar, C. Keith Cassidy, Alexandra Gabashvili, Klaus Schulten, Yishai Levin, and Michael Eisenbach: "CheY's Acetylation Sites Responsible for Generating Clockwise Flagellar Rotation in E Scherichia Coli", Molecular Microbiology, Wiley-Blackwell, Vol 95, Num 2, pp 231--244, 2014, doi:10.1111/mmi.12858

Ramya Gamini, Wei Han, John E. Stone, and Klaus Schulten: "Assembly of Nsp1 Nucleoporins Provides Insight Into Nuclear Pore Complex Gating", PLoS Comput Biol, Public Library of Science (PLoS), Vol 10, Num 3, pp e1003488, 2014, doi:10.1371/journal.pcbi.1003488

Shanmugapriya Sothiselvam, Bo Liu, Wei Han, Haripriya Ramu, Dorota Klepacki, Gemma Catherine Atkinson, Age Brauer, Maido Remm, Tanel Tenson, Klaus Schulten, Nora Vázquez-Laslop, and Alexander S. Mankin: "Macrolide Antibiotics Allosterically Predispose the Ribosome for Translation Arrest", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 111, Num 27, pp 9804--9809, 2014, doi:10.1073/pnas.1403586111

Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, and Benoît Roux: "Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD", Computer Physics Communications, Elsevier BV, Vol 185, Num 3, pp 908--916, 2014, doi:10.1016/j.cpc.2013.12.014

Zhe Wu, and Klaus Schulten: "Synaptotagmin's Role in Neurotransmitter Release Likely Involves Ca2+-induced Conformational Transition", Biophysical Journal, Elsevier BV, Vol 107, Num 5, pp 1156--1166, 2014, doi:10.1016/j.bpj.2014.07.041

Lukasz Wesolowski, Ramprasad Venkataraman, Abhishek Gupta, Jae-Seung Yeom, Keith Bisset, Yanhua Sun, Pritish Jetley, Thomas R. Quinn, and Laxmikant V. Kale: "TRAM: Optimizing Fine-Grained Communication with Topological Routing and Aggregation of Messages", Institute of Electrical & Electronics Engineers (IEEE), 2014 43rd International Conference on Parallel Processing, pp 211-220, Minneapolis, Minnesota, U.S.A., 2014, doi:10.1109/icpp.2014.30

Sarah Loebman, Jennifer Ortiz, Lee Lee Choo, Laurel Orr, Lauren Anderson, Daniel Halperin, Magdalena Balazinska, Thomas Quinn, and Fabio Governato: "Big-Data Management Use-Case", Association for Computing Machinery (ACM), Proceedings of Workshop on Data analytics in the Cloud - DanaC'14, pp 9:1-9:4, Snowbird, Utah, U.S.A., 2014, doi:10.1145/2627770.2627774

E. J. Zirnstein, J. Heerikhuisen, G. P. Zank, N. V. Pogorelov, D. J. McComas, and M. I. Desai: "Charge-Exchange Coupling Between Pickup Ions Across the Heliopause and Its Effect on Energetic Neutral Hydrogen Flux", ApJ, IOP Publishing, Vol 783, Num 2, pp 129, 2014, doi:10.1088/0004-637x/783/2/129

J. Heerikhuisen, E. J. Zirnstein, H. O. Funsten, N. V. Pogorelov, and G. P. Zank: "The Effect of New Interstellar Medium Parameters on the Heliosphere and Energetic Neutral Atoms from the Interstellar Boundary", ApJ, IOP Publishing, Vol 784, Num 1, pp 73, 2014, doi:10.1088/0004-637x/784/1/73

Ming Zhang, Pingbing Zuo, and Nikolai Pogorelov: "Heliospheric Influence on the Anisotropy of Tev Cosmic Rays", ApJ, IOP Publishing, Vol 790, Num 1, pp 5, 2014, doi:10.1088/0004-637x/790/1/5

N. V. Pogorelov, S. N. Borovikov, J. Heerikhuisen, T. K. Kim, G. P. Zank: "Time-dependent Processes in the Sheath Between the Heliospheric Termination Shock and the Heliopause", Astronomical Society of the Pacific, 8th International Conference of Numerical Modeling of Space Plasma Flows (ASTRONUM 2013), Vol 488, pp 167, Biarritz, France, 2014

S. Hirata: "Ab Initio Solid-State Chemistry", presented at the American Conference on Theoretical Chemistry, Telluride, Colorado, U.S.A., 2014

S. Hirata: "A Few Potentially Controversial Issues in Many-Body Theory", presented at the Low-scaling and Unconventional Electronic Structure Techniques Conference (LUEST), Telluride, Colorado, U.S.A., 2014

C Maffeo, J Yoo, J Comer, D B Wells, B Luan, and A Aksimentiev: "Close Encounters with DNA", Journal of Physics: Condensed Matter, IOP Publishing, Vol 26, Num 41, pp 413101, 2014, doi:10.1088/0953-8984/26/41/413101

Spencer Carson, James Wilson, Aleksei Aksimentiev, and Meni Wanunu: "Smooth DNA Transport Through a Narrowed Pore Geometry", Biophysical Journal, Elsevier BV, Vol 107, Num 10, pp 2381--2393, 2014, doi:10.1016/j.bpj.2014.10.017

Xu, X. L. and Hua, J. F. and Li, F. and Zhang, C. J. and Yan, L. X. and Du, Y. C. and Huang, W. H. and Chen, H. B. and Tang, C. X. and Lu, W. and Yu, P. and An, W. and Joshi, C. and Mori, W. B.: "Phase-Space Dynamics of Ionization Injection in Plasma-Based Accelerators", Phys. Rev. Lett., American Physical Society, Vol 112, Num 3, pp 035003, 2014, doi:10.1103/PhysRevLett.112.035003

Nikolai Pogorelov, Sergey Borovikov, Jacob Heerikhuisen, Tae Kim, Igor Kryukov, and Gary Zank: "MS-FLUKSS and Its Application to Modeling Flows of Partially Ionized Plasma in the Heliosphere", Association for Computing Machinery (ACM), Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE '14, Atlanta, GA, 2014, doi:10.1145/2616498.2616499

S. N. Borovikov, and N. V. Pogorelov: "Voyager 1 Near the Heliopause", ApJ, IOP Publishing, Vol 783, Num 1, pp L16, 2014, doi:10.1088/2041-8205/783/1/l16

T. K. Kim, N. V. Pogorelov, S. N. Borovikov, B. V. Jackson, H.-S. Yu, and M. Tokumaru: "MHD Heliosphere with Boundary Conditions from a Tomographic Reconstruction Using Interplanetary Scintillation Data", J. Geophys. Res. Space Physics, Wiley-Blackwell, Vol 119, Num 10, pp 7981--7997, 2014, doi:10.1002/2013ja019755

Kaori Nagashima, Björn Löptien,, Laurent Gizon, Aaron C. Birch, Robert Cameron, Sebastien Couvidat, Sanja Danilovic, Bernhard Fleck, and Robert Stein: "Interpreting the Helioseismic and Magnetic Imager (HMI) Multi-Height Velocity Measurements", Solar Physics, Springer Science + Business Media, Vol 289, Num 9, pp 3457--3481, 2014, doi:10.1007/s11207-014-0543-5

Matthew Ferringer, Marc DiPrinzio, Timothy Thompson, Kyle Hanifen, and Patrick Reed: "A Framework for the Discovery of Passive-Control, Minimum Energy Satellite Constellations", American Institute of Aeronautics and Astronautics (AIAA), 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, Wiley-Blackwell, Vol 50, Num 10, pp 8367--8373, 2014, doi:10.1002/2014wr015976

G. K. Tobin, M. C. Ferriss, K. D. Launey, T. Dytrych, J. P. Draayer, A. C. Dreyfuss, and C. Bahri: "Symplectic No-Core Shell-Model Approach to Intermediate-Mass Nuclei", Phys. Rev. C, American Physical Society (APS), Vol 89, Num 3, 2014, doi:10.1103/physrevc.89.034312

K D Launey, A C Dreyfuss, J P Draayer, T Dytrych, and R Baker: "Emergence of Cluster Structures and Collectivity Within a No-Core Shell-Model Framework", J. Phys.: Conf. Ser., IOP Publishing, Vol 569, pp 012061, 2014, doi:10.1088/1742-6596/569/1/012061

K.D. Launey, S. Sarbadhicary, T. Dytrych, and J.P. Draayer: "Program in C for Studying Characteristic Properties of Two-Body Interactions in the Framework of Spectral Distribution Theory", Computer Physics Communications, Elsevier BV, Vol 185, Num 1, pp 254--267, 2014, doi:10.1016/j.cpc.2013.08.007

Scott J. Krieder, Justin M. Wozniak, Timothy Armstrong, Michael Wilde, Daniel S. Katz, Benjamin Grimmer, Ian T. Foster, and Ioan Raicu: "Design and Evaluation of the Gemtc Framework for GPU-Enabled Many-Task Computing", Association for Computing Machinery (ACM), Proceedings of the 23rd international symposium on High-performance parallel and distributed computing - HPDC '14, Vancouver, Canada, 2014, doi:10.1145/2600212.2600228

Galen Arnold, Manisha Gajbe, Seid Koric, and John Urbanic: "XSEDE OpenACC Workshop Enables Blue Waters Researchers to Accelerate Key Algorithms", Association for Computing Machinery (ACM), Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE '14, pp 28:1-28:6, Atlanta, Georgia, U.S.A., 2014, doi:10.1145/2616498.2616530

Seid Koric, Qiyue Lu, and Erman Guleryuz: "Evaluation of Massively Parallel Linear Sparse Solvers on Unstructured Finite Element Meshes", Computers & Structures, Elsevier BV, Vol 141, pp 19--25, 2014, doi:10.1016/j.compstruc.2014.05.009

Wen Huang, Seid Koric, Xin Yu, K. Jimmy Hsia, and Xiuling Li: "Precision Structural Engineering of Self-Rolled-Up 3D Nanomembranes Guided by Transient Quasi-Static FEM Modeling", Nano Letters, American Chemical Society (ACS), Vol 14, Num 11, pp 6293--6297, 2014, doi:10.1021/nl5026369

Roman Gold, Vasileios Paschalidis, Milton Ruiz, Stuart L. Shapiro, Zachariah B. Etienne, and Harald P. Pfeiffer: "Accretion Disks Around Binary Black Holes of Unequal Mass: General Relativistic MHD Simulations of Postdecoupling and Merger", Physical Review D, American Physical Society (APS), Vol 90, Num 10, pp 104030, 2014, doi:10.1103/physrevd.90.104030

Roman Gold, Vasileios Paschalidis, Zachariah B. Etienne, Stuart L. Shapiro, and Harald P. Pfeiffer: "Accretion Disks Around Binary Black Holes of Unequal Mass: General Relativistic Magnetohydrodynamic Simulations Near Decoupling", Physical Review D, American Physical Society (APS), Vol 89, Num 6, pp 064060, 2014, doi:10.1103/physrevd.89.064060

Zachariah B. Etienne, John G. Baker, Vasileios Paschalidis, Bernard J. Kelly, and Stuart L. Shapiro: "Improved Moving Puncture Gauge Conditions for Compact Binary Evolutions", Physical Review D, American Physical Society (APS), Vol 90, Num 6, pp 064032, 2014, doi:10.1103/physrevd.90.064032

Maxim Belkin, Shu-Han Chao, Gino Giannetti, and Aleksei Aksimentiev: "Modeling Thermophoretic Effects in Solid-State Nanopores", J Comput Electron, Springer Science + Business Media, Vol 13, Num 4, pp 826--838, 2014, doi:10.1007/s10825-014-0594-8

Shouvik Banerjee, James Wilson, Jiwook Shim, Manish Shankla, Elise A. Corbin, Aleksei Aksimentiev, and Rashid Bashir: "Slowing DNA Transport Using Graphene-DNA Interactions", Adv. Funct. Mater., Wiley-Blackwell, Vol 25, Num 6, pp 936--946, 2014, doi:10.1002/adfm.201403719

Haihu Liu, Albert J. Valocchi, Charles Werth, Qinjun Kang, and Mart Oostrom: "Pore-Scale Simulation of Liquid CO2 Displacement of Water Using a Two-Phase Lattice Boltzmann Model", Advances in Water Resources, Elsevier BV, Vol 73, pp 144--158, 2014, doi:10.1016/j.advwatres.2014.07.010

Alexandra Jones, and Larry Di Girolamo: "A New Spectrally Integrating 3D Monte Carlo Radiative Transfer Model", presented at the American Meteorological Society 14th Conference on Atmospheric Radiation, Boston, Massachusetts, U.S.A., 2014

Andre Schleife, Erik W. Draeger, Victor M. Anisimov, Alfredo A. Correa, and Yosuke Kanai: "Quantum Dynamics Simulation of Electrons in Materials on High-Performance Computers", Comput. Sci. Eng., Institute of Electrical & Electronics Engineers (IEEE), Vol 16, Num 5, pp 54--60, 2014, doi:10.1109/mcse.2014.55

Lucas K. Wagner, and Peter Abbamonte: "Effect of Electron Correlation on the Electronic Structure and Spin-Lattice Coupling of High-Tc Cuprates: Quantum Monte Carlo Calculations", Phys. Rev. B, American Physical Society (APS), Vol 90, Num 12, 2014, doi:10.1103/physrevb.90.125129

L. Orf, R. Wilhelmson, L. Wicker, B. Lee, and C. Finley: "Genesis and Maintenance of a Long-Track EF5 Tornado Embedded within a Simulated Supercell", presented at the American Meteorological Society 27th Conference on Severe Local Storms, Madison, Wisconsin, U.S.A., 2014

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

Mahmoud Moradi, and Emad Tajkhorshid: "Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 10, Num 7, pp 2866--2880, 2014, doi:10.1021/ct5002285

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", presented at the 8th European Continuous Casting Conference (ECCC 2014), Graz, Austria, 2014

Sharon Hammes-Schiffer: "Presentation: Proton-Coupled Electron Transfer in Catalysis and Energy Conversion (Illinois)", Colloquium, Northwestern University, Evanston, IL, 2014

Jens Glaser, Pavani Medapuram, Thomas M. Beardsley, Mark W. Matsen, and David C. Morse: "Universality of Block Copolymer Melts", Phys. Rev. Lett., American Physical Society (APS), Vol 113, Num 6, 2014, doi:10.1103/physrevlett.113.068302

Mohammad Zaved Kaiser Khan, Rajeshwar Mehrotra, Ashish Sharma, and A. Sankarasubramanian: "Global Sea Surface Temperature Forecasts Using an Improved Multimodel Approach", Journal of Climate, American Meteorological Society, Vol 27, Num 10, pp 3505--3515, 2014, doi:10.1175/jcli-d-13-00486.1

C. D. Meyer, D. S. Balsara, B. Burkhart, and A. Lazarian: "Observational Diagnostics for Two-Fluid Turbulence in Molecular Clouds as Suggested by Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 439, Num 3, pp 2197--2210, 2014, doi:10.1093/mnras/stt1893

Kris Beckwith, Seth Veitzer, Stephen F. McCormick, John W. Ruge, Luke N. Olson, and Jon C. Calhoun: "Fully-Implicit Ultrascale Physics Solvers and Application to Ion Source Modelling", Institute of Electrical & Electronics Engineers (IEEE), 2014 IEEE 41st International Conference on Plasma Sciences (ICOPS) held with 2014 IEEE International Conference on High-Power Particle Beams (BEAMS), pp 1-8, Washington, D.C., U.S.A., 2014, doi:10.1109/plasma.2014.7012726

G.M. McFarquhar and J. Um: "The Impact of Natural Variations of Ice Crystal Aspect Ratios on Single-Scattering Radiative Properties", presented at the 14th Conference on Atmospheric Radiation (American Meteorological Society), Boston, Massachusetts, U.S.A., 2014

Junshik Um, and Greg M. McFarquhar: "Formation of Atmospheric Halos by Hexagonal Ice Crystals", presented at 14th Conference on Atmospheric Radiation, American Meteorological Society, Boston, Massachusetts, U.S.A., 2014

Amir Barati Farimani, Kyoungmin Min, and Narayana R. Aluru: "DNA Base Detection Using a Single-Layer MoS 2", ACS Nano, American Chemical Society (ACS), Vol 8, Num 8, pp 7914--7922, 2014, doi:10.1021/nn5029295

Dhawal Buaria, Pui-Kuen Yeung, and Brian Sawford: "Direct Numerical Simulations of the Dispersion of Molecules in Isotropic Turbulence", presented at the 19th Australasian Fluid Mechanics Conference, Melbourne, Australia, 2014

Anthony Agelastos, Benjamin Allan, Jim Brandt, Paul Cassella, Jeremy Enos, Joshi Fullop, Ann Gentile, Steve Monk, Nichamon Naksinehaboon, Jeff Ogden, Mahesh Rajan, Michael Showerman, Joel Stevenson, Narate Taerat, and Tom Tucker: "The Lightweight Distributed Metric Service: A Scalable Infrastructure for Continuous Monitoring of Large Scale Computing Systems and Applications", IEEE, SC14: International Conference for High Performance Computing, Networking, Storage and Analysis, pp 154-165, New Orleans, Louisiana, U.S.A., 2014, doi:10.1109/sc.2014.18

J Enos, G Bauer, R Brunner, S Islam, R Fiedler, M Steed, and D Jackson: "Topology-Aware Job Scheduling Strategies for Torus Networks", presented at CUG 2014, Lugano, Switzerland, 2014, doi:10.13140/2.1.2693.6001

B. D. Semeraro, Robert Sisneros, Joshi Fullop, and Gregory H. Bauer: "It Takes a Village: Monitoring the Blue Waters Supercomputer", IEEE, 2014 IEEE International Conference on Cluster Computing (CLUSTER), pp 392-399, 2014, doi:10.1109/cluster.2014.6968671

R. Sisneros, K. Chadalavada: "Toward Understanding Congestion Protection Events on Blue Waters Via Visual Analytics", presented at CUG 2014, Lugano, Switzerland, 2014

J. Fullop, R. Sisneros: "A Diagnostic Utility For Analyzing Periods Of Degraded Job Performance", presented at CUG 2014, Lugano, Switzerland, 2014

Alvaro Luiz Fazenda, Celso L. Mendes, Laxmikant V. Kale, Jairo Panetta, and Eduardo Rocha Rodrigues: "Dynamic Load Balancing in GPU-Based Systems for a MPI Program", IEEE, 2014 International Conference on High Performance Computing & Simulation (HPCS), pp 154-161, Bologna, Italy, 2014, doi:10.1109/hpcsim.2014.6903681

Andy Loftus, Alex Parga: "Clearing the Obstacles to Backup PiB-Size Filesystems", presented at CUG 2014, Lugano, Switzerland, 2014

Celso L. Mendes, Brett Bode, Gregory H. Bauer, Jeremy Enos, Cristina Beldica, and William T. Kramer: "Deploying a Large Petascale System: The Blue Waters Experience", Procedia Computer Science, Elsevier BV, Vol 29, pp 198--209, 2014, doi:10.1016/j.procs.2014.05.018

Bauer, Gregory and Mendes, Celso and Kramer, William and Fiedler, Robert: "Expanding Blue Waters with Improved Acceleration Capability", presented at CUG 2014, Lugano, Switzerland, 2014

Anisimov, Victor M. and Bauer, Gregory H. and Chadalavada, Kalyana and Olson, Ryan M. and Glenski, Joseph W. and Kramer, William T. C. and Aprà, Edoardo and Kowalski, Karol: "Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures", Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 10, Num 10, pp 4307--4316, 2014, doi:10.1021/ct500404c

Cappello, Franck and Al, Geist and Gropp, William and Kale, Sanjay and Kramer, Bill and Snir, Marc: "Toward Exascale Resilience: 2014 Update", Supercomputing Frontiers and Innovations, FSAEIHE South Ural State University (National Research University), Vol 1, Num 1, pp 5--28, 2014, doi:10.14529/jsfi140101

Catello Di Martino, Zbigniew Kalbarczyk, Ravishankar K. Iyer, Fabio Baccanico, Joseph Fullop, and William Kramer: "Lessons Learned from the Analysis of System Failures at Petascale: The Case of Blue Waters", IEEE, 2014 44th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, pp 610-621, Atlanta, Georgia, U.S.A., 2014, doi:10.1109/dsn.2014.62

Kramer, William, Butler, Michelle, Bauer, Gregory, Chadalavada, Kalyana and Mendes, Celso: "National Center for Supercomputing Applications", Chapman and Hall/CRC, High Performance Parallel I/O, pp 17-31, 2014

S. Koric, and B. G. Thomas: "Visco-plasic Multi-Physics Modeling of Steel Solidification", presented at the 20th International Symposium on Plasticity and its Current Applications, Freeport, Bahamas, 2014

Y. Cai, J. Steinbuks, J.W. Elliott, and T.W. Hertel: "The Effect of Climate and Technological Uncertainty in Crop Yields on the Optimal Path of Global Land Use", The World Bank Group, Policy Research Working Paper 7009, 2014

Taishan Zhu, and Elif Ertekin: "Phonon Transport on Two-Dimensional Graphene/boron Nitride Superlattices", Phys. Rev. B, American Physical Society (APS), Vol 90, Num 19, pp 195209, 2014, doi:10.1103/physrevb.90.195209

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, Nature Publishing Group, Vol 5, pp 5152, 2014, doi:10.1038/ncomms6152

Thomas Primer, Doug Toussaint, Aida El-Khadra, Elvira Gámiz, James Simone: "Kaon and D Meson Semileptonic Form Factors from Lattice QCD", Proceedings of Science, Proceedings, 32nd International Symposium on Lattice Field Theory (Lattice 2014), pp 374, Brookhaven, New York, U.S.A., 2014

Paul R. Woodward, Falk Herwig, and Pei-Hung Lin: "Hydrodynamic Simulations of H Entrainment at the Top of He-Shell Flash Convection", Astrophysical Journal, IOP Publishing, Vol 798, Num 1, pp 49, 2014, doi:10.1088/0004-637x/798/1/49

A. Bazavov, C. Bernard, N. Brown, C. DeTar, J. Foley, S. Gottlieb, U.M. Heller, J.E. Hetrick, J. Komijani, J. Laiho, L. Levkova, M. Oktay, R.L. Sugar, D. Toussaint, R.S. Van de Water, R. Zhou: "Gradient Flow Analysis on MILC HISQ Ensembles", Proceedings of Science, Proceedings, 32nd International Symposium on Lattice Field Theory (Lattice 2014), pp 090, Brookhaven, New York, U.S.A., 2014

Greg L. Bryan and Michael L. Norman and Brian W. O'Shea and Tom Abel and John H. Wise and Matthew J. Turk and Daniel R.Reynolds and David C. Collins and Peng Wang and Samuel W. Skillman and Britton Smith and Robert P. Harkness and JamesBordner and Ji-hoon Kim and Michael Kuhlen and Hao Xu and Nathan Goldbaum and Cameron Hummels and Alexei G.Kritsuk and Elizabeth Tasker and Stephen Skory and Christine M. Simpson and Oliver Hahn and Jeffrey S. Oishi and Geoffrey C.So and Fen Zhao and Renyue Cen and Yuan Li and The Enzo Collaboration: "Enzo: An Adaptive Mesh Refinement Code for Astrophysics", The Astrophysical Journal Supplement Series, IOP Publishing, Vol 211, Num 2, pp 19, 2014, doi:10.1088/0067-0049/211/2/19

E. Seidel, G. Allen, M. Freemon, C.F. Gammie, A.J. Kemball, R. Pennington, and D. Petravick: "Computing and Data Challenges for Multi-Messenger Astronomy", presented at the American Astronomical Society Topical Conference Series 2 Exascale Radio Astronomy 2014, Vol 46, Num 3, Monterey, California, U.S.A., 2014

Bazavov, A., C. Bernard, C. Bouchard, C. DeTar, D. Du, A.X. El-Khadra, J. Foley, E.D. Freeland, E. Gámiz, S. Gottlieb, U.M. Heller, J. Kim, J. Komijani, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint: "Charmed and Light Pseudoscalar Meson Decay Constants from HISQ Simulations", Proceedings of Science, Proceedings, 32nd International Symposium on Lattice Field Theory (Lattice 2014), pp 382, Brookhaven, New York, U.S.A., 2014

Miguel Zilhão, and Scott C Noble: "Dynamic Fisheye Grids for Binary Black Hole Simulations", Class. Quantum Grav., IOP Publishing, Vol 31, Num 6, pp 065013, 2014, doi:10.1088/0264-9381/31/6/065013

Daniel Langr, Pavel Tvrdík, Tomáš Dytrych, and Jerry P. Draayer: "Algorithm 947", ACM Transactions on Mathematical Software, Association for Computing Machinery (ACM), Vol 41, Num 1, pp 1--26, 2014, doi:10.1145/2669372

Chen-Yu Li, Jejoong Yoo, and Aleksei Aksimentiev: "Ion Conductivity, Structural Dynamics and the Effective Force in DNA Origami Nanopores", Biophysical Journal, Elsevier BV, Vol 106, Num 2, pp 414a, 2014, doi:10.1016/j.bpj.2013.11.2331

M. Salmani-Jelodar, J. D. Bermeol, S. Kim, and G. Klimeck: "ITRS Tool on NanoHUB", presented at NanoHUB User Conference, Phoenix, Arizona, U.S.A., 2014

Milton Ruiz, Vasileios Paschalidis, and Stuart L. Shapiro: "Pulsar Spin-Down Luminosity: Simulations in General Relativity", Physical Review D, American Physical Society (APS), Vol 89, Num 8, pp 084045, 2014, doi:10.1103/physrevd.89.084045

J. Um: "Calculations of Microphysical and Radiative Properties of Ice Clouds", National Institute of Meteorological Research, KMA, Jeju, Republic of Korea, 2014

P. K. Yeung, and K. R. Sreenivasan: "Direct Numerical Simulation of Turbulent Mixing at Very Low Schmidt Number with a Uniform Mean Gradient", Physics of Fluids, AIP Publishing, Vol 26, Num 1, pp 015107, 2014, doi:10.1063/1.4861070

Manish Shankla, and Aleksei Aksimentiev: "Conformational Transitions and Stop-and-Go Nanopore Transport of Single-Stranded DNA on Charged Graphene", Nature Communications, Nature Publishing Group, Vol 5, pp 5171, 2014, doi:10.1038/ncomms6171

Jon Calhoun, Luke Olson, and Marc Snir: "FlipIt: An LLVM Based Fault Injector for HPC", Springer Science + Business Media, Lecture Notes in Computer Science, pp 547--558, 2014, doi:10.1007/978-3-319-14325-5_47

Brian H. Solis, and Sharon Hammes-Schiffer: "Proton-Coupled Electron Transfer in Molecular Electrocatalysis: Theoretical Methods and Design Principles", Inorganic Chemistry, American Chemical Society (ACS), Vol 53, Num 13, pp 6427--6443, 2014, doi:10.1021/ic5002896

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and G Vedovato and J Veitch and P J Veitch and K Venkateswara and D Verkindt and S S Verma and F Vetrano and AViceré and R Vincent-Finley and J-Y Vinet and S Vitale and T Vo and H Vocca and C Vorvick and W D Vousden and S P Vyachanin and A Wade and LWade and M Wade and M Walker and L Wallace and M Wang and X Wang and R L Ward and M Was and B Weaver and L-W Wei and M Weinert and A JWeinstein and R Weiss and T Welborn and L Wen and P Wessels and M West and T Westphal and K Wette and J T Whelan and S E Whitcomb and D JWhite and B F Whiting and K Wiesner and C Wilkinson and K Williams and L Williams and R Williams and T Williams and A R Williamson and JL Willis and B Willke and M Wimmer and W Winkler and C C Wipf and A G Wiseman and H Wittel and G Woan and J Worden and J Yablon and IYakushin and H Yamamoto and C C Yancey and H Yang and Z Yang and S Yoshida and M Yvert and A Zadrożny and M Zanolin and J-P Zendri and FanZhang and L Zhang and C Zhao and X J Zhu and M E Zucker and S Zuraw and J Zweizig and M Boyle and B Brügmann and L T Buchman and MCampanelli and T Chu and Z B Etienne and M Hannam and J Healy and I Hinder and L E Kidder and P Laguna and Y T Liu and L London and C OLousto and G Lovelace and I MacDonald and P Marronetti and P Mösta and D Müller and B C Mundim and H Nakano and V Paschalidis and LPekowsky and D Pollney and H P Pfeiffer and M Ponce and M Pürrer and G Reifenberger and C Reisswig and L Santamaría and M A Scheel and SL Shapiro and D Shoemaker and C F Sopuerta and U Sperhake and B Szilágyi and N W Taylor and W Tichy and P Tsatsin and Y Zlochower: "The NINJA-2 Project: Detecting and Characterizing Gravitational Waveforms Modelled Using Numerical Binary Black Hole Simulations", Class. Quantum Grav., IOP Publishing, Vol 31, Num 11, pp 115004, 2014, doi:10.1088/0264-9381/31/11/115004

Efecan Poyraz, Heming Xu, and Yifeng Cui: "Application-Specific I/O Optimizations on Petascale Supercomputers", Procedia Computer Science, Elsevier BV, Vol 29, pp 910--923, 2014, doi:10.1016/j.procs.2014.05.082

M. Salmani-Jelodar, S. Kim, K. Ng, and G. Klimeck: "Transistor Roadmap Projection Using Predictive Full-Band Atomistic Modeling", Appl. Phys. Lett., AIP Publishing, Vol 105, Num 8, pp 083508, 2014, doi:10.1063/1.4894217

Yu He, Yu Wang, Gerhard Klimeck, and Tillmann Kubis: "Non-Equilibrium Green's Functions Method: Non-Trivial and Disordered Leads", Appl. Phys. Lett., AIP Publishing, Vol 105, Num 21, pp 213502, 2014, doi:10.1063/1.4902504

Lijun Liu: "Rejuvenation of Appalachian Topography Caused by Subsidence-Induced Differential Erosion", Nature Geoscience, Nature Publishing Group, Vol 7, Num 7, pp 518--523, 2014, doi:10.1038/ngeo2187

2015

Catello Di Martino, Saurabh Jha, William Kramer, Zbigniew Kalbarczyk, and Ravishankar K. Iyer: "LogDiver: A Tool for Measuring Resilience of Extreme-Scale Systems and Applications", Association for Computing Machinery (ACM), Proceedings of the 5th Workshop on Fault Tolerance for HPC at eXtreme Scale - FTXS '15, pp 11--18, Portland, Oregon, U.S.A., 2015, doi:10.1145/2751504.2751511

Peter L. Walters, and Nancy Makri: "Quantum-Classical Path Integral Simulation of Ferrocene-Ferrocenium Charge Transfer in Liquid Hexane", J. Phys. Chem. Lett., American Chemical Society (ACS), Vol 6, Num 24, pp 4959--4965, 2015, doi:10.1021/acs.jpclett.5b02265

B. B. Pollock, F. S. Tsung, F. Albert, J. L. Shaw, C. E. Clayton, A. Davidson, N. Lemos, K. A. Marsh, A. Pak, J. E. Ralph, W. B. Mori, and C. Joshi: "Formation of Ultrarelativistic Electron Rings from a Laser-Wakefield Accelerator", Phys. Rev. Lett., American Physical Society (APS), Vol 115, Num 5, pp 055004, 2015, doi:10.1103/physrevlett.115.055004

S. Corde, E. Adli, J. M. Allen, W. An, C. I. Clarke, C. E. Clayton, J. P. Delahaye, J. Frederico, S. Gessner, S. Z. Green, M. J. Hogan, C. Joshi, N. Lipkowitz, M. Litos, W. Lu, K. A. Marsh, W. B. Mori, M. Schmeltz, N. Vafaei-Najafabadi, D. Walz, V. Yakime: "Multi-Gigaelectronvolt Acceleration of Positrons in a Self-Loaded Plasma Wakefield", Nature, Nature Publishing Group, Vol 524, Num 7566, pp 442--445, 2015, doi:10.1038/nature14890

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

Xu, Xinlu, Lu, Wei, Mori, Warren, Joshi, Chan: "Intrinsic phase space discretization of charge in laser-triggered ionization injection in plasma accelerators", 57th Annual Meeting of the APS Division of Plasma Physics, Vol 60, Num 19, Savannah, Georgia, U.S.A., 2015

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, American Physical Society (APS), Vol 92, Num 23, pp 235209, 2015, doi:10.1103/physrevb.92.235209

Rodrigo Galindo-Murillo, Daniel R. Roe, and Thomas E. Cheatham: "Convergence and Reproducibility in Molecular Dynamics Simulations of the DNA Duplex d(GCACGAACGAACGAACGC)", Biochimica et Biophysica Acta (BBA) - General Subjects, Elsevier BV, Vol 1850, Num 5, pp 1041--1058, 2015, doi:10.1016/j.bbagen.2014.09.007

Lijun Liu, and Quan Zhou: "Deep Recycling of Oceanic Asthenosphere Material During Subduction", Geophys. Res. Lett., Wiley-Blackwell, Vol 42, Num 7, pp 2204--2211, 2015, doi:10.1002/2015gl063633

Ted Wetherbee, Elizabeth Jones, Michael Knox, Stou Sandalski, and Paul Woodward: "In-Core Volume Rendering for Cartesian Grid Fluid Dynamics Simulations", Association for Computing Machinery (ACM), Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15, St. Louis, Mo, 2015, doi:10.1145/2792745.2792780

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", presented at the 68th Annual Meeting of the APS Division of Fluid Dynamics, Bulletin of the American Physical Society, Vol 60, Num 21, Boston, Massachusetts, U.S.A., 2015

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, Oxford University Press (OUP), Vol 449, Num 4, pp 4105--4116, 2015, doi:10.1093/mnras/stv575

Robert Thompson, Romeel Davé, and Kentaro Nagamine: "The rise and fall of a challenger: the Bullet Cluster in Λ cold dark matter simulations", Mon. Not. R. Astron. Soc., Oxford University Press (OUP), Vol 452, Num 3, pp 3030--3037, 2015, doi:10.1093/mnras/stv1433

Tiziana Di Matteo: "The First Quasars", presented at the IAU General Assembly, Meeting #29, Honolulu, Hawai'i, U.S.A., 2015

Tiziana Di Matteo: "AGN Feedback in Simulations of Structure Formation", presented at the IAU General Assembly, Meeting #29, Honolulu, Hawai'i, U.S.A., 2015

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., IOP Publishing, Vol 597, pp 012054, 2015, doi:10.1088/1742-6596/597/1/012054

D. Buaria, Brian L. Sawford, and P. K. Yeung: "Characteristics of Backward and Forward Two-Particle Relative Dispersion in Turbulence at Different Reynolds Numbers", Physics of Fluids, AIP Publishing, Vol 27, Num 10, pp 105101, 2015, doi:10.1063/1.4931602

P. K. Yeung, X. M. Zhai, and Katepalli R. Sreenivasan: "Extreme Events in Computational Turbulence", Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 112, Num 41, pp 12633--12638, 2015, doi:10.1073/pnas.1517368112

Huihuo Zheng, and Lucas K. Wagner: "Computation of the Correlated Metal-Insulator Transition in Vanadium Dioxide from First Principles", Phys. Rev. Lett., American Physical Society (APS), Vol 114, Num 17, 2015, doi:10.1103/physrevlett.114.176401

Yigit Isbiliroglu, Ricardo Taborda, and Jacobo Bielak: "Coupled Soil-Structure Interaction Effects of Building Clusters During Earthquakes", Earthquake Spectra, Earthquake Engineering Research Institute, Vol 31, Num 1, pp 463--500, 2015, doi:10.1193/102412eqs315m

Ernazar Abdikamalov, Christian D. Ott, David Radice, Luke F. Roberts, Roland Haas, Christian Reisswig, Philipp Mösta, Hannah Klion, and Erik Schnetter: "Neutrino-Driven Turbulent Convection and Standing Accretion Shock Instability in Three-Dimensional Core-Collapse Supernovae", The Astrophysical Journal, IOP Publishing, Vol 808, Num 1, pp 70, 2015, doi:10.1088/0004-637x/808/1/70

Hotaka Shiokawa, Julian H. Krolik, Roseanne M. Cheng, Tsvi Piran, and Scott C. Noble: "General Relativistic Hydrodynamic Simulation of Accretion Flow from a Stellar Tidal Disruption", ApJ, IOP Publishing, Vol 804, Num 2, pp 85, 2015, doi:10.1088/0004-637x/804/2/85

Chad W. Hopkins, Scott Le Grand, Ross C. Walker, and Adrian E. Roitberg: "Long-Time-Step Molecular Dynamics Through Hydrogen Mass Repartitioning", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 4, pp 1864--1874, 2015, doi:10.1021/ct5010406

Cheng-Tsung Lai, Huei-Jiun Li, Weixuan Yu, Sonam Shah, Gopal R. Bommineni, Victoria Perrone, Miguel Garcia-Diaz, Peter J. Tonge, and Carlos Simmerling: "Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium Tuberculosis InhA", Biochemistry, American Chemical Society (ACS), Vol 54, Num 30, pp 4683--4691, 2015, doi:10.1021/acs.biochem.5b00284

Christina Bergonzo, and Thomas E. Cheatham: "Improved Force Field Parameters Lead to a Better Description of RNA Structure", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 9, pp 3969--3972, 2015, doi:10.1021/acs.jctc.5b00444

Christina Bergonzo, Kathleen B. Hall, and Thomas E. Cheatham: "Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg 2+ Bound Structure in the Presence of Monovalent Ions", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 119, Num 38, pp 12355--12364, 2015, doi:10.1021/acs.jpcb.5b05190

Christina Bergonzo, Niel M. Henriksen, Daniel R. Roe, and Thomas E. Cheatham: "Highly Sampled Tetranucleotide and Tetraloop Motifs Enable Evaluation of Common RNA Force Fields", RNA, Cold Spring Harbor Laboratory Press, Vol 21, Num 9, pp 1578--1590, 2015, doi:10.1261/rna.051102.115

George M. Giambaşu, Darrin M. York, and David A. Case: "Structural Fidelity and NMR Relaxation Analysis in a Prototype RNA Hairpin", RNA, Cold Spring Harbor Laboratory Press, Vol 21, Num 5, pp 963--974, 2015, doi:10.1261/rna.047357.114

Hai Nguyen, Alberto Pérez, Sherry Bermeo, and Carlos Simmerling: "Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins", Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 11, Num 8, pp 3714--3728, 2015, doi:10.1021/acs.jctc.5b00271

James A. Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E. Hauser, and Carlos Simmerling: "ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 8, pp 3696--3713, 2015, doi:10.1021/acs.jctc.5b00255

James C. Robertson, and Thomas E Cheatham: "DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 119, Num 44, pp 14111--14119, 2015, doi:10.1021/acs.jpcb.5b08486

R. Galindo-Murillo, J. C. Garcia-Ramos, L. Ruiz-Azuara, T. E. Cheatham, and F. Cortes-Guzman: "Intercalation Processes of Copper Complexes in DNA", Nucleic Acids Research, Oxford University Press (OUP), Vol 43, Num 11, pp 5364--5376, 2015, doi:10.1093/nar/gkv467

Thakshila Dissanayake, Jason M. Swails, Michael E. Harris, Adrian E. Roitberg, and Darrin M. York: "Interpretation of pH-Activity Profiles for Acid-Base Catalysis from Molecular Simulations", Biochemistry, American Chemical Society (ACS), Vol 54, Num 6, pp 1307--1313, 2015, doi:10.1021/bi5012833

Thomas E. Cheatham, and Daniel R. Roe: "The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis", Comput. Sci. Eng., Institute of Electrical & Electronics Engineers (IEEE), Vol 17, Num 2, pp 30--39, 2015, doi:10.1109/mcse.2015.7

A. Tankasala, Y. Wang, G. Klimeck, and R. Rahman: "Atomistic Configuration Interaction Simulations of Two-electron States of Donors in Silicon", presented at the American Physical Society March meeting 2015, Vol 60, Num 1, San Antonio, Texas, U.S.A., 2015

A. Tankasala, Y. Wang, J. Bocquel, B. Voison, M. Usman, S. Rogge, M. Simmons, L. Hollenberg, R. Rahman, and G. Klimeck: "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

Bozidar Novakovic, and Gerhard Klimeck: "Atomistic Quantum Transport Approach to Time-Resolved Device Simulations", Institute of Electrical & Electronics Engineers (IEEE), 2015 International Conference on Simulation of Semiconductor Processes and Devices (SISPAD), Washington, D.C., U.S.A., 2015, doi:10.1109/sispad.2015.7292245

Fan W. Chen, Luis A. Jauregui, Yaohua Tan, Michael Manfra, Gerhard Klimeck, Yong P. Chen, and Tillmann Kubis: "In-Surface Confinement of Topological Insulator Nanowire Surface States", Appl. Phys. Lett., AIP Publishing, Vol 107, Num 12, pp 121605, 2015, doi:10.1063/1.4931975

Mehdi Salmani-Jelodar, Saumitra R. Mehrotra, Hesameddin Ilatikhameneh, and Gerhard Klimeck: "Design Guidelines for Sub-12 Nm Nanowire MOSFETs", IEEE Transactions on Nanotechnology, Institute of Electrical & Electronics Engineers (IEEE), Vol 14, Num 2, pp 210--213, 2015, doi:10.1109/tnano.2015.2395441

Parijat Sengupta, Tillmann Kubis, Yaohua Tan, and Gerhard Klimeck: "Proximity Induced Ferromagnetism, Superconductivity, and Finite-Size Effects on the Surface States of Topological Insulator Nanostructures", J. Appl. Phys., AIP Publishing, Vol 117, Num 4, pp 044304, 2015, doi:10.1063/1.4906842

Ravi Pramod Vedula, Saumitra Mehrotra, Tillmann Kubis, Michael Povolotskyi, Gerhard Klimeck, and Alejandro Strachan: "Optimal Ge/SiGe Nanofin Geometries for Hole Mobility Enhancement: Technology Limit from Atomic Simulations", J. Appl. Phys., AIP Publishing, Vol 117, Num 17, pp 174312, 2015, doi:10.1063/1.4919091

Yaohua P. Tan, Michael Povolotskyi, Tillmann Kubis, Timothy B. Boykin, and Gerhard Klimeck: "Tight-Binding Analysis of Si and GaAs Ultrathin Bodies with Subatomic Wave-Function Resolution", Phys. Rev. B, American Physical Society (APS), Vol 92, Num 8, 2015, doi:10.1103/physrevb.92.085301

David J. Wilson, Jozef J. Dudek, Robert G. Edwards, and Christopher E. Thomas: "Resonances in coupled π K, η K scattering from lattice QCD", Physical Review D, American Physical Society (APS), Vol 91, Num 5, 2015, doi:10.1103/physrevd.91.054008

David J. Wilson, Raúl A. Briceño, Jozef J. Dudek, Robert G. Edwards, and Christopher E. Thomas: "Coupled ππ, K ¯ K scattering in P-wave and the ρ resonance from lattice QCD", Physical Review D, American Physical Society (APS), Vol 92, Num 9, pp 094502, 2015, doi:10.1103/physrevd.92.094502

Briceño, Raúl A., Jozef J. Dudek, Robert G. Edwards, Christian J. Shultz, Christopher E. Thomas, and David J. Wilson: "The resonant π+γ → π+π⁰ amplitude from Quantum Chromodynamics", Phys. Rev. Lett., American Physical Society (APS), Vol 115, Num 24, pp 242001, 2015, doi:10.1103/physrevlett.115.242001

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", presented at NRC Meeting on Computations for Science and Technology, Dallas, Texas, U.S.A., 2015

K. A. Reed, J. T. Bacmeister, N. A. Rosenbloom, M. F. Wehner, S. C. Bates, P. H. Lauritzen, J. E. Truesdale, and C. Hannay: "Impact of the Dynamical Core on the Direct Simulation of Tropical Cyclones in a High-Resolution Global Model", Geophys. Res. Lett., Wiley-Blackwell, Vol 42, Num 9, pp 3603--3608, 2015, doi:10.1002/2015gl063974

Fan Guo, Yi-Hsin Liu, William Daughton, and Hui Li: "Particle Acceleration and Plasma Dynamics During Magnetic Reconnection in the Magnetically-Dominated Regime", ApJ, IOP Publishing, Vol 806, Num 2, pp 167, 2015, doi:10.1088/0004-637x/806/2/167

K. D. Makwana, V. Zhdankin, H. Li, W. Daughton, and F. Cattaneo: "Energy Dynamics and Current Sheet Structure in Fluid and Kinetic Simulations of Decaying Magnetohydrodynamic Turbulence", Physics of Plasmas, AIP Publishing, Vol 22, Num 4, pp 042902, 2015, doi:10.1063/1.4916492

M. Wan, W. H. Matthaeus, V. Roytershteyn, H. Karimabadi, T. Parashar, P. Wu, and M. Shay: "Intermittent Dissipation and Heating in 3D Kinetic Plasma Turbulence", Phys. Rev. Lett., American Physical Society (APS), Vol 114, Num 17, 2015, doi:10.1103/physrevlett.114.175002

V. Roytershteyn, H. Karimabadi, and A. Roberts: "Generation of Magnetic Holes in Fully Kinetic Simulations of Collisionless Turbulence", Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, The Royal Society, Vol 373, Num 2041, pp 20140151--20140151, 2015, doi:10.1098/rsta.2014.0151

M. Zingale, C. M. Malone, A. Nonaka, A. S. Almgren, and J. B. Bell: "Comparisons of Two- and Three-Dimensional Convection in Type I X-Ray Bursts", ApJ, IOP Publishing, Vol 807, Num 1, pp 60, 2015, doi:10.1088/0004-637x/807/1/60

Brian W. O'Shea, John H. Wise, Hao Xu, and Michael L. Norman: "Probing the Ultraviolet Luminosity Function of the Earliest Galaxies with the Renaissance Simulations", ApJ, IOP Publishing, Vol 807, Num 1, pp L12, 2015, doi:10.1088/2041-8205/807/1/l12

Britton D. Smith, John H. Wise, Brian W. O'Shea, Michael L. Norman, and Sadegh Khochfar: "The First Population II Stars Formed in Externally Enriched Mini-Haloes", Mon. Not. R. Astron. Soc., Oxford University Press (OUP), Vol 452, Num 3, pp 2822--2836, 2015, doi:10.1093/mnras/stv1509

Kyungjin Ahn, Hao Xu, Michael L. Norman, Marcelo A. Alvarez, and John H. Wise: "Spatially Extended 21 Cm Signal from Strongly Clustered UV and X-Ray Sources in the Early Universe", ApJ, IOP Publishing, Vol 802, Num 1, pp 8, 2015, doi:10.1088/0004-637x/802/1/8

Michael L. Norman, Daniel R. Reynolds, Geoffrey C. So, Robert P. Harkness, and John H. Wise: "Fully Coupled Simulation of Cosmic Reionization. I. Numerical Methods and Tests", ApJS, IOP Publishing, Vol 216, Num 1, pp 16, 2015, doi:10.1088/0067-0049/216/1/16

Boon Chong Goh, Juan R. Perilla, Matthew R. England, Katrina J. Heyrana, Rebecca C. Craven, and Klaus Schulten: "Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis", Structure, Elsevier BV, Vol 23, Num 8, pp 1414--1425, 2015, doi:10.1016/j.str.2015.05.017

C Keith Cassidy, Benjamin A Himes, Frances J Alvarez, Jun Ma, Gongpu Zhao, Juan R Perilla, Klaus Schulten, and Peijun Zhang: "CryoEM and Computer Simulations Reveal a Novel Kinase Conformational Switch in Bacterial Chemotaxis Signaling", eLife, eLife Sciences Organisation, Ltd., Vol 4, 2015, doi:10.7554/elife.08419

David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten: "Multilevel Summation Method for Electrostatic Force Evaluation", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 2, pp 766--779, 2015, doi:10.1021/ct5009075

Juan R Perilla, Boon Chong Goh, C Keith Cassidy, Bo Liu, Rafael C Bernardi, Till Rudack, Hang Yu, Zhe Wu, and Klaus Schulten: "Molecular Dynamics Simulations of Large Macromolecular Complexes", Current Opinion in Structural Biology, Elsevier BV, Vol 31, pp 64--74, 2015, doi:10.1016/j.sbi.2015.03.007

Juan R. Perilla, Boon Chong Goh, John Stone, and Klaus Schulten: "Chemical Visualization of Human Pathogens: the Retroviral Capsids", presented at the The International Conference for High Performance Computing, Networking, Storage and Analysis (SC15), Austin, Texas, U.S.A., 2015

Rafael C. Bernardi, Marcelo C.R. Melo, and Klaus Schulten: "Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems", Biochimica et Biophysica Acta (BBA) - General Subjects, Elsevier BV, Vol 1850, Num 5, pp 872--877, 2015, doi:10.1016/j.bbagen.2014.10.019

Wen Ma, and Klaus Schulten: "Mechanism of Substrate Translocation by a Ring-Shaped ATPase Motor at Millisecond Resolution", J. Am. Chem. Soc., American Chemical Society (ACS), Vol 137, Num 8, pp 3031--3040, 2015, doi:10.1021/ja512605w

F. Governato, D. Weisz, A. Pontzen, S. Loebman, D. Reed, A. M. Brooks, P. Behroozi, C. Christensen, P. Madau, L. Mayer, S. Shen, M. Walker, T. Quinn, B. W. Keller, and J. Wadsley: "Faint Dwarfs as a Test of DM Models: WDM Versus CDM", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 448, Num 1, pp 792--803, 2015, doi:10.1093/mnras/stu2720

Harshitha Menon, Lukasz Wesolowski, Gengbin Zheng, Pritish Jetley, Laxmikant Kale, Thomas Quinn, and Fabio Governato: "Adaptive Techniques for Clustered N-Body Cosmological Simulations", Comput. Astrophys., Springer Science + Business Media, Vol 2, Num 1, 2015, doi:10.1186/s40668-015-0007-9

M. Tremmel, F. Governato, M. Volonteri, and T. R. Quinn: "Off the Beaten Path: A New Approach to Realistically Model the Orbital Decay of Supermassive Black Holes in Galaxy Formation Simulations", Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol 451, Num 2, pp 1868--1874, 2015, doi:10.1093/mnras/stv1060

J. Heerikhuisen, Eric Zirnstein, and Nikolai Pogorelov: "κ-distributed protons in the solar wind and their charge-exchange coupling to energetic hydrogen", Journal of Geophysical Research: Space Physics, Wiley-Blackwell, Vol 120, Num 3, pp 1516--1525, 2015, doi:10.1002/2014ja020636

Ming Zhang, Xi Luo, and Nikolai Pogorelov: "Where Is the Cosmic-Ray Modulation Boundary of the Heliosphere?", Physics of Plasmas, AIP Publishing, Vol 22, Num 9, pp 091501, 2015, doi:10.1063/1.4928945

N. V. Pogorelov, and S. N. Borovikov: "Mixing of the Interstellar and Solar Plasmas at the Heliospheric Interface", Astronomical Society of the Pacific, Numerical Modeling of Space Plasma Flows: ASTRONUM-2014, Vol 498, pp 160, 2015

Sean M. Couch, and Christian D. Ott: "The Role of Turbulence in Neutrino-Driven Core-Collapse Supernova Explosions", ApJ, IOP Publishing, Vol 799, Num 1, pp 5, 2015, doi:10.1088/0004-637x/799/1/5

Vasileios Paschalidis, Milton Ruiz, and Stuart L. Shapiro: "Relativistic Simulations of Black Hole-Neutron Star Coalescence: The Jet Emerges", ApJ, IOP Publishing, Vol 806, Num 1, pp L14, 2015, doi:10.1088/2041-8205/806/1/l14

Yan Li, Miroslav Hodak, and J. Bernholc: "Enzymatic Mechanism of Copper-Containing Nitrite Reductase", Biochemistry, American Chemical Society (ACS), Vol 54, Num 5, pp 1233--1242, 2015, doi:10.1021/bi5007767

Yongyang Cai, Kenneth Judd, and Jevgenijs Steinbuks: "A nonlinear certainty equivalent approximation method for dynamic stochastic problems", Quantitative Economics, Blackwell Publishing Ltd, Vol 8, Num 1, pp 117--147, 2015, doi:10.3982/QE533

N. V. Pogorelov, S. N. Borovikov, J. Heerikhuisen, and M. Zhang: "The Heliotail", ApJ, IOP Publishing, Vol 812, Num 1, pp L6, 2015, doi:10.1088/2041-8205/812/1/l6

P Manoharan, T Kim, N V Pogorelov, C N Arge, and P K Manoharan: "Modeling Solar Wind with Boundary Conditions from Interplanetary Scintillations", J. Phys.: Conf. Ser., IOP Publishing, Vol 642, pp 012016, 2015, doi:10.1088/1742-6596/642/1/012016

R L Fermo, N V Pogorelov, and L F Burlaga: "Transient Shocks Beyond the Heliopause", J. Phys.: Conf. Ser., IOP Publishing, Vol 642, pp 012008, 2015, doi:10.1088/1742-6596/642/1/012008

Xi Luo, Ming Zhang, Marius Potgieter, Xueshang Feng, and N. V. Pogorelov: "A Numerical Simulation of Cosmic-Ray Modulation Near the Heliopause", ApJ, IOP Publishing, Vol 808, Num 1, pp 82, 2015, doi:10.1088/0004-637x/808/1/82

E. Briggs, W. Lu, M. Hodak, Y. Li, C.T. Kelley, and J. Bernholc: "Petascale Electronic Structure Code with a New Parallel Eigensolver", presented at the APS March Meeting 2015, American Physical Society (APS), Vol 60, Num 1, San Antonio, Texas, U.S.A., 2015

Rui Dong, V. Ranjan, Marco Buongiorno Nardelli, and J. Bernholc: "Atomistic Simulations of Aromatic Polyurea and Polyamide for Capacitive Energy Storage", Phys. Rev. B, American Physical Society (APS), Vol 92, Num 2, pp 024203, 2015, doi:10.1103/physrevb.92.024203

Yash Thakur, Rui Dong, Minren Lin, Shan Wu, Zhaoxi Cheng, Ying Hou, J. Bernholc, and Q.M. Zhang: "Optimizing Nanostructure to Achieve High Dielectric Response with Low Loss in Strongly Dipolar Polymers", Nano Energy, Elsevier BV, Vol 16, pp 227--234, 2015, doi:10.1016/j.nanoen.2015.06.021

Unknown: "Flux Emergence and Active Region Formation", NORDITA invited talk, Stockholm, Sweden, 2015

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., Copernicus GmbH, Vol 19, Num 7, pp 3239--3251, 2015, doi:10.5194/hess-19-3239-2015

Nathaniel W. Chaney, Joshua K. Roundy, Julio E. Herrera-Estrada, and Eric F. Wood: "High-Resolution Modeling of the Spatial Heterogeneity of Soil Moisture: Applications in Network Design", Water Resources Research, Wiley-Blackwell, Vol 51, Num 1, pp 619--638, 2015, doi:10.1002/2013wr014964

Patrick M Reed, Nathaniel W Chaney, Jonathan D Herman, Matthew P Ferringer, and Eric F Wood: "Internationally Coordinated Multi-Mission Planning Is Now Critical to Sustain the Space-Based Rainfall Observations Needed for Managing Floods Globally", Environ. Res. Lett., IOP Publishing, Vol 10, Num 2, pp 024010, 2015, doi:10.1088/1748-9326/10/2/024010

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., IOP Publishing, Vol 578, pp 012010, 2015, doi:10.1088/1742-6596/578/1/012010

J. P. Draayer, T. Dytrych, K. D. Launey, A. C. Dreyfuss, and D. Langr: "HPC-Enabled Nuclear Structure Studies - Description and Applications of the Symmetry-Adapted No-Core Shell Model", J. Phys.: Conf. Ser., IOP Publishing, Vol 580, pp 012044, 2015, doi:10.1088/1742-6596/580/1/012044

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, World Scientific Pub Co Pte Lt, Vol 24, Num 05, pp 1530005, 2015, doi:10.1142/s0218301315300052

T Dytrych, K D Launey, J P Draayer, P Maris, J P Vary, D Langr, and T Oberhuber: "Emergence of Simple Patterns in Complex Atomic Nuclei from First Principles", J. Phys.: Conf. Ser., IOP Publishing, Vol 639, pp 012008, 2015, doi:10.1088/1742-6596/639/1/012008

T. Dytrych, A. C. Hayes, K. D. Launey, J. P. Draayer, P. Maris, J. P. Vary, D. Langr, and T. Oberhuber: "Electron-Scattering Form Factors for Li-6 in the Ab Initio Symmetry-Guided Framework", Phys. Rev. C, American Physical Society (APS), Vol 91, Num 2, 2015, doi:10.1103/physrevc.91.024326

Thomas S. Lontzek, Yongyang Cai, Kenneth L. Judd, and Timothy M. Lenton: "Stochastic Integrated Assessment of Climate Tipping Points Indicates the Need for Strict Climate Policy", Nature Climate Change, Nature Publishing Group, Vol 5, Num 5, pp 441--444, 2015, doi:10.1038/nclimate2570

Yongyang Cai, Kenneth L. Judd, Timothy M. Lenton, Thomas S. Lontzek, and Daiju Narita: "Environmental Tipping Points Significantly Affect the Cost-Benefit Assessment of Climate Policies", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 112, Num 15, pp 4606--4611, 2015, doi:10.1073/pnas.1503890112

Sohan Kale, Ankit Saharan, Seid Koric, and Martin Ostoja-Starzewski: "Scaling and Bounds in Thermal Conductivity of Planar Gaussian Correlated Microstructures", J. Appl. Phys., AIP Publishing, Vol 117, Num 10, pp 104301, 2015, doi:10.1063/1.4914128

Sohan Kale, Seid Koric, and Martin Ostoja-Starzewski: "Stochastic Continuum Damage Mechanics Using Spring Lattice Models", AMM, Trans Tech Publications, Vol 784, pp 350--357, 2015, doi:10.4028/www.scientific.net/amm.784.350

Vladimir Puzyrev, and Seid Koric: "3D Multi-Source CSEM Simulations: Feasibility and Comparison of Parallel Direct Solvers", Society of Exploration Geophysicists, SEG Technical Program Expanded Abstracts 2015, 2015, doi:10.1190/segam2015-5864005.1

Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev: "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field", ACS Nano, American Chemical Society (ACS), Vol 9, Num 2, pp 1420--1433, 2015, doi:10.1021/nn505825z

Jejoong Yoo, and Aleksei Aksimentiev: "Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating", J. Phys. Chem. Lett., American Chemical Society (ACS), Vol 6, Num 23, pp 4680--4687, 2015, doi:10.1021/acs.jpclett.5b01964

Maxim Belkin, Shu-Han Chao, Magnus P. Jonsson, Cees Dekker, and Aleksei Aksimentiev: "Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA", ACS Nano, American Chemical Society (ACS), Vol 9, Num 11, pp 10598--10611, 2015, doi:10.1021/acsnano.5b04173

Yue-xiao Shen, Wen Si, Mustafa Erbakan, Karl Decker, Rita De Zorzi, Patrick O. Saboe, You Jung Kang, Sheereen Majd, Peter J. Butler, Thomas Walz, Aleksei Aksimentiev, Jun-li Hou, and Manish Kumar: "Highly Permeable Artificial Water Channels That Can Self-Assemble Into Two-Dimensional Arrays", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 112, Num 32, pp 9810--9815, 2015, doi:10.1073/pnas.1508575112

Lusheng Liang, Larry Di Girolamo, and Wenbo Sun: "Bias in MODIS Cloud Drop Effective Radius for Oceanic Water Clouds as Deduced from Optical Thickness Variability Across Scattering Angles", Journal of Geophysical Research: Atmospheres, Wiley-Blackwell, Vol 120, Num 15, pp 7661--7681, 2015, doi:10.1002/2015jd023256

J. Kwack, S. Kang, G. Bhatt, and A. Masud,: "Outflow Boundary Conditions for Non-Newtonian Models for Blood", Springer, Modeling and Simulation in Science, Engineering and Technology Book Series, 2015

Jared C. Weddell, JaeHyuk Kwack, P. I. Imoukhuede, and Arif Masud: "Hemodynamic Analysis in an Idealized Artery Tree: Differences in Wall Shear Stress Between Newtonian and Non-Newtonian Blood Models", PLOS ONE, Public Library of Science (PLoS), Vol 10, Num 4, pp e0124575, 2015, doi:10.1371/journal.pone.0124575

Tyler M. Earnest, Jonathan Lai, Ke Chen, Michael J. Hallock, James R. Williamson, and Zaida Luthey-Schulten: "Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly", Biophysical Journal, Elsevier BV, Vol 109, Num 6, pp 1117--1135, 2015, doi:10.1016/j.bpj.2015.07.030

Yan Y. Liu, and Shaowen Wang: "A Scalable Parallel Genetic Algorithm for the Generalized Assignment Problem", Parallel Computing, Elsevier BV, Vol 46, pp 98--119, 2015, doi:10.1016/j.parco.2014.04.008

Rupert Croft, Tiziana Di Matteo, Nishikanta Khandai, and Yu Feng: "Petascale Cosmology: Simulations of Structure Formation", Comput. Sci. Eng., Institute of Electrical & Electronics Engineers (IEEE), Vol 17, Num 2, pp 40--46, 2015, doi:10.1109/mcse.2015.5

Yu Feng, Mark Straka, Tiziana Di Matteo, and Rupert Croft: "Sorting at Scale on BlueWaters in a Cosmological Simulation", presented at CUG 2015, Chicago, Illinois, U.S.A., 2015

Yu Feng, Tiziana Di Matteo, Rupert Croft, Ananth Tenneti, Simeon Bird, Nicholas Battaglia, and Stephen Wilkins: "The Formation of Milky Way-Mass Disk Galaxies in the First 500 Million Years of a Cold Dark Matter Universe", ApJ, IOP Publishing, Vol 808, Num 1, pp L17, 2015, doi:10.1088/2041-8205/808/1/l17

Yu Feng, Tiziana Di Matteo, Rupert A. Croft, Simeon Bird, Nicholas Battaglia, and Stephen Wilkins: "The BlueTides Simulation: First Galaxies and Reionization", Mon. Not. R. Astron. Soc., Oxford University Press (OUP), Vol 455, Num 3, pp 2778--2791, 2015, doi:10.1093/mnras/stv2484

Joel B Varley, and André Schleife: "Bethe-Salpeter Calculation of Optical-Absorption Spectra of In2O3 and Ga2O3", Semiconductor Science and Technology, IOP Publishing, Vol 30, Num 2, pp 024010, 2015, doi:10.1088/0268-1242/30/2/024010

Boris Capitanu, Ted Underwood, Peter Organisciak, Sayan Bhattacharyya, Loretta Auvil, Colleen Fallaw, and J. Stephen Downie: "Extracted Feature Dataset from 4.8 Million HathiTrust Digital Library Public Domain Volumes", HathiTrust Research Center, 2015, doi:10.13012/j8td9v7m

Jing Li, Po-Chao Wen, Mahmoud Moradi, and Emad Tajkhorshid: "Computational Characterization of Structural Dynamics Underlying Function in Active Membrane Transporters", Current Opinion in Structural Biology, Elsevier BV, Vol 31, pp 96-105, 2015, doi:10.1016/j.sbi.2015.04.001

Mahmoud Moradi, Giray Enkavi, and Emad Tajkhorshid: "Atomic-Level Characterization of Transport Cycle Thermodynamics in the Glycerol-3-Phosphate:phosphate Antiporter", Nature Communications, Nature Publishing Group, Vol 6, pp 8393, 2015, doi:10.1038/ncomms9393

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, Springer Science + Business Media, Vol 47, Num 1, pp 548--565, 2015, doi:10.1007/s11663-015-0525-5

Xiao Chen, Xiongjie Yu, Gil Young Cho, Bryan K. Clark, and Eduardo Fradkin: "Many-Body Localization Transition in Rokhsar-Kivelson-Type Wave Functions", Phys. Rev. B, American Physical Society (APS), Vol 92, Num 21, pp 214204, 2015, doi:10.1103/physrevb.92.214204

Soohaeng Yoo Willow, Michael A. Salim, Kwang S. Kim, and So Hirata: "Ab Initio Molecular Dynamics of Liquid Water Using Embedded-Fragment Second-Order Many-Body Perturbation Theory Towards Its Accurate Property Prediction", Sci. Rep., Nature Publishing Group, Vol 5, pp 14358, 2015, doi:10.1038/srep14358

Andrew Sirjoosingh, Michael V. Pak, Kurt R. Brorsen, and Sharon Hammes-Schiffer: "Quantum Treatment of Protons with the Reduced Explicitly Correlated Hartree-Fock Approach", The Journal of Chemical Physics, AIP Publishing, Vol 142, Num 21, pp 214107, 2015, doi:10.1063/1.4921303

Kurt R. Brorsen, Andrew Sirjoosingh, Michael V. Pak, and Sharon Hammes-Schiffer: "Nuclear-Electronic Orbital Reduced Explicitly Correlated Hartree-Fock Approach: Restricted Basis Sets and Open-Shell Systems", The Journal of Chemical Physics, AIP Publishing, Vol 142, Num 21, pp 214108, 2015, doi:10.1063/1.4921304

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, American Chemical Society (ACS), Vol 119, Num 6, pp 2758--2768, 2015, doi:10.1021/jp5126969

Amanda Bienz, Jon Calhoun, Luke Olson, Marc Snir, and William D. Gropp: "Analyzing the Performance of a Sparse Matrix Vector Multiply for Extreme Scale Computers", presented at the International Conference for High Performance Computing, Networking, Storage and Analysis (SC15), Poster., Austin, Texas, U.S.A., 2015

D. Guo, W. Gropp, and L. N. Olson: "A Hybrid Format for Better Performance of Sparse Matrix-Vector Multiplication on a GPU", International Journal of High Performance Computing Applications, SAGE Publications, Vol 30, Num 1, pp 103--120, 2015, doi:10.1177/1094342015593156

P. Eller and W. Gropp: "Exploiting Nonblocking Collective Operations in Conjugate Gradient", Abstract for 2015 Copper Mountain Meeting, 2015

Sohan Kale, Ankit Saharan, Seid Koric, and Martin Ostoja-Starzewski: "Scaling and Bounds in Thermal Conductivity of Planar Gaussian Correlated Microstructures", J. Appl. Phys., AIP Publishing, Vol 117, Num 10, pp 104301, 2015, doi:10.1063/1.4914128

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, American Physical Society (APS), Vol 91, Num 20, pp 205429, 2015, doi:10.1103/physrevb.91.205429

Abhilash Harpale, Marco Panesi, and Huck Beng Chew: "Communication: Surface-to-Bulk Diffusion of Isolated Versus Interacting C Atoms in Ni(111) and Cu(111) Substrates: A First Principle Investigation", The Journal of Chemical Physics, AIP Publishing, Vol 142, Num 6, pp 061101, 2015, doi:10.1063/1.4907716

Haoran Wang, Binyue Hou, Xueju Wang, Shuman Xia, and Huck Beng Chew: "Atomic-Scale Mechanisms of Sliding Along an Interdiffused Li-Si-Cu Interface", Nano Letters, American Chemical Society (ACS), Vol 15, Num 3, pp 1716--1721, 2015, doi:10.1021/nl5043837

Haoran Wang, Xueju Wang, Shuman Xia, and Huck Beng Chew: "Brittle-to-Ductile Transition of Lithiated Silicon Electrodes: Crazing to Stable Nanopore Growth", The Journal of Chemical Physics, AIP Publishing, Vol 143, Num 10, pp 104703, 2015, doi:10.1063/1.4930856

Ruizhi Li, and Huck Beng Chew: "Closed and Open-Ended Stacking Fault Tetrahedra Formation Along the Interfaces of Cu-Al Nanolayered Metals", Philosophical Magazine, Informa UK Limited, Vol 95, Num 25, pp 2747--2763, 2015, doi:10.1080/14786435.2015.1077283

Ruizhi Li, and Huck Beng Chew: "Planar-to-Wavy Transition of Cu-Ag Nanolayered Metals: A Precursor Mechanism to Twinning", Philosophical Magazine, Informa UK Limited, Vol 95, Num 10, pp 1029--1048, 2015, doi:10.1080/14786435.2015.1006290

Jens Glaser, Trung Dac Nguyen, Joshua A. Anderson, Pak Lui, Filippo Spiga, Jaime A. Millan, David C. Morse, and Sharon C. Glotzer: "Strong Scaling of General-Purpose Molecular Dynamics Simulations on GPUs", Computer Physics Communications, Elsevier BV, Vol 192, pp 97--107, 2015, doi:10.1016/j.cpc.2015.02.028

Zhanpeng Zhang, Ryan L. Marson, Zhishen Ge, Sharon C. Glotzer, and Peter X. Ma: "Simultaneous Nano- and Microscale Control of Nanofibrous Microspheres Self-Assembled from Star-Shaped Polymers", Adv. Mater., Wiley-Blackwell, Vol 27, Num 26, pp 3947--3952, 2015, doi:10.1002/adma.201501329

A. Sharma, H.J.S. Fernando, A. F. Hamlet, J.J. Hellmann, M. Barlage, and F. Chen: "Sensitivity of WRF Model to Landuse, with Applications to Chicago Metropolitan Urban Heat Island and Lake Breeze", AGU Fall Meeting Abstracts, American Geophysical Union, San Francisco, CA, 2015

Patrick Conry, Ashish Sharma, Mark J. Potosnak, Laura S. Leo, Edward Bensman, Jessica J. Hellmann, and Harindra J. S. Fernando: "Chicago's Heat Island and Climate Change: Bridging the Scales via Dynamical Downscaling", J. Appl. Meteor. Climatol., American Meteorological Society, Vol 54, Num 7, pp 1430--1448, 2015, doi:10.1175/jamc-d-14-0241.1

Poya Yasaei, Arman Fathizadeh, Reza Hantehzadeh, Arnab K. Majee, Ahmed El-Ghandour, David Estrada, Craig Foster, Zlatan Aksamija, Fatemeh Khalili-Araghi, and Amin Salehi-Khojin: "Bimodal Phonon Scattering in Graphene Grain Boundaries", Nano Letters, American Chemical Society (ACS), Vol 15, Num 7, pp 4532--4540, 2015, doi:10.1021/acs.nanolett.5b01100

Sudip Garain, Dinshaw S. Balsara, and John Reid: "Comparing Coarray Fortran (CAF) with MPI for Several Structured Mesh PDE Applications", Journal of Computational Physics, Elsevier BV, Vol 297, pp 237--253, 2015, doi:10.1016/j.jcp.2015.05.020

Gaurav Shukla, Zhongqing Wu, Han Hsu, Andrea Floris, Matteo Cococcioni, and Renata M. Wentzcovitch: "Thermoelasticity of Fe 2+ -Bearing Bridgmanite", Geophys. Res. Lett., Wiley-Blackwell, Vol 42, Num 6, pp 1741--1749, 2015, doi:10.1002/2014gl062888

Michel L. Marcondes, and Renata M. Wentzcovitch: "Hybrid Ab-Initio/experimental High Temperature Equations of State: Application to the NaCl Pressure Scale", J. Appl. Phys., AIP Publishing, Vol 117, Num 21, pp 215902, 2015, doi:10.1063/1.4921904

Ryan J. Wu, Mehmet Topsakal, Tony Low, Matthew C. Robbins, Nazila Haratipour, Jong Seok Jeong, Renata M. Wentzcovitch, Steven J. Koester, and K. Andre Mkhoyan: "Atomic and Electronic Structure of Exfoliated Black Phosphorus", Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, American Vacuum Society, Vol 33, Num 6, pp 060604, 2015, doi:10.1116/1.4926753

Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper: "Numerical Investigation of Aero-Optical Distortions Over a Hemisphere-on-Cylinder Turret with Gaps", American Institute of Aeronautics and Astronautics (AIAA), 46th AIAA Plasmadynamics and Lasers Conference, Dallas, Texas, U.S.A., 2015, doi:10.2514/6.2015-3248

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

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., Springer Science + Business Media, Vol 2, Num 1, 2015, doi:10.1186/s40668-015-0011-0

Viktoriya Morozova, Anthony L. Piro, Mathieu Renzo, Christian D. Ott, Drew Clausen, Sean M. Couch, Justin Ellis, and Luke F. Roberts: "Light Curves of Core-Collapse Supernovae with Substantial Mass Loss Using the New Open-Source Supernova Explosion Code (SNEC)", ApJ, IOP Publishing, Vol 814, Num 1, pp 63, 2015, doi:10.1088/0004-637x/814/1/63

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

George M. Slota, and Kamesh Madduri: "Parallel Color-Coding", Parallel Computing, Elsevier BV, Vol 47, pp 51--69, 2015, doi:10.1016/j.parco.2015.02.004

George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri: "High-Performance Graph Analytics on Manycore Processors", Institute of Electrical & Electronics Engineers (IEEE), 2015 IEEE International Parallel and Distributed Processing Symposium, Hyderabad, India, 2015, doi:10.1109/ipdps.2015.54

Eugene Palovcak, Lucie Delemotte, Michael L. Klein, and Vincenzo Carnevale: "Comparative Sequence Analysis Suggests a Conserved Gating Mechanism for TRP Channels", The Journal of General Physiology, Rockefeller University Press, Vol 146, Num 1, pp 37--50, 2015, doi:10.1085/jgp.201411329

Khaled Elokely, Phanindra Velisetty, Lucie Delemotte, Eugene Palovcak, Michael L. Klein, Tibor Rohacs, and Vincenzo Carnevale: "Understanding TRPV1 Activation by Ligands: Insights from the Binding Modes of Capsaicin and Resiniferatoxin", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 113, Num 2, pp E137--E145, 2015, doi:10.1073/pnas.1517288113

Luca Ponzoni, Guido Polles, Vincenzo Carnevale, and Cristian Micheletti: "SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets", Structure, Elsevier BV, Vol 23, Num 8, pp 1516--1525, 2015, doi:10.1016/j.str.2015.05.022

Saurabh S. Sawant, Burak Korkut, Ozgur Tumuklu, and Deborah A. Levin: "Development of an AMR Octree DSMC Approach for Shock Dominated Flows", American Institute of Aeronautics and Astronautics (AIAA), 53rd AIAA Aerospace Sciences Meeting, Kissimmee, Florida, U.S.A., 2015, doi:10.2514/6.2015-0070

J. Um, and G. M. McFarquhar: "Applicability of Geometric Optics Method for Calculations of Single-Scattering Properties of Atmospheric Ice Crystals", Blue Waters Symposium 2015, 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, Elsevier BV, Vol 165, pp 134--152, 2015, doi:10.1016/j.jqsrt.2015.07.001

D. Ackerman, and B. Ganapathysubramanian: "Parallel Framework for Wormlike Chains Using Self Consistent Field Theory", ASME 2015 Applied Mechanics and Materials Conference, Seattle, Washington, U.S.A., 2015

C. D. Sudheer, and Ashok Srinivasan: "Efficient Barrier Implementation on the POWER8 Processor", Institute of Electrical & Electronics Engineers (IEEE), 2015 IEEE 22nd International Conference on High Performance Computing (HiPC), Bangalore, India, 2015, doi:10.1109/hipc.2015.51

A. Barati Farimani, M. Heiranian, and N. R. Aluru: "Electromechanical Signatures for DNA Sequencing Through a Mechanosensitive Nanopore", J. Phys. Chem. Lett., American Chemical Society (ACS), Vol 6, Num 4, pp 650--657, 2015, doi:10.1021/jz5025417

Jaehyung Yu, Lucas K. Wagner, 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, AIP Publishing, Vol 143, Num 22, pp 224707, 2015, doi:10.1063/1.4937421

Miguel Zilhão, Scott C. Noble, Manuela Campanelli, Yosef Zlochower: "Resolving the Relative Influence of Strong Field Spacetime Dynamics and MHD on Circumbinary Disk Physics", Physical Review D, American Physical Society (APS), Vol 91, Num 2, pp 024034, 2015, doi:10.1103/PhysRevD.91.024034

Yan Y. Liu, Wendy K. Tam Cho, and Shaowen Wang: "A Scalable Computational Approach to Political Redistricting Optimization", ACM Press, Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15, pp 6:1, St Louis, Missouri, U.S.A., 2015, doi:10.1145/2792745.2792751

S. Aseeri, O. Batrasev, M. Icardi, B. Leu, A. Liu, N. Li, B. K. Muite, E. Muller, B. Palen, M. Quell, H. Servat, P. Sheth, M. Van Moer, and J. Vienne: "Solving the Klein-Gordon equation using fourier spectral methods: a benchmark test for computer performance", Society for Computer Simulation International, Proceedings of the Symposium on High Performance Computing, Vol HPC '15, pp 182--191, Alexandria, Virginia, 2015

Jon Calhoun, Marc Snir, Luke Olson, and Maria Garzaran: "Understanding the Propagation of Error Due to a Silent Data Corruption in a Sparse Matrix Vector Multiply", IEEE, 2015 IEEE International Conference on Cluster Computing, pp 541-542, 2015, doi:10.1109/cluster.2015.101

Constantin Schoeler, Rafael C. Bernardi, Klara H. Malinowska, Ellis Durner, Wolfgang Ott, Edward A. Bayer, Klaus Schulten, Michael A. Nash, and Hermann E. Gaub: "Mapping Mechanical Force Propagation Through Biomolecular Complexes", Nano Letters, American Chemical Society (ACS), Vol 15, Num 11, pp 7370--7376, 2015, doi:10.1021/acs.nanolett.5b02727

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, AIP Publishing, Vol 142, Num 23, pp 234702, 2015, doi:10.1063/1.4922491

Lijun Liu: "The Ups and Downs of North America: Evaluating the Role of Mantle Dynamic Topography Since the Mesozoic", Rev. Geophys., Wiley-Blackwell, Vol 53, Num 3, pp 1022--1049, 2015, doi:10.1002/2015rg000489

Kartik P. Iyer, Katepalli R. Sreenivasan, and P. K. Yeung: "Refined Similarity Hypothesis Using Three-Dimensional Local Averages", Physical Review E, American Physical Society (APS), Vol 92, Num 6, pp 063024, 2015, doi:10.1103/physreve.92.063024

Philipp Mösta, Christian D. Ott, David Radice, Luke F. Roberts, Erik Schnetter, and Roland Haas: "A Large-Scale Dynamo and Magnetoturbulence in Rapidly Rotating Core-Collapse Supernovae", Nature, Nature Publishing Group, Vol 528, Num 7582, pp 376--379, 2015, doi:10.1038/nature15755

Celso L. Mendes, Brett Bode, Gregory H. Bauer, Jeremy Enos, Cristina Beldica, and William T. Kramer: "Deployment and Testing of the Sustained Petascale Blue Waters System", Journal of Computational Science, Elsevier BV, Vol 10, pp 327--337, 2015, doi:10.1016/j.jocs.2015.03.007

Robert Sisneros: "A Feature-First Approach to Clustering for Highlighting Regions of Interest in Scientific Data", Procedia Computer Science, Elsevier BV, Vol 51, pp 2207--2216, 2015, doi:10.1016/j.procs.2015.05.497

R. Sisneros: "Visualizing the Big (and Large) Data from an HPC Resource", Astronomical Society of the Pacific, Numerical Modeling of Space Plasma Flows ASTRONUM-2014, Vol 498, pp 240, 2015

M. Gajbe, K. Chadalavada, G. Bauer, W. Kramer: "Benchmarking and Performance Studies of Mapreduce, Hadoop Framework on Blue Waters Supercomputer", presented at WorldComp 2015 - ABDA '15 International Conference on Advances in Big Data Analytics, Las Vegas, Nevada, U.S.A., 2015

Catello Di Martino, William Kramer, Zbigniew Kalbarczyk, and Ravishankar Iyer: "Measuring and Understanding Extreme-Scale Application Resilience: A Field Study of 5,000,000 HPC Application Runs", IEEE, 2015 45th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, pp 25-36, Rio de Janeiro, Brazil, 2015, doi:10.1109/dsn.2015.50

S. Byna, R. Sisneros, K. Chadalavada, Q. Koziol: "Tuning Parallel I/O on Blue Waters for Writing 10 Trillion Particles", presented at CUG 2015, Chicago, Illinois, U.S.A., 2015

M. Giles, S. Koric, and E. Burness: "U. S. Industrial Supercomputing at NCSA", Chapman and Hall/CRC Press, Industrial Applications of High-Performance Computing, pp 179-194, 2015

J. Calhoun, L. Olson, M. Snir, and W.D. Gropp: "Towards a More Fault Resilient Multigrid Solver", Society for Computer Simulation International, Proceedings of the High Performance Computing Symposium (HPC '15), pp 1-8, Alexandria, Virginia, U.S.A., 2015

Peter L. Walters, and Nancy Makri: "Quantum-Classical Path Integral Simulation of Ferrocene-Ferrocenium Charge Transfer in Liquid Hexane", The Journal of Physical Chemistry Letters, American Chemical Society (ACS), Vol 6, Num 24, pp 4959--4965, San Diego, CA, 2015, doi:10.1021/acs.jpclett.5b02265

Xu, X. L. and Hua, J. F. and Wu, Y. P. and Zhang, C. J. and Li, F. and Wan, Y. and Pai, C.-H. and Lu, W. and An, W. and Yu, P. and Hogan, M. J. and Joshi, C. and Mori, W. B.: "Physics of Phase Space Matching for Staging Plasma and Traditional Accelerator Components Using Longitudinally Tailored Plasma Profiles", Physical Review Letters, American Physical Society (APS), Vol 116, Num 12, pp 124801, Richmond, VA, 2015, doi:10.1103/PhysRevLett.116.124801

E. Mathews, K. Wang, M. Wang, and E. J. Jumper: "LES Prediction and Analysis of the Aero-optical Environment Around a 3-D Turret", presented at 68th Annual Meeting of the APS Division of Fluid Dynamics, Boston, Massachusetts, U.S.A., 2015

Eric J. Lentz and Stephen W. Bruenn and W. Raphael Hix and Anthony Mezzacappa and O. E. Bronson Messer and EirikEndeve and John M. Blondin and J. Austin Harris and Pedro Marronetti and Konstantin N. Yakunin: "Three-dimensional Core-collapse Supernova Simulated Using a 15 M ⊙ Progenitor", The Astrophysical Journal Letters, IOP Publishing, Vol 807, Num 2, pp L31, 2015, doi:10.1088/2041-8205/807/2/L31

A. Bazavov, C. Bernard, C. Bouchard, N. Brown, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, E. Gámiz, Steven Gottlieb, U.M. Heller, J. Komijani, A.S. Kronfeld, J. Laiho, L. Levkova, P.B. Mackenzie, C. Monahan, T. Primer, Heechang Na, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint, R.S. Van de Water, and R. Zhou: "Decay Constants fB and fBs from HISQ Simulations", Proceedings of Science, Proceedings, 33rd International Symposium on Lattice Field Theory (Lattice 2015), pp 331, Kobe, Japan, 2015

Thomas Primer, Claude Bernard, Carleton DeTar, Aide El-Khadra, Elvira Gamiz, Javad Komijani, Andreas Kronfeld, James Simone, Doug Toussaint, and Ruth S. Van de Water (Fermilab Lattice and MILC Collaborations): "D-meson Semileptonic Form Factors at Zero Momentum Transfer in (2+1+1)-Flavor Lattice QCD", Proceedings of Science, Proceedings, 33rd International Symposium on Lattice Field Theory (Lattice 2015), pp 338, Kobe, Japan, 2015

Erik Schnetter, Marek Blazewicz, Steven R. Brandt, David M. Koppelman, and Frank Löffler: "Chemora: A PDE-Solving Framework for Modern High-Performance Computing Architectures", Computing in Science & Engineering, Institute of Electrical and Electronics Engineers (IEEE), Vol 17, Num 2, pp 53--64, 2015, doi:10.1109/mcse.2015.2

Blakesley Burkhart, A. Lazarian, D. Balsara, C. Meyer, and J. Cho: "Alfevénic Turbulence Beyond the Ambipolar Diffusion Scale", ApJ, IOP Publishing, Vol 805, Num 2, pp 118, 2015, doi:10.1088/0004-637x/805/2/118

Kristin Muterspaw, Tara Urner, Ruth Lewis, Ivan Babic, Deeksha Srinath, and Charles Peck: "Multidisciplinary Research and Education with Open Tools", ACM Press, Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure (XSEDE '15), pp 22:1--22:8, St. Louis, Missouri, U.S.A., 2015, doi:10.1145/2792745.2792767

P. Eller: "Non-Blocking Preconditioned Conjugate Gradient Methods for Extreme-Scale Computing", IEEE Press, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '16), pp 18:1--18:12, Piscataway, N.J., U.S.A., 2015

K. Jin, S. P. Vanka, and B. G. Thomas: "Three-Dimensional Flow in a Driven Cavity Subjected to an External Magnetic Field", Journal of Fluids Engineering, ASME International, Vol 137, Num 7, pp 071104, 2015, doi:10.1115/1.4029731

A Jones and L.Di Girolamo: "High Accuracy 3D Radiative Transfer in Cloudy Atmospheres", Blue Waters Symposium, Sunriver, OR, 2015

Ariana Minot, and Na Li: "A Fully Distributed State Estimation Using Matrix Splitting Methods", Institute of Electrical & Electronics Engineers (IEEE), 2015 American Control Conference (ACC), pp 2488-2493, Chicago, Illinois, U.S.A., 2015, doi:10.1109/acc.2015.7171105

Ariana Minot, Yue M. Lu, and Na Li: "A Distributed Gauss-Newton Method for Power System State Estimation", IEEE Transactions on Power Systems, Institute of Electrical & Electronics Engineers (IEEE), Vol 31, Num 5, pp 3804-3815, 2015, doi:10.1109/tpwrs.2015.2497330

Vivek Kale: "Low-Overhead Scheduling for Improving Performance of Scientific Applications", Ph.D. Thesis, 2015

2016

Saurabh Jha, Valerio Formicola, Catello Di Martino, Zbigniew Kalbarczyk, William T. Kramer, Ravishankar K. Iyer: "Analysis of Gemini Interconnect Recovery Mechanisms: Methods and Observations", presented at CUG 2016, London, England, U.K., 2016

Phuong Cao, Eric C. Badger, Zbigniew T. Kalbarczyk, and Ravishankar K. Iyer: "A Framework for Generation, Replay, and Analysis of Real-World Attack Variants", Association for Computing Machinery (ACM), Proceedings of the Symposium and Bootcamp on the Science of Security - HotSos '16, pp 28--37, Pittsburgh, Pennsylvania, U.S.A., 2016, doi:10.1145/2898375.2898392

Subho S. Banerjee, Arjun P. Athreya, Liudmila S. Mainzer, C. Victor Jongeneel, Wen-Mei Hwu, Zbigniew T. Kalbarczyk, and Ravishankar K. Iyer: "Efficient and Scalable Workflows for Genomic Analyses", Association for Computing Machinery (ACM), Proceedings of the ACM International Workshop on Data-Intensive Distributed Computing - DIDC '16, pp 27--36, Kyoto, Japan, 2016, doi:10.1145/2912152.2912156

David J. Luitz: "Long Tail Distributions Near the Many-Body Localization Transition", Phys. Rev. B, American Physical Society (APS), Vol 93, Num 13, 2016, doi:10.1103/physrevb.93.134201

F. S. Tsung, R. Lehmberg, and J. Weaver: "Controlling Laser Plasma Interactions with Temporal Bandwidths", presented at the 46th annual Anomalous Absorption Conference, Old Saybrook, Connecticut, U.S.A., 2016

Peicheng Yu, Xinlu Xu, Asher Davidson, Adam Tableman, Thamine Dalichaouch, Fei Li, Michael D. Meyers, Weiming An, Frank S. Tsung, Viktor K. Decyk, Frederico Fiuza, Jorge Vieira, Ricardo A. Fonseca, Wei Lu, Luis O. Silva, and Warren B. Mori: "Enabling Lorentz Boosted Frame Particle-in-Cell Simulations of Laser Wakefield Acceleration in Quasi-3D Geometry", Journal of Computational Physics, Elsevier BV, Vol 316, pp 747--759, 2016, doi:10.1016/j.jcp.2016.04.014

Joshua S. Méndez Harper, and Josef Dufek: "The Effects of Granular Dynamics on the Triboelectric Charging of Volcanic ash: Experiments and Numerical Simulations", presented at the 2016 Electrostatics Joint Conference, West Lafayette, Indiana, U.S.A., 2016

Samuel R. Totorica, Tom Abel, and Frederico Fiuza: "Nonthermal Electron Energization from Magnetic Reconnection in Laser-Driven Plasmas", Phys. Rev. Lett., American Physical Society (APS), Vol 116, Num 9, pp 095003, 2016, doi:10.1103/physrevlett.116.095003

Colin M. Zarzycki, Kevin A. Reed, Julio T. Bacmeister, Anthony P. Craig, Susan C. Bates, and Nan A. Rosenbloom: "Impact of Surface Coupling Grids on Tropical Cyclone Extremes in High-Resolution Atmospheric Simulations", Geoscientific Model Development, Copernicus GmbH, Vol 9, Num 2, pp 779--788, 2016, doi:10.5194/gmd-9-779-2016

Jiashun Hu, Lijun Liu, Armando Hermosillo, and Quan Zhou: "Simulation of Late Cenozoic South American Flat-Slab Subduction Using Geodynamic Models with Data Assimilation", Earth and Planetary Science Letters, Elsevier BV, Vol 438, pp 1--13, 2016, doi:10.1016/j.epsl.2016.01.011

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, Geological Society of America, Vol 128, Num 5-6, pp 973--988, 2016, doi:10.1130/b31431.1

Tiffany Leonard, and Lijun Liu: "The Role of a Mantle Plume in the Formation of Yellowstone Volcanism", Geophys. Res. Lett., Wiley-Blackwell, Vol 43, Num 3, pp 1132--1139, 2016, doi:10.1002/2015gl067131

Gregory M. Laskowski, James Kopriva, Vittorio Michelassi, Sriram Shankaran, Umesh Paliath, Rathakrishnan Bhaskaran, Qiqi Wang, Chaitanya Talnikar, Zhi J. Wang, and Feilin Jia: "Future Directions of High Fidelity CFD for Aerothermal Turbomachinery Analysis and Design", American Institute of Aeronautics and Astronautics (AIAA), 46th AIAA Fluid Dynamics Conference, 2016, doi:10.2514/6.2016-3322

Jason Jaacks, Steven L. Finkelstein, and Kentaro Nagamine: "Connecting the Dots: Tracking Galaxy Evolution Using Constant Cumulative Number Density at 3 ≤ z ≤ 7", ApJ, American Astronomical Society, Vol 817, Num 2, pp 174, 2016, doi:10.3847/0004-637x/817/2/174

Minseung Kim, Navneet Rai, Violeta Zorraquino, and Ilias Tagkopoulos: "Multi-Omics Integration Accurately Predicts Cellular State in Unexplored Conditions for Escherichia Coli", Nature Communications, Springer Nature, Vol 7, pp 13090, 2016, doi:10.1038/ncomms13090

Hatch, Dylan: "Networking Architecture for the Distributed Simulation of Manned and Autonomous Vehicles", Simulation-Based Engineering Lab (SBEL) Technical Reports, University of Wisconsin-Madison, Num TR-2016-06, 2016

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., Oxford University Press (OUP), Vol 205, Num 3, pp 1342--1364, 2016, doi:10.1093/gji/ggw085

John M. A. Grime, James F. Dama, Barbie K. Ganser-Pornillos, Cora L. Woodward, Grant J. Jensen, Mark Yeager, and Gregory A. Voth: "Coarse-Grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly", Nature Communications, Springer Nature, Vol 7, pp 11568, 2016, doi:10.1038/ncomms11568

Christina Bergonzo, Kathleen B. Hall, and Thomas E. Cheatham: "Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics", J. Chem. Theory Comput., American Chemical Society (ACS), Vol 12, Num 7, pp 3382--3389, 2016, doi:10.1021/acs.jctc.6b00173

James T. Waters, Xiang-Jun Lu, Rodrigo Galindo-Murillo, James C. Gumbart, Harold D. Kim, Thomas E. Cheatham, and Stephen C. Harvey: "Transitions of Double-Stranded DNA Between the A- and B-Forms", The Journal of Physical Chemistry B, American Chemical Society (ACS), 2016, doi:10.1021/acs.jpcb.6b02155

Lucía Álvarez, Ariel Lewis-Ballester, Adrián Roitberg, Darío A. Estrin, Syun-Ru Yeh, Marcelo A. Marti, and Luciana Capece: "Structural Study of a Flexible Active Site Loop in Human Indoleamine 2, 3-Dioxygenase and Its Functional Implications", Biochemistry, American Chemical Society (ACS), Vol 55, Num 19, pp 2785--2793, 2016, doi:10.1021/acs.biochem.6b00077

Rodrigo Galindo-Murillo, Darrell R. Davis, and Thomas E. Cheatham: "Probing the Influence of Hypermodified Residues Within the tRNA3Lys Anticodon Stem Loop Interacting with the A-Loop Primer Sequence from HIV-1", Biochimica et Biophysica Acta (BBA) - General Subjects, Elsevier BV, Vol 1860, Num 3, pp 607--617, 2016, doi:10.1016/j.bbagen.2015.11.009

Galindo-Murillo, Rodrigo and Robertson, James C. and Zgarbová, Marie and Šponer, Jiří and Otyepka, Michal and Jurečka, Petr and Cheatham, Thomas E.: "Assessing the Current State of Amber Force Field Modifications for DNA", Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 12, Num 8, pp 4114-4127, 2016, doi:10.1021/acs.jctc.6b00186

Sheel C. Dodani, Gert Kiss, Jackson K. B. Cahn, Ye Su, Vijay S. Pande, and Frances H. Arnold: "Discovery of a Regioselectivity Switch in Nitrating P450s Guided by Molecular Dynamics Simulations and Markov Models", Nature Chemistry, Nature Publishing Group, Vol 8, Num 5, pp 419--425, 2016, doi:10.1038/nchem.2474

James Charles, Prasad Sarangapani, Roksana Golizadeh-Mojarad, Robert Andrawis, Daniel Lemus, Xinchen Guo, Daniel Mejia, James E. Fonseca, Michael Povolotskyi, Tillmann Kubis, and Gerhard Klimeck: "Incoherent Transport in NEMO5: Realistic and Efficient Scattering on Phonons", J Comput Electron, Springer Nature, 2016, doi:10.1007/s10825-016-0845-y

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A. Bazavov, C. Bernard, N. Brown, J. Komijani, C. DeTar, J. Foley, L. Levkova, Steven Gottlieb, U.M. Heller, J. Laiho, R.L. Sugar, D. Toussaint, and R.S. Van de Water: "Gradient Flow and Scale Setting on MILC HISQ Ensembles", Physical Review D, American Physical Society (APS), Vol 93, Num 9, 2016, doi:10.1103/physrevd.93.094510

Kai Germaschewski, William Fox, Stephen Abbott, Narges Ahmadi, Kristofor Maynard, Liang Wang, Hartmut Ruhl, and Amitava Bhattacharjee: "The Plasma Simulation Code: A Modern Particle-in-Cell Code with Patch-Based Load-Balancing", Journal of Computational Physics, Elsevier BV, Vol 318, pp 305--326, 2016, doi:10.1016/j.jcp.2016.05.013

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Chuang Liu, Juan R. Perilla, Jiying Ning, Manman Lu, Guangjin Hou, Ruben Ramalho, Benjamin A. Himes, Gongpu Zhao, Gregory J. Bedwell, In-Ja Byeon, Jinwoo Ahn, Angela M. Gronenborn, Peter E. Prevelige, Itay Rousso, Christopher Aiken, Tatyana Polenova, Klau: "Cyclophilin a Stabilizes the HIV-1 Capsid Through a Novel Non-Canonical Binding Site", Nature Communications, Nature Publishing Group, Vol 7, pp 10714, 2016, doi:10.1038/ncomms10714

John E. Stone and Melih Sener and Kirby L. Vandivort and Angela Barragan and Abhishek Singharoy and Ivan Teo and João V. Ribeiro and Barry Isralewitz and Bo Liu and Boon Chong Goh and James C. Phillips and Craig MacGregor-Chatwin and Matthew P. Johnson and Lena F. Kourkoutis and C. Neil Hunter and Klaus Schulten: "Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing", Parallel Computing, Elsevier BV, Vol 55, pp 17--27, 2016, doi:10.1016/j.parco.2015.10.015

E. J. Zirnstein, J. Heerikhuisen, H. O. Funsten, G. Livadiotis, D. J. McComas, and N. V. Pogorelov: "Local Interstellar Magnetic Field Determined from the Interstellar Boundary Explorer Ribbon", ApJ, American Astronomical Society, Vol 818, Num 1, pp L18, 2016, doi:10.3847/2041-8205/818/1/l18

N. V. Pogorelov: "The Heliotail: Theory and Modeling", J. Phys.: Conf. Ser., IOP Publishing, Vol 719, pp 012013, 2016, doi:10.1088/1742-6596/719/1/012013

P. Forai, G. Peretti-Pezzi, B. Bode, K. Hoste: "Making Scientific Software Installation Reproducible on Cray Systems Using EasyBuild", presented at CUG 2016, London, England, U.K., 2016

Stephen W. Bruenn and Eric J. Lentz and W. Raphael Hix and Anthony Mezzacappa and J. Austin Harris and O. E. BronsonMesser and Eirik Endeve and John M. Blondin and Merek Austin Chertkow and Eric J. Lingerfelt and PedroMarronetti and Konstantin N. Yakunin: "The Development of Explosions in Axisymmetric Ab Initio Core-collapse Supernova Simulations of 12-25 M ⊙ Stars", The Astrophysical Journal, IOP Publishing, Vol 818, Num 2, pp 123, 2016, doi:10.3847/0004-637X/818/2/123

Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha: "Direct Evidence for Sequence-Dependent Attraction Between Double-Stranded DNA Controlled by Methylation", Nature Communications, Springer Nature, Vol 7, pp 11045, 2016, doi:10.1038/ncomms11045

Jejoong Yoo, James Wilson, and Aleksei Aksimentiev: "Improved Model of Hydrated Calcium Ion for Molecular Dynamics Simulations Using Classical Biomolecular Force Fields", Biopolymers, Wiley-Blackwell, Vol 105, Num 10, pp 752--763, 2016, doi:10.1002/bip.22868

Abhilash Harpale, Marco Panesi, and Huck Beng Chew: "Plasma-Graphene Interaction and Its Effects on Nanoscale Patterning", Phys. Rev. B, American Physical Society (APS), Vol 93, Num 3, 2016, doi:10.1103/physrevb.93.035416

Yongyang Cai, Timothy M. Lenton, and Thomas S. Lontzek: "Risk of Multiple Interacting Tipping Points Should Encourage Rapid CO2 Emission Reduction", Nature Climate Change, Nature Publishing Group, Vol 6, Num 5, pp 520--525, 2016, doi:10.1038/nclimate2964

J. Kwack, G. H Bauer, and S. Koric: "Performance Test of Parallel Linear Equation Solvers on Blue Waters – Cray XE6/XK7 system", presented at CUG 2016, London, England, U.K., 2016

R. I. Barabash, V. Agarwal, S. Koric, I. Jasiuk, and J. Z. Tischler: "Finite Element Simulation and X-Ray Microdiffraction Study of Strain Partitioning in a Layered Nanocomposite", Journal of Crystallography, Hindawi Publishing Corporation, Vol 2016, pp 1--11, 2016, doi:10.1155/2016/4351347

Seid Koric, and Anshul Gupta: "Sparse Matrix Factorization in the Implicit Finite Element Method on Petascale Architecture", Computer Methods in Applied Mechanics and Engineering, Elsevier BV, Vol 302, pp 281--292, 2016, doi:10.1016/j.cma.2016.01.011

Vladimir Puzyrev, Seid Koric, and Scott Wilkin: "Evaluation of Parallel Direct Sparse Linear Solvers in Electromagnetic Geophysical Problems", Computers & Geosciences, Elsevier BV, Vol 89, pp 79--87, 2016, doi:10.1016/j.cageo.2016.01.009

Milton Ruiz, Ryan N. Lang, Vasileios Paschalidis, and Stuart L. Shapiro: "Binary Neutron Star Mergers: A Jet Engine for Short Gamma-Ray Burst", ApJ, American Astronomical Society, Vol 824, Num 1, pp L6, 2016, doi:10.3847/2041-8205/824/1/l6

Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev: "De Novo Reconstruction of DNA Origami Structures Through Atomistic Molecular Dynamics Simulation", Nucleic Acids Res, Oxford University Press (OUP), Vol 44, Num 7, pp 3013--3019, 2016, doi:10.1093/nar/gkw155

Tyler M. Earnest, John A. Cole, Joseph R. Peterson, Michael J. Hallock, Thomas E. Kuhlman, and Zaida Luthey-Schulten: "Ribosome Biogenesis in Replicating Cells: Integration of Experiment and Theory", Biopolymers, Wiley-Blackwell, Vol 105, Num 10, pp 735, 2016, doi:10.1002/bip.22892

Dacen Waters, Stephen M. Wilkins, Tiziana Di Matteo, Yu Feng, Rupert Croft, and Daisuke Nagai: "Monsters in the Dark: Predictions for Luminous Galaxies in the Early Universe from the BlueTides Simulation", Monthly Notices of the Royal Astronomical Society: Letters, Oxford University Press (OUP), Vol 461, Num 1, pp L51--L55, 2016, doi:10.1093/mnrasl/slw100

Stephen M. Wilkins, Yu Feng, Tiziana Di Matteo, Rupert Croft, Elizabeth R. Stanway, Andrew Bunker, Dacen Waters, and Christopher Lovell: "The Photometric Properties of Galaxies in the Early Universe", Mon. Not. R. Astron. Soc., Oxford University Press (OUP), Vol 460, Num 3, pp 3170--3178, 2016, doi:10.1093/mnras/stw1154

Stephen M. Wilkins, Yu Feng, Tiziana Di Matteo, Rupert Croft, Elizabeth R. Stanway, Rychard J. Bouwens, and Peter Thomas: "The Lyman-Continuum Photon Production Efficiency in the High-Redshift Universe", Monthly Notices of the Royal Astronomical Society: Letters, Oxford University Press (OUP), Vol 458, Num 1, pp L6--L9, 2016, doi:10.1093/mnrasl/slw007

Leigh Orf, Robert Wilhelmson, Bruce Lee, Cathy Finley, and Adam Houston: "Evolution of a Long-Track Violent Tornado Within a Simulated Supercell", Bulletin of the American Meteorological Society, American Meteorological Society, Vol 98, Num 1, pp 45, 2016, doi:10.1175/bams-d-15-00073.1

Kai Jin, Surya P. Vanka, Brian G. Thomas, and Xiaoming Ruan: "Large Eddy Simulations of the Effects of Double-Ruler Electromagnetic Braking and Nozzle Submergence Depth on Molten Steel Flow in a Commercial Continuous Casting Mold", Wiley-Blackwell, CFD Modeling and Simulation in Materials Processing 2016, pp 159--166, 2016, doi:10.1002/9781119274681.ch20

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, AIP Publishing, Vol 144, Num 20, pp 204503, 2016, doi:10.1063/1.4951687

S. Hirata, K. Gilliard, X. He, M. Keçeli, J. Li, M. A. Salim, O. Sode, and K. Yagi: "Ab Initio Ice, Dry Ice, and Liquid Water", Wiley, Chichester, Fragmentation: Toward Accurate Calculations on Complex Molecular Systems, 2016

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., American Chemical Society (ACS), Vol 7, Num 4, pp 680--684, 2016, doi:10.1021/acs.jpclett.5b02430

Puja Goyal, Christine A. Schwerdtfeger, Alexander V. Soudackov, and Sharon Hammes-Schiffer: "Proton Quantization and Vibrational Relaxation in Nonadiabatic Dynamics of Photoinduced Proton-Coupled Electron Transfer in a Solvated Phenol-Amine Complex", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 120, Num 9, pp 2407--2417, 2016, doi:10.1021/acs.jpcb.5b12015

Carlo Pierleoni, Miguel A. Morales, Giovanni Rillo, Markus Holzmann, and David M. Ceperley: "Liquid-Liquid Phase Transition in Hydrogen by Coupled Electron-Ion Monte Carlo Simulations", Proceedings of the National Academy of Sciences, National Academy of Sciences, Vol 113, Num 18, pp 4953--4957, 2016, doi:10.1073/pnas.1603853113

Yashar D. Hezaveh and Neal Dalal and Daniel P. Marrone and Yao-Yuan Mao and Warren Morningstar and Di Wen and Roger D.Blandford and John E. Carlstrom and Christopher D. Fassnacht and Gilbert P. Holder and Athol Kemball and Philip J.Marshall and Norman Murray and Laurence Perreault Levasseur and Joaquin D. Vieira and Risa H. Wechsler: "Detection of Lensing Substructure Using Alma Observations of the Dusty Galaxy SDP.81", ApJ, American Astronomical Society, Vol 823, Num 1, pp 37, 2016, doi:10.3847/0004-637x/823/1/37

A Sharma, P Conry, H J S Fernando, Alan F Hamlet, J J Hellmann, and F Chen: "Green and Cool Roofs to Mitigate Urban Heat Island Effects in the Chicago Metropolitan Area: Evaluation with a Regional Climate Model", Environ. Res. Lett., IOP Publishing, Vol 11, Num 6, pp 064004, 2016, doi:10.1088/1748-9326/11/6/064004

Ashish Sharma, Harindra J.S. Fernando, Alan F. Hamlet, Jessica J. Hellmann, Michael Barlage, and Fei Chen: "Urban Meteorological Modeling Using WRF: A Sensitivity Study", International Journal of Climatology, Wiley-Blackwell, 2016, doi:10.1002/joc.4819

Dinshaw S. Balsara, Takanobu Amano, Sudip Garain, and Jinho Kim: "A High-Order Relativistic Two-Fluid Electrodynamic Scheme with Consistent Reconstruction of Electromagnetic Fields and a Multidimensional Riemann Solver for Electromagnetism", Journal of Computational Physics, Elsevier BV, Vol 318, pp 169--200, 2016, doi:10.1016/j.jcp.2016.05.006

Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper: "LES of an Aero-Optical Turret Flow at High Reynolds Number", American Institute of Aeronautics and Astronautics (AIAA), 54th AIAA Aerospace Sciences Meeting, San Diego, California, U.S.A., 2016, doi:10.2514/6.2016-1461

David Radice, Christian D. Ott, Ernazar Abdikamalov, Sean M. Couch, Roland Haas, and Erik Schnetter: "Neutrino-Driven Convection in Core-Collapse Supernovae: High-Resolution Simulations", ApJ, American Astronomical Society, Vol 820, Num 1, pp 76, 2016, doi:10.3847/0004-637x/820/1/76

David Radice, Filippo Galeazzi, Jonas Lippuner, Luke F. Roberts, Christian D. Ott, and Luciano Rezzolla: "Dynamical Mass Ejection from Binary Neutron Star Mergers", Mon. Not. R. Astron. Soc., Oxford University Press (OUP), Vol 460, Num 3, pp 3255--3271, 2016, doi:10.1093/mnras/stw1227

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

Alireza Samimi, and Jamesina Simpson: "Parallelization of 3-D Global FDTD Earth-Ionosphere Waveguide Models at Resolutions on the Order of ~1 Km and Higher", Antennas Wirel. Propag. Lett., Institute of Electrical & Electronics Engineers (IEEE), pp 1959 - 1962, 2016, doi:10.1109/lawp.2016.2545526

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, American Chemical Society (ACS), 2016, doi:10.1021/acs.jpcb.6b01327

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", presented at International Symposium on Radiation 2016, Auckland, New Zealand, 2016

J. Um, and G. M. McFarquhar: "Light Scattering by Atmospheric Ice Crystals: Application to Forward Scattering Probes", presented at International Symposium on Radiation 2016, Auckland, New Zealand, 2016

Amir Barati Farimani, Narayana R. Aluru, Emad Tajkhorshid, and Eric Jakobsson: "Computational Approach to Designing Antibody for Ebola Virus", Biophysical Journal, Elsevier BV, Vol 110, Num 3, pp 537a, 2016, doi:10.1016/j.bpj.2015.11.2877

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, Wiley-Blackwell, Vol 121, Num 1, pp 586--601, 2016, doi:10.1002/2015jc011226

Diwakar Shukla, Ariana Peck, and Vijay S. Pande: "Conformational Heterogeneity of the Calmodulin Binding Interface", Nature Communications, Nature Publishing Group, Vol 7, pp 10910, 2016, doi:10.1038/ncomms10910

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

Nam-Phuong Nguyen, Tandy Warnow, Mihai Pop, and Bryan White: "A Perspective on 16S rRNA Operational Taxonomic Unit Clustering Using Sequence Similarity", npj Biofilms and Microbiomes, Nature Publishing Group, Vol 2, pp 16004, 2016, doi:10.1038/npjbiofilms.2016.4

K. Jin, P. Kumar, S. P. Vanka, and B. G. Thomas: "Rise of an Argon Bubble in Liquid Steel in the Presence of a Transverse Magnetic Field", Physics of Fluids, AIP Publishing, Vol 28, Num 9, pp 093301, 2016, doi:10.1063/1.4961561

Kai Jin, Surya P. Vanka, and Brian G. Thomas: "Large Eddy Simulations of the Effects of EMBr and SEN Submergence Depth on Turbulent Flow in the Mold Region of a Steel Caster", Metallurgical and Materials Transactions B, Springer Nature, Vol 48, Num 1, pp 162--178, 2016, doi:10.1007/s11663-016-0801-z

Brian M. Sandroff, Curtis L. Johnson, and Robert W. Motl: "Exercise Training Effects on Memory and Hippocampal Viscoelasticity in Multiple Sclerosis: A Novel Application of Magnetic Resonance Elastography", Neuroradiology, Springer Nature, Vol 59, Num 1, pp 61--67, 2016, doi:10.1007/s00234-016-1767-x

Marianne J Bezaire, Ivan Raikov, Kelly Burk, Dhrumil Vyas, and Ivan Soltesz: "Interneuronal Mechanisms of Hippocampal Theta Oscillations in a Full-Scale Model of the Rodent CA1 Circuit", eLife, eLife Sciences Organisation, Ltd., Vol 5, 2016, doi:10.7554/elife.18566

Kerstin Göpfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser: "Large-Conductance Transmembrane Porin Made from DNA Origami", ACS Nano, American Chemical Society (ACS), Vol 10, Num 9, pp 8207--8214, 2016, doi:10.1021/acsnano.6b03759

Kalyan Immadisetty, Jeevapani Hettige, and Mahmoud Moradi: "What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT?", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 15, pp 3644--3656, 2016, doi:10.1021/acs.jpcb.6b09733

Cole M. Johnson, Alexander E. Doran, Jinmei Zhang, Edward F. Valeev, and So Hirata: "Monte Carlo Explicitly Correlated Second-Order Many-Body Perturbation Theory", The Journal of Chemical Physics, AIP Publishing, Vol 145, Num 15, pp 154115, 2016, doi:10.1063/1.4964854

Yan Y. Liu, Wendy K. Tam Cho, and Shaowen Wang: "PEAR: A Massively Parallel Evolutionary Computation Approach for Political Redistricting Optimization and Analysis", Swarm and Evolutionary Computation, Elsevier BV, Vol 30, pp 78--92, 2016, doi:10.1016/j.swevo.2016.04.004

A. Perez, J. A. Morrone, E. Brini, J. L. MacCallum, and K. A. Dill: "Blind Protein Structure Prediction Using Accelerated Free-Energy Simulations", Science Advances, American Association for the Advancement of Science (AAAS), Vol 2, Num 11, pp e1601274--e1601274, 2016, doi:10.1126/sciadv.1601274

T. Dytrych, P. Maris, K.D. Launey, J.P. Draayer, J.P. Vary, D. Langr, E. Saule, M.A. Caprio, U. Catalyurek, and M. Sosonkina: "Efficacy of the SU(3) Scheme for Ab Initio Large-Scale Calculations Beyond the Lightest Nuclei", Computer Physics Communications, Elsevier BV, Vol 207, pp 202--210, 2016, doi:10.1016/j.cpc.2016.06.006

Hui Li, and Ryan L. Sriver: "Effects of Ocean Grid Resolution on Tropical Cyclone-Induced Upper Ocean Responses Using a Global Ocean General Circulation Model", Journal of Geophysical Research: Oceans, Wiley-Blackwell, Vol 121, Num 11, pp 8305--8319, 2016, doi:10.1002/2016jc011951

Som Dutta, Paul Fischer, and Marcelo Garcia: "Large Eddy Simulation (LES) of Flow and Bedload Transport at an Idealized 90-Degree Diversion: Insight Into Bulle-Effect", CRC Press, River Flow 2016, pp 101-109, 2016, doi:10.1201/9781315644479-20

L. Liu, and D. Hasterok: "High-Resolution Lithosphere Viscosity and Dynamics Revealed by Magnetotelluric Imaging", Science, American Association for the Advancement of Science (AAAS), Vol 353, Num 6307, pp 1515--1519, 2016, doi:10.1126/science.aaf6542

Sirish Namilae, Ashok Srinivasan, C.D. Sudheer, Anuj Mubayi, Robert Pahle, and Mathew Scotch: "Self-Propelled Pedestrian Dynamics Model for Studying Infectious Disease Propagation During Air-Travel", Journal of Transport & Health, Elsevier BV, Vol 3, Num 2, pp S40, 2016, doi:10.1016/j.jth.2016.05.090

Xiongjie Yu, David J. Luitz, and Bryan K. Clark: "Bimodal Entanglement Entropy Distribution in the Many-Body Localization Transition", Physical Review B, American Physical Society (APS), Vol 94, Num 18, pp 184202, 2016, doi:10.1103/physrevb.94.184202

David J. Luitz, and Yevgeny Bar Lev: "Anomalous Thermalization in Ergodic Systems", Physical Review Letters, American Physical Society (APS), Vol 117, Num 17, pp 170404, 2016, doi:10.1103/physrevlett.117.170404

Ketan Date, and Rakesh Nagi: "GPU-Accelerated Hungarian Algorithms for the Linear Assignment Problem", Parallel Computing, Elsevier BV, Vol 57, Num C, pp 52, 2016, doi:10.1016/j.parco.2016.05.012

Yoo, Jejoong and Aksimentiev, Aleksei: "The structure and intermolecular forces of DNA condensates", Nucleic Acids Research, Oxford University Press, Vol 44, Num 5, pp 2036, 2016, doi:10.1093/nar/gkw081

Thuy T. M. Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei Aksimentiev, and Taekjip Ha: "Effects of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability", Nature Communications, Springer Nature, Vol 7, pp 10813, 2016, doi:10.1038/ncomms10813

Jejoong Yoo, and Aleksei Aksimentiev: "Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields", Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 12, Num 1, pp 430--443, 2016, doi:10.1021/acs.jctc.5b00967

Carson, Spencer and Wilson, James and Aksimentiev, Aleksei and Weigele, Peter R. and Wanunu, Meni: "Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA", Nucleic Acids Research, Oxford University Press, Vol 44, Num 5, pp 2085, 2016, doi:10.1093/nar/gkv1199

S. Slone, J. Yoo, C.-Y. Li, and A. Aksimentiev: "Molecular Mechanics of DNA Bricks: In Situ Structure, Mechanical Properties and Ionic Conductivity", New Journal of Physics, IOP Publishing Ltd and Deutsche Physikalische Gesellschaft, Vol 18, Num 5, pp 055012, 2016

Maxim Belkin, and Aleksei Aksimentiev: "Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores", ACS Applied Materials & Interfaces, American Chemical Society (ACS), Vol 8, Num 20, pp 12599--12608, 2016, doi:10.1021/acsami.6b00463

Sergii Pud, Shu-Han Chao, Maxim Belkin, Daniel Verschueren, Teun Huijben, Casper van Engelenburg, Cees Dekker, and Aleksei Aksimentiev: "Mechanical Trapping of DNA in a Double-Nanopore System", Nano Letters, American Chemical Society (ACS), Vol 16, Num 12, pp 8021--8028, 2016, doi:10.1021/acs.nanolett.6b04642

Krishna Kumar, Hitesh J. Changlani, Bryan K. Clark, and Eduardo Fradkin: "Numerical Evidence for a Chiral Spin Liquid in the XXZ Antiferromagnetic Heisenberg Model on the Kagome Lattice Atm=23magnetization", Physical Review B, American Physical Society (APS), Vol 94, Num 13, pp 134410, 2016, doi:10.1103/physrevb.94.134410

Amanda Bienz, Robert D. Falgout, William Gropp, Luke N. Olson, and Jacob B. Schroder: "Reducing Parallel Communication in Algebraic Multigrid Through Sparsification", SIAM Journal on Scientific Computing, Society for Industrial & Applied Mathematics (SIAM), Vol 38, Num 5, pp S332--S357, 2016, doi:10.1137/15m1026341

Guangyu Zhao, Larry Di Girolamo, David J. Diner, Carol J. Bruegge, Kevin J. Mueller, and Dong L. Wu: "Regional Changes in Earth's Color and Texture as Observed from Space Over a 15-Year Period", IEEE Transactions on Geoscience and Remote Sensing, Institute of Electrical and Electronics Engineers (IEEE), Vol 54, Num 7, pp 4240--4249, 2016, doi:10.1109/tgrs.2016.2538723

Tanner Culpitt, Kurt R. Brorsen, Michael V. Pak, and Sharon Hammes-Schiffer: "Multicomponent Density Functional Theory Embedding Formulation", The Journal of Chemical Physics, AIP Publishing, Vol 145, Num 4, pp 044106, 2016, doi:10.1063/1.4958952

Kristina D. Launey, Tomas Dytrych, and Jerry P. Draayer: "Symmetry-Guided Large-Scale Shell-Model Theory", Progress in Particle and Nuclear Physics, Elsevier BV, Vol 89, pp 101--136, 2016, doi:10.1016/j.ppnp.2016.02.001

Jiashun Hu, and Lijun Liu: "Abnormal Seismological and Magmatic Processes Controlled by the Tearing South American Flat Slabs", Earth and Planetary Science Letters, Elsevier BV, Vol 450, pp 40--51, 2016, doi:10.1016/j.epsl.2016.06.019

Leigh Orf, Robert Wilhelmson, and Louis Wicker: "A Numerical Simulation of a Long-Track EF5 Tornado Embedded Within a Supercell", presented at the American Meteorological Society Special Symposium on Severe Local Storms: The Current State of the Science and Understanding Impacts, Atlanta, Georgia, U.S.A., 2016

T. K. Kim and N. V. Pogorelov and G. P. Zank and H. A. Elliott and D. J. McComas: "Modeling the Solar Wind at the Ulysses, Voyager, and New Horizons Spacecraft", The Astrophysical Journal, The American Astronomical Society, Vol 832, Num 1, pp 72, 2016, doi:10.3847/0004-637X/832/1/72

Jacob Heerikhuisen and Konstantin V. Gamayunov and Eric J. Zirnstein and Nikolai V. Pogorelov: "Neutral Atom Properties in the Direction of the IBEX Ribbon", The Astrophysical Journal, The American Astronomical Society, Vol 831, Num 2, pp 137, 2016, doi:10.3847/0004-637X/831/2/137

N. V. Pogorelov and M. C. Bedford and I. A. Kryukov and G. P. Zank: "Pickup Ion Effect of the Solar Wind Interaction with the Local Interstellar Medium", Journal of Physics: Conference Series, IOP Publishing Ltd, Vol 767, Num 1, pp 012020, 2016, doi:10.1088/1742-6596/767/1/012020

Luke F. Roberts, Christian D. Ott, Roland Haas, Evan P. O'Connor, Peter Diener, and Erik Schnetter: "General Relativistic Three-Dimensional Multi-Group Neutrino Radiation-Hydrodynamics Simulations of Core-Collapse Supernovae", The Astrophysical Journal, The American Astronomical Society, Vol 831, Num 1, pp 98, 2016, doi:10.3847/0004-637X/831/1/98

Viktoriya Morozova and Anthony L. Piro and Mathieu Renzo and Christian D. Ott: "Numerical Modeling of the Early Light Curves of Type IIP Supernovae", The Astrophysical Journal, The American Astronomical Society, Vol 829, Num 2, pp 109, 2016, doi:10.3847/0004-637X/829/2/109

Christian D. Ott: "Massive Computation for Understanding Core-Collapse Supernova Explosions", Computing in Science & Engineering, Institute of Electrical and Electronics Engineers (IEEE), Vol 18, Num 5, pp 78--92, 2016, doi:10.1109/mcse.2016.81

Shuai Zhang, Kevin P. Driver, François Soubiran, and Burkhard Militzer: "Path Integral Monte Carlo Simulations of Warm Dense Sodium", High Energy Density Physics, Elsevier BV, Vol 21, pp 16--19, 2016, doi:10.1016/j.hedp.2016.09.004

S. X. Hu, B. Militzer, L. A. Collins, K. P. Driver, and J. D. Kress: "First-Principles Prediction of the Softening of the Silicon Shock Hugoniot Curve", Physical Review B, American Physical Society (APS), Vol 94, Num 9, pp 094109, 2016, doi:10.1103/physrevb.94.094109

Ashraf Idkaidek, and Iwona Jasiuk: "Cortical Bone Fracture Analysis Using XFEM - Case Study", International Journal for Numerical Methods in Biomedical Engineering, Wiley-Blackwell, Vol 33, Num 4, pp e2809, 2016, doi:10.1002/cnm.2809

Scott Lathrop: "A Call to Action to Prepare the High-Performance Computing Workforce", Computing in Science & Engineering, Institute of Electrical and Electronics Engineers (IEEE), Vol 18, Num 6, pp 80--83, 2016, doi:10.1109/mcse.2016.101

JaeHyuk Kwack, Soonpil Kang, Geetha Bhat, and Arif Masud: "Time-Dependent Outflow Boundary Conditions for Blood Flow in the Arterial System", Springer International Publishing, Advances in Computational Fluid-Structure Interaction and Flow Simulation, pp 359--377, 2016, doi:10.1007/978-3-319-40827-9_28

Matthieu Dorier, Gabriel Antoniu, Franck Cappello, Marc Snir, Robert Sisneros, Orcun Yildiz, Shadi Ibrahim, Tom Peterka, and Leigh Orf: "Damaris: Addressing Performance Variability in Data Management for Post-Petascale Simulations", ACM Transactions on Parallel Computing, Association for Computing Machinery (ACM), Vol 3, Num 3, pp 15:1--15:43, 2016, doi:10.1145/2987371

JaeHyuk Kwack, Arif Masud, and K. R. Rajagopal: "Stabilized Mixed Three-Field Formulation for a Generalized Incompressible Oldroyd-B Model", International Journal for Numerical Methods in Fluids, Wiley-Blackwell, Vol 83, Num 9, pp 704--734, 2016, doi:10.1002/fld.4287

John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten: "High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL", IEEE, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp 1014-1023, 2016, doi:10.1109/ipdpsw.2016.127

Robert Sisneros, and David Pugmire: "Tuned to Terrible: A Study of Parallel Particle Advection State of the Practice", IEEE, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp 1058-1067, 2016, doi:10.1109/ipdpsw.2016.173

Matthieu Dorier, Robert Sisneros, Leonardo Bautista Gomez, Tom Peterka, Leigh Orf, Lokman Rahmani, Gabriel Antoniu, and Luc Bouge: "Adaptive Performance-Constrained in Situ Visualization of Atmospheric Simulations", IEEE, 2016 IEEE International Conference on Cluster Computing (CLUSTER), pp 269-278, Taipei, Taiwan, 2016, doi:10.1109/cluster.2016.25

Julio T. Bacmeister, Kevin A. Reed, Cecile Hannay, Peter Lawrence, Susan Bates, John E. Truesdale, Nan Rosenbloom, and Michael Levy: "Projected Changes in Tropical Cyclone Activity Under Future Warming Scenarios Using a High-Resolution Climate Model", Climatic Change, Springer Nature, 2016, doi:10.1007/s10584-016-1750-x

Nancy Makri: "Blip-Summed Quantum-Classical Path Integral with Cumulative Quantum Memory", Faraday Discussions, Royal Society of Chemistry (RSC), Vol 195, pp 81--92, 2016, doi:10.1039/c6fd00142d

Michael Nute, and Tandy Warnow: "Scaling Statistical Multiple Sequence Alignment to Large Datasets", BMC Genomics, Springer Nature, Vol 17, Num S10, pp 764, 2016, doi:10.1186/s12864-016-3101-8

Nam-phuong Nguyen, Michael Nute, Siavash Mirarab, and Tandy Warnow: "HIPPI: Highly Accurate Protein Family Classification with Ensembles of HMMs", BMC Genomics, Springer Nature, Vol 17, Num S10, pp 765, 2016, doi:10.1186/s12864-016-3097-0

Dacen Waters, Tiziana Di Matteo, Yu Feng, Stephen M. Wilkins, and Rupert A.C. Croft: "Forecasts for the WFIRST High Latitude Survey using the BlueTides Simulation", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 463, Num 4, pp 3520-3530, 2016, doi:10.1093/mnras/stw2000

John D Lueck, Adam L Mackey, Daniel T Infield, Jason D Galpin, Jing Li, Benoît Roux, and Christopher A Ahern: "Atomic Mutagenesis in Ion Channels with Engineered Stoichiometry", eLife, eLife Sciences Organisation, Ltd., Vol 5, 2016, doi:10.7554/elife.18976

Pei-Hung Lin, and Paul R. Woodward: "Transforming the Multifluid PPM Algorithm to Run on GPUs", Journal of Parallel and Distributed Computing, Elsevier BV, Vol 93-94, pp 56--65, 2016, doi:10.1016/j.jpdc.2016.04.005

Seong-Mook Cho, Brian G. Thomas, and Seon-Hyo Kim: "Transient Two-Phase Flow in Slide-Gate Nozzle and Mold of Continuous Steel Slab Casting with and Without Double-Ruler Electro-Magnetic Braking", Metallurgical and Materials Transactions B, Springer Nature, Vol 47, Num 5, pp 3080--3098, 2016, doi:10.1007/s11663-016-0752-4

Cho, Seong Mook and Thomas, Brian G. and Lee, Hyoung Jun and Kim, Seon Hyo: "Effect of nozzle port angle on mold surface flow in steel slab casting", Association for Iron and Steel Technology, AISTECH, AISTech 2016 - Proceedings of the Iron and Steel Technology Conference, Vol 3, pp 2651--2662, 2016

T. Primer, A. Bazavov, C. Bernard, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, E. Gamiz, S. Gottlieb, U.M. Heller, J. Komijani, A.S. Kronfeld, J. Laiho, P.B. Mackenzie, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint, R.S. Van de Water, R. Zhou and Fermilab Lattice and MILC Collaborations: "D meson semileptonic form factors with HISQ valence and sea quarks", Proceedings of Science, Proceedings, 34th International Symposium on Lattice Field Theory (Lattice 2016), pp 305, Southhampton, England, U.K., 2016

Paul R. Eller, and William Gropp: "Scalable Non-Blocking Preconditioned Conjugate Gradient Methods", IEEE, SC16: International Conference for High Performance Computing, Networking, Storage and Analysis, pp 204-215, 2016, doi:10.1109/sc.2016.17

William Gropp, Luke N. Olson, and Philipp Samfass: "Modeling MPI Communication Performance on SMP Nodes: Is it Time to Retire the Ping Pong Test?", ACM Press, Proceedings of the 23rd European MPI Users' Group Meeting on - EuroMPI 2016, pp 41-50, 2016, doi:10.1145/2966884.2966919

João V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C. Phillips, Peter L. Freddolino & Klaus Schulten: "QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts", Scientific Reports, Springer Nature, Vol 6, Num 1, 2016, doi:10.1038/srep26536

David Radice, Sebastiano Bernuzzi, and Christian D. Ott: "One-Armed Spiral Instability in Neutron Star Mergers and Its Detectability in Gravitational Waves", Physical Review D, American Physical Society (APS), Vol 94, Num 6, 2016, doi:10.1103/physrevd.94.064011

Sebastiano Bernuzzi, David Radice, Christian D. Ott, Luke F. Roberts, Philipp Mösta, and Filippo Galeazzi: "How Loud Are Neutron Star Mergers?", Physical Review D, American Physical Society (APS), Vol 94, Num 2, pp 024023, 2016, doi:10.1103/physrevd.94.024023

A. Cerjanic, J. L. Holtrop, G-C. Ngo, B. Leback, G. Arnold, M. Van Moer, G. LaBelle, J. A. Fessler, and B. P. Sutton: "PowerGrid: A Open Source Library for Accelerated Iterative Magnetic Resonance Image Reconstruction", Proceedings of the 24th annual meeting of the International Society for Magnetic Resonance in Medicine, pp 525, Singapore, 2016

Robert Sisneros, Mohammad Raji, Mark W. Van Moer, and David Bock: "Chasing Rainbows: A Color-Theoretic Framework for Improving and Preserving Bad Colormaps", Springer International Publishing, Advances in Visual Computing, pp 391--402, 2016, doi:10.1007/978-3-319-50835-1_36

Ashok Srinivasan, C. D. Sudheer, and Sirish Namilae: "Optimizing Massively Parallel Simulations of Infection Spread Through Air-Travel for Policy Analysis", IEEE, 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), pp 136-145, Cartagena, Colombia, 2016, doi:10.1109/ccgrid.2016.23

Rafael O. Tinoco, and Giovanni Coco: "A Laboratory Study on Sediment Resuspension Within Arrays of Rigid Cylinders", Advances in Water Resources, Elsevier BV, Vol 92, pp 1--9, 2016, doi:10.1016/j.advwatres.2016.04.003

Xu, S. Byna, V. Venkatesan, R. Sisneros, O. Kulkarni, M. Chaarawi, K. Chadalavada: "LIOProf: Exposing Lustre File System Behavior for I/O Middleware", presented at CUG 2016, London, England, U.K., 2016

Nawrin Sultana, Alexander Calvert, Jeffrey L. Overbey, and Galen Arnold: "From OpenACC to OpenMP 4", ACM Press, Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16, pp 44:1--44:8, 2016, doi:10.1145/2949550.2949654

Xu, X. L. and Pai, C.-H. and Zhang, C. J. and Li, F. and Wan, Y. and Wu, Y. P. and Hua, J. F. and Lu, W. and An, W. and Yu, P. and Joshi, C. and Mori, W. B.: "Nanoscale Electron Bunching in Laser-Triggered Ionization Injection in Plasma Accelerators", Physical Review Letters, American Physical Society (APS), Vol 117, Num 3, pp 034801, 2016, doi:10.1103/physrevlett.117.034801

Schweitzer, Andreas and Aufderheide, Antje and Rudack, Till and Beck, Florian and Pfeifer, Günter and Plitzko, Jürgen M. and Sakata, Eri and Schulten, Klaus and Förster, Friedrich and Baumeister, Wolfgang: "Structure of the human 26S proteasome at a resolution of 3.9 Å", Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol 113, Num 28, pp 7816-7821, 2016, doi:10.1073/pnas.1608050113

Patricia M. Gregg, and J. Cory Pettijohn: "A Multi-Data Stream Assimilation Framework for the Assessment of Volcanic Unrest", Journal of Volcanology and Geothermal Research, Elsevier BV, Vol 309, pp 63--77, 2016, doi:10.1016/j.jvolgeores.2015.11.008

Huilan Zhang, Guangjin Hou, Manman Lu, Jinwoo Ahn, In-Ja L. Byeon, Christopher J. Langmead, Juan R. Perilla, Ivan Hung, Peter L. Gor'kov, Zhehong Gan, William W. Brey, David A. Case, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova: "HIV-1 Capsid Function Is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD", Journal of the American Chemical Society, American Chemical Society (ACS), Vol 138, Num 42, pp 14066--14075, 2016, doi:10.1021/jacs.6b08744

Thieker, David F. and Hadden, Jodi A. and Schulten, Klaus and Woods, Robert J.: "3D implementation of the symbol nomenclature for graphical representation of glycans", Glycobiology, Oxford University Press, Vol 26, Num 8, pp 786-787, 2016, doi:10.1093/glycob/cww076

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", The Astrophysical Journal, IOP Publishing, Vol 827, Num 1, pp 84, 2016

E. Gámiz, A. Bazavov, C. Bernard, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, Steven Gottlieb, U.M. Heller, J. Komijani, A.S. Kronfeld, J. Laiho, P.B. Mackenzie, E.T. Neil, T. Primer, J.N. Simone, R. Sugar, D. Toussaint, R.S. Van de Water, Ran Zhou: "Kaon semileptonic decays with Nf=2+1+1 HISQ fermions and physical light-quark masses", Proceedings of Science, Proceedings, 34th International Symposium on Lattice Field Theory (Lattice 2016), pp 286, Southampton, England, U.K., 2016

Yosef Zlochower, Hiroyuki Nakano, Bruno C. Mundim, Manuela Campanelli, Scott Noble, and Miguel Zilhão: "Inspiraling Black-Hole Binary Spacetimes: Challenges in Transitioning from Analytical to Numerical Techniques", Physical Review D, American Physical Society (APS), Vol 93, Num 12, pp 124072, 2016, doi:10.1103/physrevd.93.124072

John E. Stone, William R. Sherman, and Klaus Schulten: "Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering", IEEE, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Chicago, Illinois, U.S.A., 2016, doi:10.1109/ipdpsw.2016.121

D. Roten, Y. Cui, K. Olsen, S. Day, K. Withers, W. Savran, and P. Wang: "High-Frequency Nonlinear Earthquake Simulations on Petascale Heterogeneous Supercomputers", IEEE Press, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '16), pp 82:1--82:12, Salt Lake City, Utah, U.S.A., 2016

Anshul Gupta, Natalia Gimelshein, Seid Koric, and Steven Rennich: "Effective Minimally-Invasive GPU Acceleration of Distributed Sparse Matrix Factorization", Springer International Publishing, Euro-Par 2016: Parallel Processing, pp 672--683, Grenoble, France, 2016, doi:10.1007/978-3-319-43659-3_49

Hao Xu, John H. Wise, Michael L. Norman, Kyungjin Ahn, and Brian W. O'Shea: "Galaxy Properties and UV Escape Fractions During Epoch of Reionization: Results from the Renaissance Simulations", The Astrophysical Journal, The American Astronomical Society, Vol 833, Num 1, pp 84, 2016, doi:10.3847/1538-4357/833/1/84

A. L. Jones: "Development of an Accurate 3D Monte Carlo Broadband Atmospheric Radiative Transfer Model", Ph.D. Dissertation, University of Illinois, 2016

J. Komijani, A. Bazavov, C. Bernard, N. Brambilla, N. Brown, C. DeTar, D. Du, A.X. El-Khadra, E.D. Freeland, E. Gámiz, Steven Gottlieb, U.M. Heller, A.S. Kronfeld, J. Laiho, P.B. Mackenzie, C. Monahan, Heechang Na, E.T. Neil, J.N. Simone, R.L. Sugar, D. Toussaint, A. Vairo, R.S. Van de Water: "Decay constants fB and fBs and quark masses mb and mc from HISQ simulations", Proceedings of Science, Proceedings, 34th International Symposium on Lattice Field Theory (Lattice 2016), pp 294, Southampton, England, United Kingdom, 2016

Daniel R. Bolton, Raúl A. Briceño, and David J. Wilson: "Connecting Physical Resonant Amplitudes and Lattice QCD", Physics Letters B, Elsevier BV, Vol 757, pp 50--56, 2016, doi:10.1016/j.physletb.2016.03.043

Yanbin Wu, Lucas K. Wagner, and Narayana R. Aluru: "Hexagonal Boron Nitride and Water Interaction Parameters", The Journal of Chemical Physics, AIP Publishing, Vol 144, Num 16, pp 164118, 2016, doi:10.1063/1.4947094

Hesameddin Ilatikhameneh, Tarek A. Ameen, Gerhard Klimeck, and Rajib Rahman: "Universal Behavior of Atomistic Strain in Self-Assembled Quantum Dots", IEEE Journal of Quantum Electronics, Institute of Electrical and Electronics Engineers (IEEE), Vol 52, Num 7, pp 1--8, 2016, doi:10.1109/jqe.2016.2573959

Ariana Minot, Yue M. Lu, and Na Li: "A Parallel Primal-Dual Interior-Point Method for DC Optimal Power Flow", IEEE, 2016 Power Systems Computation Conference (PSCC), pp 1-7, Genoa, Italy, 2016, doi:10.1109/pscc.2016.7540826

Wendy K. Tam Cho, and Yan Y. Liu: "A Parallel Evolutionary Algorithm for Subset Selection in Causal Inference Models", ACM Press, Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale, pp 7:1-7:8, Miami, Florida, U.S.A., 2016, doi:10.1145/2949550.2949568

Leigh Orf, Robert Wilhelmson, and Louis Wicker: "Visualization of a Simulated Long-Track EF5 Tornado Embedded Within a Supercell Thunderstorm", Parallel Computing, Elsevier BV, Vol 55, pp 28--34, 2016, doi:10.1016/j.parco.2015.10.014

Kamdar, Harshil M. and Turk, Matthew J. and Brunner, Robert J.: "Machine learning and cosmological simulations – II. Hydrodynamical simulations", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 457, Num 2, pp 1162-1179, 2016, doi:10.1093/mnras/stv2981

Kamdar, Harshil M. and Turk, Matthew J. and Brunner, Robert J.: "Machine learning and cosmological simulations – I. Semi-analytical models", Monthly Notices of the Royal Astronomical Society, The Royal Astronomical Society, Vol 455, Num 1, pp 642-658, 2016, doi:10.1093/mnras/stv2310

Haoran Wang, and Huck Beng Chew: "Molecular Dynamics Simulations of Plasticity and Cracking in Lithiated Silicon Electrodes", Extreme Mechanics Letters, Elsevier BV, Vol 9, Num Part 3, pp 503--513, 2016, doi:10.1016/j.eml.2016.02.020

Robert J. Trapp, and Kimberly A. Hoogewind: "The Realization of Extreme Tornadic Storm Events Under Future Anthropogenic Climate Change", Journal of Climate, American Meteorological Society, Vol 29, Num 14, pp 5251--5265, 2016, doi:10.1175/jcli-d-15-0623.1

Justin A. Drake, Robert C. Harris, and B. Montgomery Pettitt: "Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility", Biophysical Journal, Elsevier BV, Vol 111, Num 4, pp 756--767, 2016, doi:10.1016/j.bpj.2016.07.013

Alexander E. Doran, and So Hirata: "Monte Carlo MP2 on Many Graphical Processing Units", Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 12, Num 10, pp 4821--4832, 2016, doi:10.1021/acs.jctc.6b00588

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., Oxford University Press (OUP), Vol 205, Num 2, pp 856--863, 2016, doi:10.1093/gji/ggw050

2017

David J. Luitz, and Yevgeny Bar Lev: "Information Propagation in Isolated Quantum Systems", Physical Review B, American Physical Society (APS), Vol 96, Num 2, pp 020406, 2017, doi:10.1103/physrevb.96.020406

John E. Stone, Juan R. Perilla, C. Keith Cassidy, and Klaus Schulten: "GPU-Accelerated Molecular Dynamics Clustering Analysis with OpenACC", Elsevier, Parallel Programming with OpenACC, pp 215--240, 2017, doi:10.1016/b978-0-12-410397-9.00011-1

Julie M. Allen, Bret Boyd, Nam-Phuong Nguyen, Pranjal Vachaspati, Tandy Warnow, Daisie I. Huang, Patrick G. S. Grady, Kayce C. Bell, Quentin C. B. Cronk, Lawrence Mugisha, Barry R. Pittendrigh, M. Soledad Leonardi, David L. Reed, Kevin P. Johnson: "Phylogenomics from Whole Genome Sequences Using aTRAM", Systematic Biology, Oxford University Press, Vol 66, Num 5, pp 786–798, 2017, doi:10.1093/sysbio/syw105

David Pekker, and Bryan K. Clark: "Encoding the Structure of Many-Body Localization with Matrix Product Operators", Physical Review B, American Physical Society (APS), Vol 95, Num 3, pp 035116, 2017, doi:10.1103/physrevb.95.035116

Pekker, David and Clark, Bryan K. and Oganesyan, Vadim and Refael, Gil: "Fixed Points of Wegner-Wilson Flows and Many-Body Localization", Phys. Rev. Lett., American Physical Society, Vol 119, Num 7, pp 075701, 2017, doi:10.1103/PhysRevLett.119.075701

Greg Bauer, Victor Anisimov, Galen Arnold, Brett Bode, Robert Brunner, Tom Cortese, Roland Haas, Andriy Kot, William Kramer, JaeHyuk Kwack, Jing Li, Celso Mendes, Ryan Mokos, Craig Steffen: "Updating the SPP Benchmark Suite for Extreme-Scale Systems", presented at CUG 2017, Redmond, Washington, U.S.A., 2017

Cong Xu, Shane Snyder, Vishwanath Venkatesan, Philip Carns, Omkar Kulkarni, Suren Byna, Robert Sisneros, Kalyana Chadalavada: "DXT: Darshan eXtended Tracing", presented at CUG 2017, Redmond, Washington, U.S.A., 2017

Saurabh Jha, Jim Brandt, Ann Gentile, Zbigniew Kalbarczyk, Greg Bauer, Jeremy Enos, Michael Showerman, Larry Kaplan, Brett Bode, Annette Greiner, Amanda Bonnie, Mike Mason, William Kramer and Ravishankar Iyer: "Holistic Measurement Driven System Assessment", IEEE, 2017 IEEE International Conference on Cluster Computing (CLUSTER), pp 797-800, Honolulu, Hawai'i, U.S.A., 2017, doi:10.1109/CLUSTER.2017.124

A. C. Dreyfuss, K. D. Launey, T. Dytrych, J. P. Draayer, R. B. Baker, C. M. Deibel, and C. Bahri: "Understanding Emergent Collectivity and Clustering in Nuclei from a Symmetry-Based No-Core Shell-Model Perspective", Physical Review C, American Physical Society (APS), Vol 95, Num 4, pp 044312, 2017, doi:10.1103/physrevc.95.044312

Amir Barati Farimani, Mohammad Heiranian, Kyoungmin Min, and Narayana R. Aluru: "Antibody Subclass Detection Using Graphene Nanopores", The Journal of Physical Chemistry Letters, American Chemical Society (ACS), Vol 8, Num 7, pp 1670--1676, 2017, doi:10.1021/acs.jpclett.7b00385

K. Jin, S.P. Vanka, R.K. Agarwal, and B.G. Thomas: "GPU Accelerated Simulations of Three-Dimensional Flow of Power-Law Fluids in a Driven Cube", International Journal of Computational Fluid Dynamics, Informa UK Limited, Vol 31, Num 1, pp 36--56, 2017, doi:10.1080/10618562.2016.1270449

S. R. Totorica, T. Abel, and F. Fiuza: "Particle Acceleration in Laser-Driven Magnetic Reconnection", Physics of Plasmas, AIP Publishing, Vol 24, Num 4, pp 041408, 2017, doi:10.1063/1.4978627

Kartik P. Iyer, Katepalli R. Sreenivasan, and P. K. Yeung: "Reynolds Number Scaling of Velocity Increments in Isotropic Turbulence", Physical Review E, American Physical Society (APS), Vol 95, Num 2, pp 021101, 2017, doi:10.1103/physreve.95.021101

Hillary Schwarb, Curtis L. Johnson, Ana M. Daugherty, Charles H. Hillman, Arthur F. Kramer, Neal J. Cohen, and Aron K. Barbey: "Aerobic Fitness, Hippocampal Viscoelasticity, and Relational Memory Performance", NeuroImage, Elsevier BV, Vol 153, pp 179--188, 2017, doi:10.1016/j.neuroimage.2017.03.061

Yongyang Cai, Kenneth Judd, and Jevgenijs Steinbuks: "A Nonlinear Certainty Equivalent Approximation Method for Dynamic Stochastic Problems", Quantitative Economics, The Econometric Society, Vol 8, Num 1, pp 117--147, 2017, doi:10.3982/qe533

Sevin Yeltekin, Yongyang Cai, and Kenneth L. Judd: "Computing Equilibria of Dynamic Games", Operations Research, Institute for Operations Research and the Management Sciences (INFORMS), Vol 65, Num 2, pp 337--356, 2017, doi:10.1287/opre.2016.1572

Jones, Alexandra L.: "Alexandraljones/Imc-Emission: Code Base Plus Select Benchmark Results", Zenodo, 2017, doi:10.5281/zenodo.574872

S. Namilae, A. Srinivasan, A. Mubayi, M. Scotch, and R. Pahle: "Self-Propelled Pedestrian Dynamics Model: Application to Passenger Movement and Infection Propagation in Airplanes", Physica A: Statistical Mechanics and its Applications, Elsevier BV, Vol 465, pp 248--260, 2017, doi:10.1016/j.physa.2016.08.028

Jiashun Hu, Manuele Faccenda, and Lijun Liu: "Subduction-Controlled Mantle Flow and Seismic Anisotropy in South America", Earth and Planetary Science Letters, Elsevier BV, Vol 470, pp 13--24, 2017, doi:10.1016/j.epsl.2017.04.027

Sung Jun Lim, Andre Schleife, and Andrew M. Smith: "Optical Determination of Crystal Phase in Semiconductor Nanocrystals", Nature Communications, Springer Nature, Vol 8, pp 14849, 2017, doi:10.1038/ncomms14849

Matthew P. Harrigan, Keri A. McKiernan, Veerabahu Shanmugasundaram, Rajiah Aldrin Denny, and Vijay S. Pande: "Markov Modeling Reveals Novel Intracellular Modulation of the Human TREK-2 Selectivity Filter", Scientific Reports, Springer Nature, Vol 7, Num 1, 2017, doi:10.1038/s41598-017-00256-y

Stuart L. Shapiro: "Black Holes, Disks, and Jets Following Binary Mergers and Stellar Collapse: The Narrow Range of Electromagnetic Luminosities and Accretion Rates", Physical Review D, American Physical Society (APS), Vol 95, Num 10, pp 101303, 2017, doi:10.1103/physrevd.95.101303

Antonios Tsokaros, Milton Ruiz, Vasileios Paschalidis, Stuart L. Shapiro, Luca Baiotti, and Koji Uryu: "Gravitational Wave Content and Stability of Uniformly, Rotating, Triaxial Neutron Stars in General Relativity", Physical Review D, American Physical Society (APS), Vol 95, Num 12, pp 124057, 2017, doi:10.1103/physrevd.95.124057

Kurt R. Brorsen, Michael V. Pak, and Sharon Hammes-Schiffer: "Calculation of Positron Binding Energies and Electron-Positron Annihilation Rates for Atomic Systems with the Reduced Explicitly Correlated Hartree-Fock Method in the Nuclear-Electronic Orbital Framework", The Journal of Physical Chemistry A, American Chemical Society (ACS), Vol 121, Num 2, pp 515--522, 2017, doi:10.1021/acs.jpca.6b10124

Kurt R. Brorsen, Yang Yang, Michael V. Pak, and Sharon Hammes-Schiffer: "Is the Accuracy of Density Functional Theory for Atomization Energies and Densities in Bonding Regions Correlated?", The Journal of Physical Chemistry Letters, American Chemical Society (ACS), Vol 8, Num 9, pp 2076--2081, 2017, doi:10.1021/acs.jpclett.7b00774

Cole M. Johnson, So Hirata, and Seiichiro Ten-no: "Explicit Correlation Factors", Chemical Physics Letters, Elsevier BV, Vol 683, pp 247--252, 2017, doi:10.1016/j.cplett.2017.02.072

Daniel Dumett Torres, Progna Banerjee, Sudhakar Pamidighantam, and Prashant K. Jain: "A Non-Natural Wurtzite Polymorph of HgSe: A Potential 3D Topological Insulator", Chemistry of Materials, American Chemical Society (ACS), 2017, doi:10.1021/acs.chemmater.7b01674

Joseph A. Morrone, Alberto Perez, Qiaolin Deng, Sookhee N. Ha, M. Katharine Holloway, Tomi K. Sawyer, Bradley S. Sherborne, Frank K. Brown, and Ken A. Dill: "Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX", Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 13, Num 2, pp 863--869, 2017, doi:10.1021/acs.jctc.6b00978

Joseph A. Morrone, Alberto Perez, Justin MacCallum, and Ken A. Dill: "Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics", Journal of Chemical Theory and Computation, American Chemical Society (ACS), Vol 13, Num 2, pp 870--876, 2017, doi:10.1021/acs.jctc.6b00977

Sherwood Richers, Christian D. Ott, Ernazar Abdikamalov, Evan O'Connor, and Chris Sullivan: "Equation of State Effects on Gravitational Waves from Rotating Core Collapse", Physical Review D, American Physical Society (APS), Vol 95, Num 6, pp 063019, 2017, doi:10.1103/physrevd.95.063019

D. Baumgardner, S. J. Abel, D. Axisa, R. Cotton, J. Crosier, P. Field, C. Gurganus, A. Heymsfield, A. Korolev, M. Krämer, P. Lawson, G. McFarquhar, Z. Ulanowski, and J. Um: "Cloud Ice Properties: In Situ Measurement Challenges", Meteorological Monographs, American Meteorological Society, Vol 58, pp 9.1--9.23, 2017, doi:10.1175/amsmonographs-d-16-0011.1

Andrew Huang, Hui Li, Ryan L. Sriver, Alexey V. Fedorov, and Chris M. Brierley: "Regional Variations in the Ocean Response to Tropical Cyclones: Ocean Mixing Versus Low Cloud Suppression", Geophysical Research Letters, Wiley-Blackwell, Vol 44, Num 4, pp 1947-1955, 2017, doi:10.1002/2016gl072023

Zachary Zobel, Jiali Wang, Donald J. Wuebbles, and V. Rao Kotamarthi: "Evaluations of High-Resolution Dynamically Downscaled Ensembles Over the Contiguous United States", Climate Dynamics, Springer Nature, 2017, doi:10.1007/s00382-017-3645-6

Bowen, D., M. Campanelli, J. Krolik, V. Mewes, S. Noble: "Relativistic Dynamics and Mass Exchange in Binary Black Hole Mini-disks", The Astrophysical Journal, The American Astronomical Society, Vol 838, Num 1, pp 42, 2017, doi:10.3847/1538-4357/aa63f3

David J. Luitz, and Yevgeny Bar Lev: "The Ergodic Side of the Many-Body Localization Transition", Annalen der Physik, Wiley-Blackwell, Vol 529, Num 7, pp 1600350, 2017, doi:10.1002/andp.201600350

Amir Barati Farimani, Payam Dibaeinia, and Narayana R. Aluru: "DNA Origami-Graphene Hybrid Nanopore for DNA Detection", ACS Applied Materials & Interfaces, American Chemical Society (ACS), Vol 9, Num 1, pp 92--100, 2017, doi:10.1021/acsami.6b11001

Karl Decker, Martin Page, Ashley Boyd, Irene MacAllister, Mark Ginsberg, and Aleksei Aksimentiev: "Selective Permeability of Truncated Aquaporin 1 in Silico", ACS Biomaterials Science & Engineering, American Chemical Society (ACS), Vol 3, Num 3, pp 342--348, 2017, doi:10.1021/acsbiomaterials.6b00583

Jahan Claes, and Bryan K. Clark: "Finite-Temperature Properties of Strongly Correlated Systems via Variational Monte Carlo", Physical Review B, American Physical Society (APS), Vol 95, Num 20, pp 205109, 2017, doi:10.1103/physrevb.95.205109

Xiongjie Yu, David Pekker, and Bryan K. Clark: "Finding Matrix Product State Representations of Highly Excited Eigenstates of Many-Body Localized Hamiltonians", Physical Review Letters, American Physical Society (APS), Vol 118, Num 1, pp 017201, 2017, doi:10.1103/physrevlett.118.017201

Puja Goyal, and Sharon Hammes-Schiffer: "Tuning the Ultrafast Dynamics of Photoinduced Proton-Coupled Electron Transfer in Energy Conversion Processes", ACS Energy Letters, American Chemical Society (ACS), Vol 2, Num 2, pp 512--519, 2017, doi:10.1021/acsenergylett.6b00723

Saurabh Shukla, Zahra Shamsi, Alexander S. Moffett, Balaji Selvam, and Diwakar Shukla: "Application of Hidden Markov Models in Biomolecular Simulations", Methods in Molecular Biology, Springer New York, Hidden Markov Models, pp 29--41, 2017, doi:10.1007/978-1-4939-6753-7_3

Jerry P. Draayer, Tomas Dytrych, and Kristina D. Launey: "Symmetry-adapted No-core Shell Model — the Ab Initio Picture of Nuclear Collectivity", World Scientific, Emergent Phenomena in Atomic Nuclei from Large-Scale Modeling, pp 229--263, 2017, doi:10.1142/9789813146051_0008

J P Draayer and K D Launey and T Dytrych and A C Dreyfuss and R B Baker and M E Miora: "No-core Symplectic Model: Exploiting Hidden Symmetry in Atomic Nuclei", Journal of Physics: Conference Series, IOP Publishing Ltd, Vol 863, Num 1, pp 012008, 2017

James W. Mazzuca, and Chase P. Schultz: "Quantum Mechanical Enhancement of Rate Constants and Kinetic Isotope Effects for Water-Mediated Proton Transfer in a Model Biological System", The Journal of Physical Chemistry A, American Chemical Society (ACS), Vol 121, Num 4, pp 819--826, 2017, doi:10.1021/acs.jpca.6b10337

T. K. Kim and N. V. Pogorelov and L. F. Burlaga: "Modeling Shocks Detected by Voyager 1 in the Local Interstellar Medium", The Astrophysical Journal Letters, The American Astronomical Society, Vol 843, Num 2, pp L32, 2017, doi:10.3847/2041-8213/aa7b2b

V. López-Barquero and S. Xu and P. Desiati and A. Lazarian and N. V. Pogorelov and H. Yan: "TeV Cosmic-Ray Anisotropy from the Magnetic Field at the Heliospheric Boundary", The Astrophysical Journal, The American Astronomical Society, Vol 842, Num 1, pp 54, 2017, doi:10.3847/1538-4357/aa74d1

N. V. Pogorelov and S. N. Borovikov and I. A. Kryukov and S. T. Wu and M. S. Yalim and P. C. Colella and B. Van Straalen: "Modeling Coronal Mass Ejections with the Multi-Scale Fluid-Kinetic Simulation Suite", Journal of Physics: Conference Series, IOP Publishing Ltd, Vol 837, Num 1, pp 012014, 2017, doi:10.1088/1742-6596/837/1/012014

N. V. Pogorelov, H. Fichtner, A. Czechowski, A. Lazarian, B. Lembege, J. A. le Roux, M. S. Potgieter, K. Scherer, E. C. Stone, R. D. Strauss, T. Wiengarten, P. Wurz, G. P. Zank, and M. Zhang: "Heliosheath Processes and the Structure of the Heliopause: Modeling Energetic Particles, Cosmic Rays, and Magnetic Fields", Space Science Reviews, Springer Nature, 2017, doi:10.1007/s11214-017-0354-8

Mehmet Sarp Yalim and Nikolai Pogorelov and Yang Liu: "A data-driven MHD model of the global solar corona within Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS)", Journal of Physics: Conference Series, IOP Publishing Ltd, Vol 837, Num 1, pp 012015, 2017, doi:10.1088/1742-6596/837/1/012015

E. J. Zirnstein and J. Heerikhuisen and G. P. Zank and N. V. Pogorelov and H. O. Funsten and D. J. McComas and D. B.Reisenfeld and N. A. Schwadron: "Structure of the Heliotail from Interstellar Boundary Explorer Observations: Implications for the 11-year Solar Cycle and Pickup Ions in the Heliosheath", The Astrophysical Journal, The American Astronomical Society, Vol 836, Num 2, pp 238, 2017, doi:10.3847/1538-4357/aa5cb2

Jon Calhoun, Marc Snir, Luke N. Olson, and William D. Gropp: "Towards a More Complete Understanding of SDC Propagation", ACM Press, Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing - HPDC '17, pp 131, Washington, D.C., U.S.A., 2017, doi:10.1145/3078597.3078617

Michael A. Lively, Brandon Holybee, Michael Toriyama, and Jean Paul Allain: "Massive-Scale Molecular Dynamics of Ion-Irradiated III-v Compound Semiconductors at the Onset of Nanopatterning", Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Elsevier BV, 2017, doi:10.1016/j.nimb.2017.04.047

Michael J. Brazell, Andrew C. Kirby, and Dimitri Mavriplis: "A High-Order Discontinuous-Galerkin Octree-Based AMR Solver for Overset Simulations", American Institute of Aeronautics and Astronautics, 23rd AIAA Computational Fluid Dynamics Conference, Denver, Colorado, U.S.A., 2017, doi:10.2514/6.2017-3944

Abhilash Harpale, and Huck Beng Chew: "Hydrogen-Plasma Patterning of Multilayer Graphene: Mechanisms and Modeling", Carbon, Elsevier BV, Vol 117, pp 82--91, 2017, doi:10.1016/j.carbon.2017.02.062

Shu-Ching Ou, Justin A. Drake, and B. Montgomery Pettitt: "Nonpolar Solvation Free Energy from Proximal Distribution Functions", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 15, pp 3555--3564, 2017, doi:10.1021/acs.jpcb.6b09528

David Radice and Sebastiano Bernuzzi and Walter Del Pozzo and Luke F. Roberts and Christian D. Ott: "Probing Extreme-density Matter with Gravitational-wave Observations of Binary Neutron Star Merger Remnants", The Astrophysical Journal Letters, The American Astronomical Society, Vol 842, Num 2, pp L10, 2017, doi:10.3847/2041-8213/aa775f

Shuai Zhang, Kevin P. Driver, Fran\ccois Soubiran, and Burkhard Militzer: "First-Principles Equation of State and Shock Compression Predictions of Warm Dense Hydrocarbons", Physical Review E, American Physical Society (APS), Vol 96, Num 1, pp 013204, 2017, doi:10.1103/physreve.96.013204

K. P. Driver, and B. Militzer: "First-Principles Simulations of Warm Dense Lithium Fluoride", Physical Review E, American Physical Society (APS), Vol 95, Num 4, pp 043205, 2017, doi:10.1103/physreve.95.043205

Shuai Zhang, Kevin P. Driver, François Soubiran, and Burkhard Militzer: "Equation of state and shock compression of warm dense sodium—A first-principles study", The Journal of Chemical Physics, AIP Publishing, Vol 146, Num 7, pp 074505, 2017, doi:10.1063/1.4976559

Daniel H. Moser, and Sonia Lasher-Trapp: "The Influence of Successive Thermals on Entrainment and Dilution in a Simulated Cumulus Congestus", Journal of the Atmospheric Sciences, American Meteorological Society, Vol 74, Num 2, pp 375--392, 2017, doi:10.1175/jas-d-16-0144.1

John J. Podesta, and Vadim Roytershteyn: "The Most Intense Electrical Currents in the Solar Wind: Comparisons Between Single-Spacecraft Measurements and Plasma Turbulence Simulations", Journal of Geophysical Research: Space Physics, Wiley-Blackwell, 2017, doi:10.1002/2017ja024074

Hime, Paul Michael: "Genomic Perspectives on Amphibian Evolution across Multiple Phylogenetic Scales", Theses and Dissertations--Biology, University of Kentucky Libraries, Num 45, 2017, doi:10.13023/ETD.2017.284

Morteza Khabiri, and Peter L. Freddolino: "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 20, pp 5151--5161, 2017, doi:10.1021/acs.jpcb.6b12450

E.A. Huerta, Prayush Kumar, Bhanu Agarwal, Daniel George, Hsi-Yu Schive, Harald P. Pfeiffer, Roland Haas, Wei Ren, Tony Chu, Michael Boyle, Daniel A. Hemberger, Lawrence E. Kidder, Mark A. Scheel, and Bela Szilagyi: "Complete Waveform Model for Compact Binaries on Eccentric Orbits", Physical Review D, American Physical Society (APS), Vol 95, Num 2, pp 024038, 2017, doi:10.1103/physrevd.95.024038

Katharine J. Cahill, Scott Lathrop, and Steven Gordon: "Building a Community of Practice to Prepare the HPC Workforce", Procedia Computer Science, Elsevier BV, Vol 108, pp 2131--2140, 2017, doi:10.1016/j.procs.2017.05.059

P. Vachaspati and T. Warnow: "FastRFS: Fast and Accurate Robinson-Foulds Supertrees using Constrained Exact Optimization", Bioinformatics, Oxford University Press, Vol 33, Num 5, pp 631-639, 2017, doi:10.1093/bioinformatics/btw600

Y. Feng, and C. Modi: "A Fast Algorithm for Identifying Friends-of-Friends Halos", Astronomy and Computing, Elsevier BV, Vol 20, pp 44--51, 2017, doi:10.1016/j.ascom.2017.05.004

Di Matteo, Tiziana and Croft, Rupert A. C. and Feng, Yu and Waters, Dacen and Wilkins, Stephen: "The origin of the most massive black holes at high-z: BlueTides and the next quasar frontier", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 467, Num 4, pp 4243-4251, 2017, doi:10.1093/mnras/stx319

Yan Li, Miroslav Hodak, Wenchang Lu, and J. Bernholc: "Selective Sensing of Ethylene and Glucose Using Carbon-Nanotube-Based Sensors: An Ab Initio Investigation", Nanoscale, Royal Society of Chemistry (RSC), Vol 9, Num 4, pp 1687--1698, 2017, doi:10.1039/c6nr07371a

Chuanxu Ma, Zhongcan Xiao, Honghai Zhang, Liangbo Liang, Jingsong Huang, Wenchang Lu, Bobby G. Sumpter, Kunlun Hong, J. Bernholc, and An-Ping Li: "Controllable Conversion of Quasi-Freestanding Polymer Chains to Graphene Nanoribbons", Nature Communications, Springer Nature, Vol 8, pp 14815, 2017, doi:10.1038/ncomms14815

Yash Thakur, Bing Zhang, Rui Dong, Wenchang Lu, C. Iacob, J. Runt, J. Bernholc, and Q.M. Zhang: "Generating High Dielectric Constant Blends from Lower Dielectric Constant Dipolar Polymers Using Nanostructure Engineering", Nano Energy, Elsevier BV, Vol 32, pp 73--79, 2017, doi:10.1016/j.nanoen.2016.12.021

Natalia V. Dolgova, Corey Yu, John P. Cvitkovic, Miroslav Hodak, Kurt H. Nienaber, Kelly L. Summers, Julien J. H. Cotelesage, Jerzy Bernholc, George A. Kaminski, Ingrid J. Pickering, Graham N. George, and Oleg Y. Dmitriev: "Binding of Copper and Cisplatin to Atox1 Is Mediated by Glutathione Through the Formation of Metal-Sulfur Clusters", Biochemistry, American Chemical Society (ACS), Vol 56, Num 24, pp 3129--3141, 2017, doi:10.1021/acs.biochem.7b00293

P. J. Mendygral and N. Radcliffe and K. Kandalla and D. Porter and B. J. O’Neill and C. Nolting and P. Edmon and J. M. F.Donnert and T. W. Jones: "WOMBAT: A Scalable and High-performance Astrophysical Magnetohydrodynamics Code", The Astrophysical Journal Supplement Series, The American Astronomical Society, Vol 228, Num 2, pp 23, 2017, doi:10.3847/1538-4365/aa5b9c

Jones, S. and Andrassy, R. and Sandalski, S. and Davis, A. and Woodward, P. and Herwig, F.: "Idealized hydrodynamic simulations of turbulent oxygen-burning shell convection in 4π geometry", Monthly Notices of the Royal Astronomical Society, Oxford University Press, Vol 465, Num 3, pp 2991-3010, 2017, doi:10.1093/mnras/stw2783

Rohit Dhariwal, Sarma L. Rani, and Donald L. Koch: "Stochastic Theory and Direct Numerical Simulations of the Relative Motion of High-Inertia Particle Pairs in Isotropic Turbulence", Journal of Fluid Mechanics, Cambridge University Press (CUP), Vol 813, pp 205--249, 2017, doi:10.1017/jfm.2016.859

Juan R. Perilla, and Klaus Schulten: "Physical Properties of the HIV-1 Capsid from All-Atom Molecular Dynamics Simulations", Nature Communications, Springer Nature, Vol 8, pp 15959, 2017, doi:10.1038/ncomms15959

Tyler M. Earnest, Reika Watanabe, John E. Stone, Julia Mahamid, Wolfgang Baumeister, Elizabeth Villa, and Zaida Luthey-Schulten: "Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 15, pp 3871--3881, 2017, doi:10.1021/acs.jpcb.7b00672

Mert Hidayetogglu, Carl Pearson, Levent Gurel, Wen-Mei Hwu, and Weng Cho Chew: "Scalable Parallel DBIM Solutions of Inverse-Scattering Problems", IEEE, 2017 Computing and Electromagnetics International Workshop (CEM), pp 65-66, Barcelona, Spain, 2017, doi:10.1109/cem.2017.7991889

Mert Hidayetogglu, Carl Pearson, Weng Cho Chew, Levent Gurel, and Wen-Mei Hwu: "Large Inverse-Scattering Solutions with DBIM on GPU-Enabled Supercomputers", IEEE, 2017 International Applied Computational Electromagnetics Society Symposium - Italy (ACES), pp 1-2, Florence, Italy, 2017, doi:10.23919/ropaces.2017.7916310

M.P. Clay, D. Buaria, T. Gotoh, and P.K. Yeung: "A Dual Communicator and Dual Grid-Resolution Algorithm for Petascale Simulations of Turbulent Mixing at High Schmidt Number", Computer Physics Communications, Elsevier BV, Vol 219, pp 313-328, 2017, doi:10.1016/j.cpc.2017.06.009

J. Kwack and G. Bauer: "HPCG and HPGMG benchmark tests on Multiple Program, Multiple Data (MPMD) mode on Blue Waters", presented at CUG 2017, Redmond, Washington, U.S.A., 2017

Brett Bode, Jim Glasgow, Michelle Butler, Sean Stevens, Nate Schumann, Frank Zago: "Implementing a Hierarchical Storage Management system in a large-scale Lustre and HPSS environment", presented at CUG 2017, Redmond, Washington, U.S.A., 2017

Valerio Formicola, Saurabh Jha, Daniel Chen, Fei Deng, Amanda Bonnie, Mike Mason, Jim Brandt, Ann Gentile, Larry Kaplan, Jason Repik, Jeremy Enos, Mike Showerman, Annette Greiner, Zbigniew Kalbarczyk, Ravishankar K. Iyer, William Kramer: "Understanding Fault Scenarios and Impacts through Fault Injection Experiments in Cielo", presented at CUG 2017, Redmond, Washington, U.S.A., 2017

Tim Bouvet, Galen Arnold, Reuben Budiardja, Greg Bauer: "Application-Level Regression Testing Framework using Jenkins", presented at CUG 2017, Redmond, Washington, U.S.A., 2017

Colin Maclean: "Python Usage Metrics on Blue Waters", presented at CUG 2017, Redmond, Washington, U.S.A., 2017

Raji, Mohammad and Hota, Alok and Sisneros, Robert and Messmer, Peter and Huang, Jian: "Photo-Guided Exploration of Volume Data Features", The Eurographics Association, Eurographics Symposium on Parallel Graphics and Visualization, 2017, doi:10.2312/pgv.20171091

David Bock: "Visualization of Tropical Cyclone-Ocean Interactions", ACM Press, Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact - PEARC17, pp 79:1--79:3, New Orleans, Louisiana, U.S.A., 2017, doi:10.1145/3093338.3104149

Weiming An, Wei Lu, Chengkun Huang, Xinlu Xu, Mark J. Hogan, Chan Joshi, and Warren B. Mori: "Ion Motion Induced Emittance Growth of Matched Electron Beams in Plasma Wakefields", Physical Review Letters, American Physical Society (APS), Vol 118, Num 24, pp 244801, 2017, doi:10.1103/physrevlett.118.244801

Lisa G. Lippert, Tali Dadosh, Jodi A. Hadden, Vishakha Karnawat, Benjamin T. Diroll, Christopher B. Murray, Erika L. F. Holzbaur, Klaus Schulten, Samara L. Reck-Peterson, and Yale E. Goldman: "Angular Measurements of the Dynein Ring Reveal a Stepping Mechanism Dependent on a Flexible Stalk", Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol 114, Num 23, pp E4564--E4573, 2017, doi:10.1073/pnas.1620149114

Juan R. Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L. Byeon, Angela M. Gronenborn, Tatyana Polenova, and Peijun Zhang: "CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations", The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 15, pp 3853--3863, 2017, doi:10.1021/acs.jpcb.6b13105

Larissa J. Reames: "Diurnal Variations in Severe Weather Forecast Parameters of Rapid Update Cycle-2 Tornado Proximity Environments", Weather and Forecasting, American Meteorological Society, Vol 32, Num 2, pp 743--761, 2017, doi:10.1175/waf-d-16-0029.1

Jonathan Blackman, Scott E. Field, Mark A. Scheel, Chad R. Galley, Christian D. Ott, Michael Boyle, Lawrence E. Kidder, Harald P. Pfeiffer, and Béla Szilágyi: "Numerical Relativity Waveform Surrogate Model for Generically Precessing Binary Black Hole Mergers", Physical Review D, American Physical Society (APS), Vol 96, Num 2, pp 024058, 2017, doi:10.1103/physrevd.96.024058

Yu, Jaehyung and Wagner, Lucas K. and Ertekin, Elif: "Fixed-node diffusion Monte Carlo description of nitrogen defects in zinc oxide", Physical Review B, American Physical Society, Vol 95, Num 7, pp 075209, 2017, doi:10.1103/PhysRevB.95.075209

Pengyu Long, Michael Povolotskyi, Jun Z. Huang, James Charles, Tillmann Kubis, Gerhard Klimeck, and Mark J. W. Rodwell: "A High-Current InP-Channel Triple Heterojunction Tunnel Transistor Design", IEEE, 2017 75th Annual Device Research Conference (DRC), pp 1-2, South Bend, Indiana, U.S.A., 2017, doi:10.1109/drc.2017.7999437

Reed Hodges, Cleon Dean, and Maxim Durach: "Optical Neutrality: Invisibility Without Cloaking", Optics Letters, The Optical Society, Vol 42, Num 4, pp 691, 2017, doi:10.1364/ol.42.000691

Joseph S. Haddad, Timothy W. O'Neil, Anthony Deeter, and Zhong-Hui Duan: "An Implementation of Parallel Bayesian Network Learning", The Journal of Computational Science Education, Shodor, Vol 8, Num 2, pp 24 - 28, 2017, doi:10.22369/issn.2153-4136/8/2/4

Venkata Suhas Maringanti, Basileal Imana, and Peter Yoon: "GPU-Accelerated VLSI Routing Using Group Steiner Trees", The Journal Of Computational Science Education, Shodor, Vol 8, Num 1, pp 16 - 19, 2017, doi:10.22369/issn.2153-4136/8/1/4

Frances J. D. Alvarez, Shaoda He, Juan R. Perilla, Sooin Jang, Klaus Schulten, Alan N. Engelman, Sjors H. W. Scheres, and Peijun Zhang: "CryoEM Structure of MxB Reveals a Novel Oligomerization Interface Critical for HIV Restriction", Science Advances, American Association for the Advancement of Science (AAAS), Vol 3, Num 9, pp e1701264, 2017, doi:10.1126/sciadv.1701264

Lunan Sun, Vasileios Paschalidis, Milton Ruiz, and Stuart L. Shapiro: "Magnetorotational Collapse of Supermassive Stars: Black Hole Formation, Gravitational Waves, and Jets", Physical Review D, American Physical Society (APS), Vol 96, Num 4, pp 043006, 2017, doi:10.1103/physrevd.96.043006

C. Ritter, R. Andrassy, B. Côté, F. Herwig, P. R. Woodward, M. Pignatari, S. Jones: "Convective-reactive nucleosynthesis of K, Sc, Cl and p-process isotopes in O-C shell mergers", Monthly Notices of the Royal Astronomical Society (accepted), 2017, doi:10.1093/mnrasl/slx126

Minseung Kim, Ameen Eetemadi, and Ilias Tagkopoulos: "DeepPep: Deep Proteome Inference from Peptide Profiles", PLOS Computational Biology, Public Library of Science (PLoS), Vol 13, Num 9, pp e1005661, 2017, doi:10.1371/journal.pcbi.1005661

Small, Patrick and Gill, David and Maechling, Philip J. and Taborda, Ricardo and Callaghan, Scott and Jordan, Thomas H. and Olsen, Kim B. and Ely, Geoffrey P. and Goulet, Christine: "The SCEC Unified Community Velocity Model Software Framework", Seismological Research Letters, GeoScienceWorld, Vol 88, Num 5, 2017, doi:10.1785/0220170082

Bret M. Boyd, Julie M. Allen, Nam-Phuong Nguyen, Andrew D. Sweet, Tandy Warnow, Michael D. Shapiro, Scott M. Villa, Sarah E. Bush, Dale H. Clayton, Kevin P. Johnson: "Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola)", Systematic Biology, Oxford University Press, Vol 66, Num 6, pp 896–911, 2017, doi:10.1093/sysbio/syx027

Chao Zhang, Lian Duan, and Meelan M. Choudhari: "Effect of Wall Cooling on Boundary-Layer-Induced Pressure Fluctuations at Mach 6", Journal of Fluid Mechanics, Cambridge University Press (CUP), Vol 822, pp 5--30, 2017, doi:10.1017/jfm.2017.212

Anglés-Alcázar, Daniel; Faucher-Giguère, Claude-André; Quataert, Eliot; Hopkins, Philip F.; Feldmann, Robert; Torrey, Paul; Wetzel, Andrew; Kereš, Dušan: "Black Holes on FIRE: Stellar Feedback Limits Early Feeding of Galactic Nuclei", Monthly Notices of the Royal Astronomical Society: Letters, Oxford University Press (OUP), pp slx161, 2017, doi:10.1093/mnrasl/slx161

Alex Lindsay and Gavin Ridley and Cody Permann and Katy Huff and John W. Peterson and Andrew E Slaughter and Derek Gaston and David Andrs and Robert Carlsen and Andrei Rykhlevskii: "Arfc/moltres: 3D steady-state and 2D transient capabilities", Zenodo, 2017, doi:10.5281/zenodo.887941

Ashraf Idkaidek, Vineet Agarwal, and Iwona Jasiuk: "Finite Element Simulation of Reference Point Indentation on Bone", Journal of the Mechanical Behavior of Biomedical Materials, Elsevier BV, Vol 65, pp 574--583, 2017, doi:10.1016/j.jmbbm.2016.08.031

Ozgur Tumuklu, and Deborah A. Levin: "On the Temporal Evolution in Laminar Separated Boundary Layer Shock-Interaction Flows Using DSMC", American Institute of Aeronautics and Astronautics, 55th AIAA Aerospace Sciences Meeting, Grapevine, Texas, U.S.A., 2017, doi:10.2514/6.2017-1614

Saurabh Sawant, Ozgur Tumuklu, Revathi Jambunathan, and Deborah A. Levin: "Novel Use of AMR Unstructured Grids in DSMC Compressible Flow Simulations", American Institute of Aeronautics and Astronautics, 47th AIAA Thermophysics Conference, Denver, Colorado, U.S.A., 2017, doi:10.2514/6.2017-4028