A Visual Computing Environment for Very Large Scale Biomolecular Modeling. - Michael Zeller; James C. Phillips; Andrew Dalke; William Humphrey; Klaus Schulten; Thomas S. Huang; Vladimir Pavlovic 001; Yunxin Zhao; Zion Lo; Stephen M. Chu; Rajeev Sharma (ASAP, 1997)

NAMD: A Case Study in Multilingual Parallel Programming. - Laxmikant V. Kalé; Milind A. Bhandarkar; Robert Brunner; Neal Krawetz; James C. Phillips; Aritomo Shinozaki (LCPC, 1997)

Algebraic Constructs for the Graphical and Computational Solution to Balancing Chemical Equations. - James C. Phillips (Comput. Chem., 1998)

Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code. - James C. Phillips; Robert Brunner; Aritomo Shinozaki; Milind A. Bhandarkar; Neal Krawetz; Attila Gürsoy; Laxmikant V. Kalé; Robert D. Skeel; Klaus Schulten (Computational Molecular Dynamics, 1999)

Application Performance of a Linux Cluster Using Converse. - Laxmikant V. Kalé; Robert Brunner; James C. Phillips; Krishnan Varadarajan (IPPS/SPDP Workshops, 1999)

Scalable Molecular Dynamics for Large Biomolecular Systems. - Robert Brunner; James C. Phillips; Laxmikant V. Kalé (SC, 2000)

Speech/Gesture Interface to a Visual-Computing Environment. - Rajeev Sharma; Michael Zeller; Vladimir Pavlovic 001; Thomas S. Huang; Zion Lo; Stephen M. Chu; Yunxin Zhao; James C. Phillips; Klaus Schulten (IEEE Computer Graphics and Applications, 2000)

NAMD: biomolecular simulation on thousands of processors. - James C. Phillips; Gengbin Zheng; Sameer Kumar 001; Laxmikant V. Kalé (SC, 2002)

Scalable molecular dynamics with NAMD. - James C. Phillips; Rosemary Braun; Wei Wang 342; James C. Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant V. Kalé; Klaus Schulten (J. Comput. Chem., 2005)

Bond strain and defects at interfaces in high-k gate stacks. - Gerald Lucovsky; James C. Phillips (Microelectron. Reliab., 2005)

Poster reception - Charm++ simplifies coding for the cell processor. - David M. Kunzman; Gengbin Zheng; Eric J. Bohm; James C. Phillips; Laxmikant V. Kalé (SC, 2006)

Accelerating molecular modeling applications with graphics processors. - John E. Stone; James C. Phillips; Peter L. Freddolino; David J. Hardy; Leonardo G. Trabuco; Klaus Schulten (J. Comput. Chem., 2007)

Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations. - Robert D. Skeel; David J. Hardy; James C. Phillips (J. Comput. Phys., 2007)

Overcoming scaling challenges in biomolecular simulations across multiple platforms. - Abhinav Bhatele; Sameer Kumar 001; Chao Mei; James C. Phillips; Gengbin Zheng; Laxmikant V. Kalé (IPDPS, 2008)

Adapting a message-driven parallel application to GPU-accelerated clusters. - James C. Phillips; John E. Stone; Klaus Schulten (SC, 2008)

Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system. - Sameer Kumar 001; Chao Huang 029; Gengbin Zheng; Eric J. Bohm; Abhinav Bhatele; James C. Phillips; Hao Yu; Laxmikant V. Kalé (IBM J. Res. Dev., 2008)

GPU Computing. - John D. Owens; Mike Houston; David Luebke; Simon Green; John E. Stone; James C. Phillips (Proc. IEEE, 2008)

GPU clusters for high-performance computing. - Volodymyr V. Kindratenko; Jeremy Enos; Guochun Shi; Michael T. Showerman; Galen Wesley Arnold; John E. Stone; James C. Phillips; Wen-mei W. Hwu (CLUSTER, 2009)

Beta-sandwich - beta-barrel transformation may serve as a model of a conversion of 'normal' soluble proteins into amyloid aggregates. - Praveen K. Chandrasekharan; Alexander Kister; James C. Phillips (Int. J. Medical Eng. Informatics, 2009)

Probing Biomolecular Machines with Graphics Processors. - James C. Phillips; John E. Stone (ACM Queue, 2009)

Implementation of scientific computing applications on the Cell Broadband Engine. - Guochun Shi; Volodymyr V. Kindratenko; Ivan S. Ufimtsev; Todd J. Martínez; James C. Phillips; Steven A. Gottlieb (Sci. Program., 2009)

Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters. - Jeremy Enos; Craig P. Steffen; Joshi Fullop; Michael T. Showerman; Guochun Shi; Kenneth Esler; Volodymyr V. Kindratenko; John E. Stone; James C. Phillips (Green Computing Conference, 2010)

Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime. - Chao Mei; Yanhua Sun; Gengbin Zheng; Eric J. Bohm; Laxmikant V. Kalé; James C. Phillips; Chris Harrison 001 (SC, 2011)

NAMD (NAnoscale Molecular Dynamics). - Laxmikant V. Kalé; Abhinav Bhatele; Eric J. Bohm; James C. Phillips (Encyclopedia of Parallel Computing, 2011)

Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6. - Yanhua Sun; Gengbin Zheng; Chao Mei; Eric J. Bohm; James C. Phillips; Laximant V. Kalé; Terry R. Jones (SC, 2012)

Scalable Molecular Dynamics with NAMD. - James C. Phillips; Klaus Schulten; Abhinav Bhatele; Chao Mei; Yanhua Sun; Eric J. Bohm; Laxmikant V. Kalé (Parallel Science and Engineering Applications, 2013)

Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. - James C. Phillips; Yanhua Sun; Nikhil Jain; Eric J. Bohm; Laxmikant V. Kalé (SC, 2014)

Petascale Tcl with NAMD, VMD, and Swift/T. - James C. Phillips; John E. Stone; Kirby L. Vandivort; Timothy G. Armstrong; Justin M. Wozniak; Michael Wilde; Klaus Schulten (HPTCDL@SC, 2014)

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. - Wei Jiang; James C. Phillips; Lei Huang 019; Mikolai Fajer; Yilin Meng; James C. Gumbart; Yun Luo; Klaus Schulten; Benoît Roux (Comput. Phys. Commun., 2014)

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. - John E. Stone; Michael J. Hallock; James C. Phillips; Joseph R. Peterson; Zaida Luthey-Schulten; Klaus Schulten (IPDPS Workshops, 2016)

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms. - John E. Stone; Antti-Pekka Hynninen; James C. Phillips; Klaus Schulten (ISC Workshops, 2016)

Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. - John E. Stone; Melih Sener; Kirby L. Vandivort; Angela M. Barragan; Abhishek Singharoy; Ivan Teo; João V. Ribeiro 003; Barry Isralewitz; Bo Liu; Boon Chong Goh; James C. Phillips; Craig MacGregor-Chatwin; et al. (Parallel Comput., 2016)

What You Should Know About NAMD and Charm++ But Were Hoping to Ignore. - James C. Phillips (PEARC, 2018)

Scalable molecular dynamics with NAMD on the Summit system. - Bilge Acun; David J. Hardy; Laxmikant V. Kalé; Keqin Li 001; James C. Phillips; John E. Stone (IBM J. Res. Dev., 2018)

Theory-Software Translation: Research Challenges and Future Directions. - Caroline Jay; Robert Haines; Daniel S. Katz; Jeffrey C. Carver; James C. Phillips; Anshu Dubey; Sandra Gesing; Matthew Turk 002; Hui Wan; Hubertus Van Dam; James Howison; Vitali A. Morozov; et al. (CoRR, 2019)

The challenges of theory-software translation. - Caroline Jay; Robert Haines; Daniel S. Katz; Jeffrey C. Carver; Sandra Gesing; Steven R. Brandt; James Howison; Anshu Dubey; James C. Phillips; Hui Wan; Matthew J. Turk (F1000Research, 2020)

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. - Lorenzo Casalino; Abigail C. Dommer; Zied Gaieb; Emília P. Barros; Terra Sztain; Surl-Hee Ahn; Anda Trifan; Alexander Brace; Anthony T. Bogetti; Austin Clyde; Heng Ma; Hyungro Lee; et al. (Int. J. High Perform. Comput. Appl., 2021)

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. - Anda Trifan; Defne Gorgun; Michael Salim; Zongyi Li; Alexander Brace; Maxim Zvyagin; Heng Ma; Austin Clyde; David Clark; David J. Hardy; Tom Burnley; Lei Huang 019; et al. (Int. J. High Perform. Comput. Appl., 2022)

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. - Abigail C. Dommer; Lorenzo Casalino; Fiona L. Kearns; Mia A. Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)

AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD. - Santiago Antolínez; Peter Eugene Jones; James C. Phillips; Jodi A. Hadden-Perilla (J. Chem. Inf. Model., 2024)