James C. Phillips

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 11

Top Topics

Future Directions

Computing Platform

Affine Invariant

Molecular Dynamics

Top Venues

Int. J. High Perform. Comput. Appl.

IBM J. Res. Dev.

Publications

Santiago Antolínez, Peter Eugene Jones, James C. Phillips, Jodi A. Hadden-Perilla
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD. J. Chem. Inf. Model. 64 (2) (2024)
Abigail C. Dommer, Lorenzo Casalino, Fiona L. Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, A. Sofia F. Oliveira, Clare Morris, Anthony T. Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, S. Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders S. Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai K. Sirumalla, Michael O'connor, Frederick R. Manby, Anima Anandkumar, David J. Hardy, James C. Phillips, Abraham C. Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John D. McCalpin, Christopher J. Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E. Stone, Daniel M. Zuckerman, Adrian J. Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T. Chong, Rommie E. Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. 37 (1) (2023)
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, John D. McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey Wells, Venkatesh Mysore, Tom Gibbs, James C. Phillips, S. Chakra Chennubhotla, Ian T. Foster, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A Harris, Arvind Ramanathan
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. Int. J. High Perform. Comput. Appl. 36 (5-6) (2022)
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, Matteo Turilli, Syma Khalid, Lillian T. Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham C. Stern, Lei Huang, John D. McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int. J. High Perform. Comput. Appl. 35 (5) (2021)
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
The challenges of theory-software translation. F1000Research 9 (2020)
Caroline Jay, Robert Haines, Daniel S. Katz, Jeffrey C. Carver, James C. Phillips, Anshu Dubey, Sandra Gesing, Matthew J. Turk, Hui Wan, Hubertus Van Dam, James Howison, Vitali A. Morozov, Steven R. Brandt
Theory-Software Translation: Research Challenges and Future Directions. CoRR (2019)
Bilge Acun, David J. Hardy, Laxmikant V. Kalé, Keqin Li, James C. Phillips, John E. Stone
Scalable molecular dynamics with NAMD on the Summit system. IBM J. Res. Dev. 62 (6) (2018)
James C. Phillips
What You Should Know About NAMD and Charm++ But Were Hoping to Ignore. PEARC (2018)
John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, João V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F. Kourkoutis, C. Neil Hunter, Klaus Schulten
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. Parallel Comput. 55 (2016)
John E. Stone, Antti-Pekka Hynninen, James C. Phillips, Klaus Schulten
Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms. ISC Workshops (2016)
John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida Luthey-Schulten, Klaus Schulten
Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. IPDPS Workshops (2016)
James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, Laxmikant V. Kalé
Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. SC (2014)
James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, Klaus Schulten
Petascale Tcl with NAMD, VMD, and Swift/T. HPTCDL@SC (2014)
Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Comput. Phys. Commun. 185 (3) (2014)
Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, James C. Phillips, Laximant V. Kalé, Terry R. Jones
Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6. SC (2012)
Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kalé, James C. Phillips, Chris Harrison
Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime. SC (2011)
Jeremy Enos, Craig P. Steffen, Joshi Fullop, Michael T. Showerman, Guochun Shi, Kenneth Esler, Volodymyr V. Kindratenko, John E. Stone, James C. Phillips
Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters. Green Computing Conference (2010)
James C. Phillips, John E. Stone
Probing biomolecular machines with graphics processors. Commun. ACM 52 (10) (2009)
James C. Phillips, John E. Stone
Probing Biomolecular Machines with Graphics Processors. ACM Queue 7 (9) (2009)
Praveen K. Chandrasekharan, Alexander Kister, James C. Phillips
Beta-sandwich - beta-barrel transformation may serve as a model of a conversion of 'normal' soluble proteins into amyloid aggregates. Int. J. Medical Eng. Informatics 1 (4) (2009)
Volodymyr V. Kindratenko, Jeremy Enos, Guochun Shi, Michael T. Showerman, Galen Wesley Arnold, John E. Stone, James C. Phillips, Wen-mei W. Hwu
GPU clusters for high-performance computing. CLUSTER (2009)
Guochun Shi, Volodymyr V. Kindratenko, Ivan S. Ufimtsev, Todd J. Martínez, James C. Phillips, Steven A. Gottlieb
Implementation of scientific computing applications on the Cell Broadband Engine. Sci. Program. 17 (1-2) (2009)
John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, James C. Phillips
GPU Computing. Proc. IEEE 96 (5) (2008)
Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kalé
Overcoming scaling challenges in biomolecular simulations across multiple platforms. IPDPS (2008)
Sameer Kumar, Chao Huang, Gengbin Zheng, Eric J. Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, Laxmikant V. Kalé
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system. IBM J. Res. Dev. 52 (1-2) (2008)
James C. Phillips, John E. Stone, Klaus Schulten
Adapting a message-driven parallel application to GPU-accelerated clusters. SC (2008)
John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten
Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 28 (16) (2007)
Robert D. Skeel, David J. Hardy, James C. Phillips
Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations. J. Comput. Phys. 225 (1) (2007)
David M. Kunzman, Gengbin Zheng, Eric J. Bohm, James C. Phillips, Laxmikant V. Kalé
Poster reception - Charm++ simplifies coding for the cell processor. SC (2006)
Gerald Lucovsky, James C. Phillips
Bond strain and defects at interfaces in high-k gate stacks. Microelectron. Reliab. 45 (5-6) (2005)
James C. Phillips, Rosemary Braun, Wei Wang, James C. Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant V. Kalé, Klaus Schulten
Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (16) (2005)
James C. Phillips, Gengbin Zheng, Sameer Kumar, Laxmikant V. Kalé
NAMD: biomolecular simulation on thousands of processors. SC (2002)
Rajeev Sharma, Michael Zeller, Vladimir Pavlovic, Thomas S. Huang, Zion Lo, Stephen M. Chu, Yunxin Zhao, James C. Phillips, Klaus Schulten
Speech/Gesture Interface to a Visual-Computing Environment. IEEE Computer Graphics and Applications 20 (2) (2000)
Robert Brunner, James C. Phillips, Laxmikant V. Kalé
Scalable Molecular Dynamics for Large Biomolecular Systems. SC (2000)
Laxmikant V. Kalé, Robert Brunner, James C. Phillips, Krishnan Varadarajan
Application Performance of a Linux Cluster Using Converse. IPPS/SPDP Workshops (1999)
James C. Phillips
Algebraic Constructs for the Graphical and Computational Solution to Balancing Chemical Equations. Comput. Chem. 22 (4) (1998)
Laxmikant V. Kalé, Milind A. Bhandarkar, Robert Brunner, Neal Krawetz, James C. Phillips, Aritomo Shinozaki
NAMD: A Case Study in Multilingual Parallel Programming. LCPC (1997)
Michael Zeller, James C. Phillips, Andrew Dalke, William Humphrey, Klaus Schulten, Thomas S. Huang, Vladimir Pavlovic, Yunxin Zhao, Zion Lo, Stephen M. Chu, Rajeev Sharma
A Visual Computing Environment for Very Large Scale Biomolecular Modeling. ASAP (1997)