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Journal Articles
- 2024
[j19]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): 543-554 (2024)- 2023
- [j18]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 F. Miller III, 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): 28-44 (2023) - 2022
- [j17]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): 603-623 (2022) - 2021
- [j16]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) - 2018
- [j15]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): 4:1-4:9 (2018) - 2016
- [j14]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: 17-27 (2016) - 2014
- [j13]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): 908-916 (2014) - 2009
- [j12]James C. Phillips, John E. Stone:
Probing biomolecular machines with graphics processors. Commun. ACM 52(10): 34-41 (2009) - [j11]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): 473-489 (2009) - [j10]James C. Phillips, John E. Stone:
Probing Biomolecular Machines with Graphics Processors. ACM Queue 7(9): 30 (2009) - [j9]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): 135-151 (2009) - 2008
- [j8]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): 177-188 (2008) - [j7]John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, James C. Phillips:
GPU Computing. Proc. IEEE 96(5): 879-899 (2008) - 2007
- [j6]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): 2618-2640 (2007) - [j5]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): 1-5 (2007) - 2005
- [j4]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): 1781-1802 (2005) - [j3]Gerald Lucovsky, James C. Phillips:
Bond strain and defects at interfaces in high-k gate stacks. Microelectron. Reliab. 45(5-6): 770-778 (2005) - 2000
- [j2]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): 29-37 (2000) - 1998
- [j1]James C. Phillips:
Algebraic Constructs for the Graphical and Computational Solution to Balancing Chemical Equations. Comput. Chem. 22(4): 295-308 (1998)
Conference and Workshop Papers
- 2018
- [c17]James C. Phillips:
What You Should Know About NAMD and Charm++ But Were Hoping to Ignore. PEARC 2018: 55:1-55:6 - 2016
- [c16]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: 89-100 - [c15]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: 188-206 - 2014
- [c14]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: 6-17 - [c13]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: 81-91 - 2012
- [c12]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: 55 - 2011
- [c11]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: 61:1-61:11 - 2010
- [c10]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: 317-324 - 2009
- [c9]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: 1-8 - 2008
- [c8]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: 1-12 - [c7]James C. Phillips, John E. Stone, Klaus Schulten:
Adapting a message-driven parallel application to GPU-accelerated clusters. SC 2008: 8 - 2006
- [c6]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: 135 - 2002
- [c5]James C. Phillips, Gengbin Zheng, Sameer Kumar, Laxmikant V. Kalé:
NAMD: biomolecular simulation on thousands of processors. SC 2002: 53:1-53:18 - 2000
- [c4]Robert Brunner, James C. Phillips, Laxmikant V. Kalé:
Scalable Molecular Dynamics for Large Biomolecular Systems. SC 2000: 45 - 1999
- [c3]Laxmikant V. Kalé, Robert Brunner, James C. Phillips, Krishnan Varadarajan:
Application Performance of a Linux Cluster Using Converse. IPPS/SPDP Workshops 1999: 483-495 - 1997
- [c2]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: 3- - [c1]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: 367-381
Parts in Books or Collections
- 2013
- [p2]James C. Phillips, Klaus Schulten, Abhinav Bhatele, Chao Mei, Yanhua Sun, Eric J. Bohm, Laxmikant V. Kalé:
Scalable Molecular Dynamics with NAMD. Parallel Science and Engineering Applications 2013: 61-78 - 1999
- [p1]James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind A. Bhandarkar, Neal Krawetz, Attila Gürsoy, Laxmikant V. Kalé, Robert D. Skeel, Klaus Schulten:
Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code. Computational Molecular Dynamics 1999: 472-482
Reference Works
- 2011
- [r1]Laxmikant V. Kalé, Abhinav Bhatele, Eric J. Bohm, James C. Phillips:
NAMD (NAnoscale Molecular Dynamics). Encyclopedia of Parallel Computing 2011: 1249-1254
Informal and Other Publications
- 2020
- [i2]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: 1192 (2020) - 2019
- [i1]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 abs/1910.09902 (2019)
Coauthor Index
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