#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel GA Smith, Zhuoran Qiao, Sai Krishna Sirumalla, Michael O’Connor, Frederick Manby, Anima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel Zuckerman, Adrian Mulholland, Thomas Miller III, Shantenu Jha, Arvind Ramanathan, Lillian Chong, and Rommie Amaro. bioRxiv, 2021/11/15. doi: 10.1101/2021.11.12.468428

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Lorenzo Casalino, Abigail C Dommer, Zied Gaieb, Emilia 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 DC 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, and Rommie E Amaro. The International Journal of High Performance Computing Applications. April 2021. doi: 10.1177/10943420211006452

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, and Matthew J. Turk. F1000Research 9, 2020. doi: 10.12688/f1000research.25561.1

Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Phillips, D. Hardy, J. Maia, J. Stone, J. Ribeiro, R. Bernardi, R. Buch, G. Fiorin, J. Henin, W. Jiang, R. McGreevy, M. C. R. Melo, B. Radak, R. Skeel, A. Singharoy, Y. Wang, B. Roux, A. Aksimentiev, Z. L. Schulten, L. Kale, K. Schulten, C. Chipot, and E. Tajkhorshid. Journal of Chemical Physics, 153:044130, 2020. doi: 10.1063/5.0014475

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. A. Singharoy, C. Maffeo, K.H. Delgado-Magnero, D. J. K. Swainsbury, M.Sener, U. Kleinekathöfer, B. Isralewitz, I. Teo, D. Chandler, J. W. Vant, J. E. Stone, J. Phillips, T. V. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten, P. Tieleman, C. N. Hunter, E. Tajkhorshid, A. Aksimentiev, and K. Schulten Cell, 179:1098-1111, 2019.

Scalable Molecular Dynamics with NAMD on the Summit System. B. Acun, D. J. Hardy, L. V. Kale, K. Li, J. C. Phillips, and J. E. Stone. IBM Journal of Research and Development, Volume 62, Issue 6, Nov.-Dec. 1 2018. DOI

What You Should Know About NAMD and Charm++ But Were Hoping to Ignore. James C. Phillips. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18). ACM, New York, NY, USA, Article 55, 6 pages. 2018.

NAMD goes quantum: an integrative suite for hybrid simulations. Marcelo C R Melo, Rafael C Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C Phillips, Julio D C Maia, Gerd B Rocha, Joo V Ribeiro, John E Stone, Frank Neese, Klaus Schulten, & Zaida Luthey-Schulten. Nature Methods, volume 15, pages 351-354, 2018.

NAMD: Scalable Molecular Dynamics Based on the Charm++ Parallel Runtime System. Bilge Acun, Ronak Buch, Laxmikant Kale, and James C. Phillips. Exascale Scientific Applications: Scalability and Performance Portability, Tjerk P. Straatsma, Katerina B. Antypas, and Timothy J. Williams, editors, CRC Press, 2017.

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Brian K. Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C. Phillips, Klaus Schulten, and Benot Roux. J. Chem. Theory Comput., 2017.

Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Fuxing Zeng, Yanbo Chen, Jonathan Remis, Mrinal Shekhar, James C. Phillips, Emad Tajkhorshid, and Hong Jin. Nature, 541:554-557, 2017.

QwikMD-integrative molecular dynamics toolkit for novices and experts. Joao V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C. Phillips, Peter L. Freddolino, and Klaus Schulten. Scientific Reports, 6:26536, 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, and Klaus Schulten. International Workshop on OpenPOWER for HPC (IWOPH'16), 2016. In Press.

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, and Klaus Schulten. Parallel and Distributed Processing Symposium Workshop, 2016 (in press).

Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing. John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matt Johnson, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten. Parallel Computing, 55:17-27, 2016.

Multilevel Summation Method for Electrostatic Force Evaluation. David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten. Journal of Chemical Theory and Computation, 2015. In Press. journal

Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules. Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot. Journal of Chemical Theory and Computation, 2014. In Press. journal

Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laximant V. Kale. In Proceedings of the 2014 International Conference for High Performance Computing, Networking, Storage, and Analysis (SC14), 2014. conference, journal

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, and Klaus Schulten. In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14. IEEE Press, 2014. journal

Visualization of energy conversion processes in a light harvesting organelle at atomic detail. Melih Sener, John E. Stone, Angela Barragan, Abhishek Singharoy, Ivan Teo, Kirby L. Vandivort, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press, 2014.

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Wei Jiang, James Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James Gumbart, Yun Luo, Klaus Schulten, and Benoit Roux. Computer Physics Communications, 185:908-916, 2014.

Optimizing Fine-grained Communication in a Biomolecular Simulation Application on Cray XK6. Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, Terry Jones, Laxmikant V. Kale, and James C. Phillips. In Proceedings of the 2012 ACM/IEEE Conference on Supercomputing (SC12), 2012. journal

GPU/CPU algorithm for generalized Born / solvent-accessible surface area implicit solvent calculations. David E. Tanner, James C. Phillips, and Klaus Schulten. Journal of Chemical Theory and Computation, 8:2521-2530, 2012.

Parallel generalized Born implicit solvent calculations with NAMD. David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten. Journal of Chemical Theory and Computation, 7:3635-3642, 2011.

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. Kale, James C. Phillips, and Chris Harrison. In Proceedings of the 2011 ACM/IEEE Conference on Supercomputing (SC11), 2011. journal

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD. Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell, Jr., Klaus Schulten, and Benoit Roux. J. Phys. Chem. Lett., Vol. 2, pp. 87-92, 2011.

Probing Biomolecular Machines with Graphics Processors. James C. Phillips and John E. Stone. Communications of the ACM, Vol. 52, No. 10 (October 2009), Pages 34-41.

GPU Clusters for High-Performance Computing. Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman, Galen Arnold, John Stone, James Phillips and Wen-mei Hwu. In Proceedings of IEEE Cluster 2009, Workshop on Parallel Programming on Accelerator Clusters (PPAC), 2009.

Adapting a message-driven parallel application to GPU-accelerated clusters. James C. Phillips, John E. Stone, and Klaus Schulten. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC08), 2008.

GPU computing. John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and James C. Phillips. Proceedings of the IEEE, 96:879-899, 2008.

Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms. Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale. In Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008.

Biomolecular modeling in the era of petascale computing. Klaus Schulten, James C. Phillips, Laxmikant V. Kalé, and Abhinav Bhatele. In David Bader, editor, Petascale Computing: Algorithms and Applications, pp. 165-181. Chapman and Hall/CRC Press, Taylor and Francis Group, New York, 2008.

Scalable molecular dynamics with NAMD on the Blue Gene/L system. Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, and Laxmikant V. Kale. IBM Journal of Research and Development, Volume 52, No. 1/2, 2007.

Accelerating molecular modeling applications with graphics processors. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007.

Correcting Mesh-Based Force Calculations to Conserve Both Energy and Momentum in Molecular Dynamics Simulations. Robert D. Skeel, David J. Hardy and James C. Phillips. Journal of Computational Physics, 225:1-5, 2007.

Managing biomolecular simulations in a grid environment with NAMD-G. Michelle Gower, Jordi Cohen, James Phillips, Richard Kufrin, and Klaus Schulten. In Proceedings of the 2006 Tera Grid Conference, 2006.

Scalable molecular dynamics with NAMD. James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005.

Biomolecular modeling using parallel supercomputers. Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng. In S. Aluru, editor, Handbook of computational molecular biology, pp. 34.1-34.43. Taylor and Francis, 2005.

Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins. Amy Y. Shih, Ilia G. Denisov, James C. Phillips, Stephen G. Sligar, and Klaus Schulten. Biophysical Journal, 88:548-556, 2005.

Large scale simulation of protein mechanics and function. Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. In Frederic M. Richards, David S. Eisenberg, and John Kuriyan, editors, Advances in Protein Chemistry, 66:195-247. Elsevier Academic Press, New York, 2003.

NAMD: Biomolecular Simulation on Thousands of Processors. James C. Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant V. Kalé. Proceedings of the IEEE/ACM SC2002 Conference. IEEE Press, 2002.

Molecular dynamics study of bacteriorhodopsin and the purple membrane. Jerome Baudry, Emad Tajkhorshid, Ferenc Molnar, James Phillips, and Klaus Schulten. Journal of Physical Chemistry B, 105(5):905-918, 2001.

Scalable Molecular Dynamics for Large Biomolecular Systems. Robert K. Brunner, James C. Phillips, Laxmikant V. Kalé. Proceedings of the IEEE/ACM SC2000 Conference. IEEE Press, 2000. Reprinted as Scientific Programming, 8(3):195-207, 2000.

Speech/gesture interface to a visual-computing environment. Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo, Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten. IEEE Computer Graphics and Applications, 20:29-37, 2000.

NAMD2: Greater scalability for parallel molecular dynamics. Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. Journal of Computational Physics, 151:283-312, 1999.

Flexibility and Inter-operability in a Parallel Biomolecular Dynamics Code. Robert Brunner, Laxmikant Kal, and James Phillips. In M.E. Henderson, C.R. Anderson, and S.L. Lyons, editors, Object Oriented Methods for Interoperable Scientific and Engineering Computing, Proceedings in Applied Mathematics 99, 1999.

BioCoRE: A collaboratory for structural biology. Milind Bhandarkar, Gila Budescu, William F. Humphrey, Jesus A. Izaguirre, Sergei Izrailev, Laxmikant V. Kalé, Dorina Kosztin, Ferenc Molnar, James C. Phillips, and Klaus Schulten. In Agostino G. Bruzzone, Adelinde Uchrmacher, and Ernest H. Page, editors, Proceedings of the SCS International Conference on Web-Based Modeling and Simulation, pages 242-251, San Francisco, California, 1999.

Slow algebraic relaxation in quartic potentials and related results. R.S. Sinkovits, S. Sen, J.C. Phillips, S. Chakravarti. Physical Review E, 59(6):6497-6512, 1999.

Quantum dynamics of retinal's femtosecond photoisomerization in bacteriorhodopsin. Michal Ben-Nun, Ferenc Molnar, Hui Lu, James C. Phillips, Todd J. Martínez, and Klaus Schulten. In Faraday Discussions, No. 110, pages 447-462. Faraday Publications, December 1998.

Avoiding algorithmic obfuscation in a message-driven parallel MD code. James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. In P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich, and R. D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pages 472-482. Springer-Verlag, November 1998.

NAMD: A Case Study in Multilingual Parallel Programming. L.V. Kal, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips, and A. Shinozaki. In Z. Li, P.-C. Yew, S. Chatterjee, C.-H. Huang, P. Sadayappan, and D. Sehr, editors, Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, 1366:367-381, 1998. Springer-Verlag.

Predicting the structure of apolipoprotein A-I in reconstituted high density lipoprotein disks. James C. Phillips, Willy Wriggers, Zhigang Li, Ana Jonas, and Klaus Schulten. Biophysical Journal, 73:2337-2346, 1997.

A visual computing environment for very large scale biomolecular modeling. Michael Zeller, James C. Phillips, Andrew Dalke, William Humphrey, Klaus Schulten, Rajeev Sharma, T. S. Huang, V. I. Pavlovic, Y. Zhao, Z. Lo, and S. Chu. In Proceedings of the 1997 IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP), pages 3-12. IEEE Computer Society Press, 1997.

Speech/gesture interface to a visual computing environment for molecular biologists. R. Sharma, T. S. Huang, V. I. Pavlovic, K. Schulten, A. Dalke, J. Phillips, M. Zeller, W. Humphrey, Y. Zhao, Z. Lo, and S. Chu. In Proceedings of 13th ICPR 96, volume 3, pages 964-968, 1996.

Protein response to external electric fields: Relaxation, hysteresis and echo. Dong Xu, James Christopher Phillips, and Klaus Schulten. Journal of Physical Chemistry, 100:12108-12121, 1996.

Diffusive hysteresis at high and low driving frequencies. James Phillips and Klaus Schulten. Physical Review E, 52:2473-2477, 1995.

Relaxation in a Duffing potential. Surajit Sen and James Christopher Phillips. Physica A, 216:271-287, 1995.

Asymptotic behavior of dynamical correlations via perturbative analysis of infinite continued fractions. Surajit Sen and James Christopher Phillips. Physical Review E, 47(5):3152-3157, 1993.

Zeolite Adsorption Site Location and Shape Shown by Simulated Isodensity Surfaces. Paul R. VanTassel, James C. Phillips, H. Ted Davis, and Alon V. McCormick. Journal of Molecular Graphics 11, 180, 1993.

Visualizing Global Datasets with Explorer 2.0. James C. Phillips, Paul J. Morin, and David A. Yuen. University of Minnesota Army High Performance Computing Research Center Preprint 93-013 and University of Minnesota Supercomputer Institute Research Report UMSI 93/4, January 1993.

Visualizing Global Datasets with the Program Explorer. James C. Phillips, Paul J. Morin, and David A. Yuen. University of Minnesota Army High Performance Computing Research Center Preprint 92-069, June 1992.