James Phillips' Publications
GPU computing. John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and James C. Phillips. Proceedings of the IEEE, accepted.
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, in press.
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.
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 Kalé, 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. Kalé, 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.