- J.D. Chodera, W.C. Swope, J.W. Pitera, C. Seok, and K.A. Dill. Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. Journal of Chemical Theory and Computation, 3(1):26–41, 2007. (doi:10.1021/ct0502864)
- John D. Chodera, Nina Singhal, Vijay S. Pande, Ken A. Dill, and William C. Swope. Automatic discovery of metastable states for the construction of markov models of macromolecular conformational dynamics. The Journal of Chemical Physics, 126(15):155101, 2007. (doi:10.1063/1.2714538)
- Alan Grossfield, Scott E. Feller, and Michael C. Pitman. Convergence of molecular dynamics simulations of membrane proteins. Proteins: Structure, Function, and Bioinformatics, 67(1):31–40, 2007. (doi:10.1002/prot.21308)
- Ruhong Zhou, Maria Eleftheriou, Ajay K. Royyuru, and Bruce J. Berne. Destruction of long-range interactions by a single mutation in lysozyme. PNAS, 104(14):5824–5829, 2007. (doi:10.1073/pnas.0701249104)
- John D. Chodera, William C. Swope, Jed W. Pitera, and Ken A. Dill. Long-time protein folding dynamics from short-time molecular dynamics simulations. Multiscale Modeling & Simulation, 5(4):1214–1226, 2006. (doi:10.1137/06065146X)
- Lillian T. Chong, William C. Swope, Jed W Pitera, and Vijay S. Pande. Kinetic computational alanine scanning: Application to p53 oligomerization. Journal of Molecular Biology, 357(3):1039–1049, March 2006. (doi:10.1016/j.jmb.2005.12.083)
- M. Eleftheriou, A. Rayshubskiy, J. W. Pitera, B. G. Fitch, R. Zhou, and R. S. Germain. Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L. In Fifth IEEE International Workshop on High Performance Computational Biology, April 2006.
- Maria Eleftheriou, Robert S. Germain, Ajay K. Royyuru, and Ruhong Zhou. Thermal denaturing of mutant lysozyme with both the oplsaa and the charmm force fields. Journal of the American Chemical Society, 128(41):13388–13395, 2006. Journal of the American Chemical Society. (doi:10.1021/ja060972s)
- Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, T.J. Christopher Ward, Mark Giampapa, Michael C. Pitman, and Robert S. Germain. Molecular dynamics—blue matter: approaching the limits of concurrency for classical molecular dynamics. In SC '06: Proceedings of the 2006 ACM/IEEE conference on Supercomputing, page 87, New York, NY, USA, November 2006. ACM Press. (doi:10.1145/1188455.1188547)
- Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, T.J. Christopher Ward, Mark Giampapa, Yuri Zhestkov, Michael C. Pitman, Frank Suits, Alan Grossfield, Jed Pitera, William Swope, Ruhong Zhou, Scott Feller, and Robert S. Germain. Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L. In V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, editors, International Conference on Computational Science (ICCS 2006), volume 3992 of LNCS, pages 846–854. Springer-Verlag, 2006. (doi:10.1007/11758525_113)
- Alan Grossfield, Scott E. Feller, and Michael C. Pitman. A role for direct interactions in the modulation of rhodopsin by ω-3 polyunsaturated lipids. PNAS, 103(13):4888–4893, 2006. (doi:10.1073/pnas.0508352103)
- Alan Grossfield, Scott E. Feller, and Michael C. Pitman. Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation. J. Phys. Chem B, 110(18):8907–8909, 2006. (doi:10.1021/jp060405r)
- Edgar Larios, Jed W. Pitera, William C. Swope, and Martin Gruebele. Correlation of early orientational ordering of engineered lambda 6–85 structure with kinetics and thermodynamics. Chemical Physics, 323(1):45–53, March 2006. (doi:10.1016/j.chemphys.2005.08.048)
- K. Martinez-Mayorga, M.C. Pitman, A. Grossfield, S.E. Feller, and M.F. Brown. Retinal counterion switch mechanism in vision evaluated by molecular simulations. Journal of the American Chemical Society, 128(51):16502–16503, 2006. (doi:10.1021/ja0671971)
- Jed W. Pitera, Imran Haque, and William C. Swope. Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide. The Journal of Chemical Physics, 124(14):141102, 2006. (doi:10.1063/1.2190226)
- W. C. Swope, J. W. Pitera, and R. S. Germain. Molecular simulation and systems biology. In I. Rigoutsos and G. Stephanopoulos, editors, Genomics and Systems Biology/Networks & Models in Systems Biology. Oxford University Press, 2006.
- George Almasi, Gyan Bhanot, Dong Chen, Maria Eleftheriou, Blake Fitch, Alan Gara, Robert Germain, John Gunnels, Manish Gupta, Philip Heidelberger, Michael Pitman, Aleksandr Rayshubskiy, James Sexton, Frank Suits, Pavlos Vranas, Robert Walkup, Chris Ward, Yuriy Zhestkov, Alessandro Curioni, Wanda Andreoni, Charles Archer, Jose Moreira, Richard Loft, Henry Tufo, Theron Voran, and Katherine Riley. Early experience with scientific applications on the Blue Gene/L supercomputer. In Jose C. Cunha and Pedro D. Medeiros, editors, Euro-Par 2005 Parallel Processing: 11th International Euro-Par Conference, Lisbon, Portugal, August 30 - September 2, 2005. Proceedings, volume 3648 of Lecture Notes in Computer Science, page 560. Springer-Verlag, 2005. (doi:10.1007/11549468_63)
- M. Eleftheriou, B. Fitch, A. Rayshubskiy, T.J.C. Ward, and R.S. Germain. Performance measurements of the 3d FFT on the Blue Gene/L supercomputer. In J.C. Cunha and P.D. Medeiros, editors, Euro-Par 2005 Parallel Processing: 11th International Euro-Par Conference, Lisbon, Portugal, August 30-September 2, 2005, volume 3648 of Lecture Notes in Computer Science, pages 795–803. Springer-Verlag, 2005. (doi:10.1007/11549468_87)
- M. Eleftheriou, B.G Fitch, A. Rayshubskiy, T.J.C. Ward, and R.S. Germain. Scalable framework for 3d FFTs on the Blue Gene/L supercomputer: Implementation and early performance measurements. IBM Journal of Research and Development, 49(2/3):457–464, 2005. (doi:10.1147/rd.492.0457)
- R.F. Enenkel et al. Custom math functions for molecular dynamics. IBM Journal of Research and Development, 49(2/3):465–474, 2005. (doi:10.1147/rd.492.0465)
- Robert S. Germain, Blake Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, Michael C. Pitman, Frank Suits, Mark Giampapa, and T.J. Christopher Ward. Blue Matter on Blue Gene/L: massively parallel computation for biomolecular simulation. In CODES+ISSS '05: Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis, pages 207–212, New York, NY, USA, 2005. ACM Press. (doi:10.1145/1084834.1084888)
- R.S. Germain, Y. Zhestkov, M. Eleftheriou, A. Rayshubskiy, F. Suits, T.J.C. Ward, and B.G. Fitch. Early performance data on the Blue Matter molecular simulation framework. IBM Journal of Research and Development, 49(2/3):447–456, 2005. (doi:10.1147/rd.492.0447)
- Hans W. Horn, William C. Swope, and Jed W. Pitera. Characterization of the tip4p-ew water model: Vapor pressure and boiling point. The Journal of Chemical Physics, 123(19):194504, 2005. (doi:10.1063/1.2085031)
- Michael C. Pitman, Alan Grossfield, Frank Suits, and Scott E. Feller. Role of cholesterol and polyunsaturated chains in lipid-protein interactions: Molecular dynamics simulation of rhodopsin in a realistic membrane environment. Journal of the American Chemical Society, 127(13):4576–4577, 2005. (doi:10.1021/ja042715y)
- Michael C. Pitman, Frank Suits, Klaus Gawrisch, and Scott E. Feller. Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers. Journal of Chemical Physics, 122(24):244715, 2005. (doi:10.1063/1.1899153)
- F. Suits, M.C. Pitman, J.W. Pitera, W.C. Swope, and R.S. Germain. Overview of molecular dynamics techniques and early scientific results from the Blue Gene project. IBM Journal of Research and Development, 49(2/3):475–488, 2005. (doi:10.1147/rd.492.0475)
- Frank Suits, Michael C. Pitman, and Scott E. Feller. Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers. Journal of Chemical Physics, 122(24), 2005. (doi:10.1063/1.1899152)
- Hans W. Horn, William C. Swope, Jed W. Pitera, Jeffry D. Madura, Thomas J. Dick, Greg L. Hura, and Teresa Head-Gordon. Development of an improved four-site water model for biomolecular simulations: Tip4p-ew. The Journal of Chemical Physics, 120(20):9665–9678, 2004. (doi:10.1063/1.1683075)
- Michael C. Pitman, Frank Suits, Jr. MacKerell, Alexander D., and Scott E. Feller. Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol. Biochemistry, 43(49):15318–15328, 2004. (doi:10.1021/bi048231w)
- William C. Swope, Jed W. Pitera, and Frank Suits. Describing protein folding kinetics by molecular dynamics simulations. 1. theory. J. Phys. Chem. B, 108(21):6571 – 6581, 2004. (doi:10.1021/jp037421y)
- William C. Swope, Jed W. Pitera, Frank Suits, Mike Pitman, Maria Eleftheriou, Blake G. Fitch, Robert S. Germain, Aleksandr Rayshubskiy, T. J. C. Ward, Yuriy Zhestkov, and Ruhong Zhou. Describing protein folding kinetics by molecular dynamics simulations. 2. example applications to alanine dipeptide and a β-hairpin peptide. J. Phys. Chem. B, 108(21):6582–6594, 2004. (doi:10.1021/jp037422q)
- Wei Yuan Yang, Jed W. Pitera, William C. Swope, and Martin Gruebele. Heterogeneous folding of the trpzip hairpin: Full atom simulation and experiment. Journal of Molecular Biology, 336(1):241–251, February 2004. (doi:10.1016/j.jmb.2003.11.033)
- B.G. Fitch, R.S. Germain, M. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Sham, F. Suits, W. Swope, T.J.C. Ward, Y. Zhestkov, and R. Zhou. Blue Matter, an application framework for molecular simulation on Blue Gene. Journal of Parallel and Distributed Computing, 63:759–773, 2003. (doi:10.1016/S0743-7315(03)00084-4)
- J. Pitera and W. Swope. Understanding folding and design: replica-exchange simulations of the trp-cage miniprotein. Proc. natl. Acad. Sci. U.S.A., 100:7587–7592, 2003.
- Michael R. Shirts, Jed W. Pitera, William C. Swope, and Vijay S. Pande. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins. The Journal of Chemical Physics, 119(11):5740–5761, 2003. (doi:10.1063/1.1587119)
- Ruhong Zhou. Trp-cage: Folding free energy landscape in explicit water. Proceedings of the National Academy of Sciences, 100(23):13280–13285, November 2003. (doi:10.1073/pnas.2233312100)
- NR Adiga, G Almasi, GS Almasi, Y Aridor, R Barik, D Beece, R Bellofatto, G Bhanot, R Bickford, M Blumrich, AA Bright, J Brunheroto, C Cascaval, J Castaños, W Chan, L Ceze, P Coteus, S Chatterjee, D Chen, G Chiu, TM Cipolla, P Crumley, KM Desai, A Deutsch, T Domany, MB Dombrowa, W Donath, M Eleftheriou, C Erway, J Esch, B Fitch, J Gagliano, A Gara, R Garg, R Germain, ME Giampapa, B Gopalsamy, J Gunnels, M Gupta, F Gustavson, S Hall, RA Haring, D Heidel, P Heidelberger, LM Herger, D Hoenicke, RD Jackson, T Jamal-Eddine, GV Kopcsay, E Krevat, MP Kurhekar, AP Lanzetta, D Lieber, LK Liu, M Lu, M Mendell, A Misra, Y Moatti, L Mok, JE Moreira, BJ Nathanson, M Newton, M Ohmacht, A Oliner, V Pandit, RB Pudota, R Rand, R Regan, B Rubin, A Ruehli, S Rus, RK Sahoo, A Sanomiya, E Schenfeld, M Sharma, E Shmueli, S Singh, P Song, V Srinivasan, BD Steinmacher-Burow, K Strauss, C Surovic, R Swetz, T Takken, RB Tremaine, M Tsao, AR Umamaheshwaran, P Verma, P Vranas, TJC Ward, M Wazlowski, W Barrett, C Engel, B Drehmel, B Hilgart, D Hill, F Kasemkhani, D Krolak, CT Li, T Liebsch, J Marcella, A Muff, A Okomo, M Rouse, A Schram, M Tubbs, G Ulsh, C Wait, J Wittrup, M Bae, K Dockser, L Kissel, MK Seager, JS Vetter, and K Yates. An overview of the Blue Gene/L supercomputer. In Proceedings of the 2002 ACM/IEEE conference on Supercomputing, pages 1–22, November 2002.
- Ruhong Zhou and Bruce J. Berne. Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?. Proceedings of the National Academy of Sciences, 99(20):12777–12782, October 2002. (doi:10.1073/pnas.142430099)
- F. Allen, G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, C. Cascaval, J. Castanos, P. Coteus, P. Crumley, A. Curioni, M. Denneau, W. Donath, M. Eleftheriou, B. Fitch, B. Fleischer, C. J. Georgiou, R. Germain, M. Giampapa, D. Gresh, M. Gupta, R. Haring, H. Ho, P. Hochschild, S. Hummel, T. Jonas, D. Lieber, G. Martyna, K. Maturu, J. Moreira, D. Newns, M. Newton, R. Philhower, T. Picunko, J. Pitera, M. Pitman, R. Rand, A. Royyuru, V. Salapura, A. Sanomiya, R. Shah, Y. Sham, S. Singh, M. Snir, F. Suits, R. Swetz, W. C. Swope, N. Vishnumurthy, T. J. C. Ward, H. Warren, and R. Zhou. Blue Gene: a vision for protein science using a petaflop supercomputer. IBM Journal of Research and Development, 40(2):310–327, 2001. (doi:10.1147/sj.402.0310)
- R. Zhou, E. Harder, H. Xu, and B.J. Berne. Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems. Journal of Chemical Physics, 115(5):2348–2358, August 2001.
- Ruhong Zhou, Bruce J. Berne, and Robert Germain. The free energy landscape for beta hairpin folding in explicit water. Proceedings of the National Academy of Sciences, 98(26):14931–14936, December 2001. (doi:10.1073/pnas.201543998)
IBM publications
R. S. Germain, Y. Zhestkov, M. Eleftheriou, A. Rayshubskiy, F. Suits, T. J. C. Ward and B. G. Fitch. Early performance data on the Blue Matter molecular simulation framework. .Maria Eleftheriou, Jose E. Moreira, Blake G. Fitch and Robert S. Germain. A Volumetric FFT for Blue Gene/L. HIPC 2003 - High Performance Computing 2003. IEEE Computer Society/ACM SIGARCH, December 2003.
George L. Chiu, George S. Almasi, Gheorghe Almasi, Daniel K. Beece, Ralph E. Bellofatto, Gyan V. Bhanot, H. Randall Bickford, Matthias A. Blumrich, Arthur A. Bright, Jose R. Brunheroto, Gheorghe C. Cascaval, Jose G. Castanos, Paul W. Coteus, Siddhartha Chatterjee, Dong Chen, Thomas M. Cipolla, Paul G. Crumley, Alina Deutsch, Marc B. Dombrowa, Maria Eleftheriou, Blake G. Fitch, Joseph Gagliano, Alan Gara, Robert S. Germain, Mark E. Giampapa, Manish Gupta, Fred G. Gustavson, Shawn Hall, Rudolf A. Haring, David F. Heidel, Philip Heidelberger, Lorraine M. Herger, Dirk Hoenicke, Tarek J. Jamal-Eddine, Gerard V. Kopcsay, Alphonso P. Lanzetta, Derek Lieber, Minhua Lu, Lawrence S. Mok, Jose Moreira, Ben J. Nathanson, Martin Ohmacht, Rick A. Rand, Richard D. Regan, Ramendra K. Sahoo, Alda Sanomiya, Eugen Schenfeld, Sarabjeet Singh, Peilin S. Song, Burkhard D. Steinmacher-Burow, Richard A. Swetz, Todd Takken, Robert B. Tremaine, Michael Tsao, Pavlos Vranas, T. J. C. Ward and Michael Wazlowski. Blue Gene/L, a System-On-A-Chip. Cluster 2002, IEEE International Conference on Cluster Computing. IEEE Computer Society, September 2002.
Frank Suits, Mike C. Pitman and Scott Feller. Molecular Dynamics Investigation of the Structural Properties of Phosphatidylethanolamine Lipid Bilayers. Journal of Chemical Physics 122(24):Art. no. 244714, June 2005.
Mike C. Pitman, Frank Suits, Klaus Gawrisch and Scott Feller. Molecular Dynamics Investigation of Dynamical Properties of Phosphatidylethanolamine Lipid Bilayers. Journal of Chemical Physics 122(24):Art. no. 244715, June 2005.
Mike C. Pitman, Frank Suits, Alan Grossfield and Scott Feller. Role of Cholesterol and Polyunsaturated Chains in Lipid-Protein Interactions: Molecular Dynamics Simulation of Rhodopsin in a Realistic Membrane Environment. Journal of the American Chemical Society 127(13):4576-7, April 2005.
Mike C. Pitman, Frank Suits, Alan Grossfield and S. E. Feller. Molecular Dynamics Investigation of Dark-Adapted Rhodopsin in an Explicit 2:2:1 SDPE/SDPC/Cholesterol Environment: Membrane Structure and Dynamics. Biophysical Journal 88(1, Pt. 2, Suppl. S):579A, January 2005.
Alan Grossfield, Mike C. Pitman, Frank Suits and S. E. Feller. Molecular Dynamics Investigation of Dark-Adapted Rhodopsin in an Explicit 2:2:1 SDPE/SDPC/Cholesterol Environment: Protein Structure and Dynamics. Biophysical Journal 88(1, Pt. 2, Suppl. S):579A, January 2005.
Mike C. Pitman, Frank Suits, Alexander D. Mackerrell Jr. and Scott E. Feller. Molecular Level Organization of Saturated and Polyunsaturated Fatty Acids in a Phosphatidylcholine Bilayer Containing Cholesterol. Biochemistry 43(49):15318-28, December 2004.
T. Ebisuzaki, Robert S. Germain and M. Taiji. PetaFLOPS Computing. Communications of the ACM 47(11):42-45, November 2004.
William C. Swope, Jed W. Pitera, Frank Suits, Mike C. Pitman, Maria Eleftheriou, Blake G. Fitch, Robert S. Germain, Aleksandr Rayshubskiy, T J C Ward, Yuri Zhestkov and Ruhong Zhou. Describing Protein Folding Kinetics By Molecular Dynamics Simulations: II. Example Applications to Alanine Dipeptide and beta-Hairpin Peptide. Journal of Physical Chemistry B 108(21):6582-94, May 2004.
S. E. Feller and Mike C. Pitman. A Molecular Dynamics Study of the Interaction of Cholesterol with Saturated and Polyunsaturated Fatty Acids in a Phosphatidylcholine Lipid Bilayer. Biophysical Journal, Part 2, Suppl. S 88(1):27A, January 2004.
Mike C. Pitman and S. E. Feller. Structure and Dynamics of 1-stearoyl-2-oleoyl-phosphatidyethanolamine (SOPE) by Molecular Simulation Reveals Notable Differences Compared to 1-palmitoyi-2-oleoyl-phosphatidylcholine (POPC) due to Head Group Hydrogen Bonding in SOPE. Biophysical Journal, Part 2, Suppl. S 86(1):414A-415A, January 2004.
Blake G. Fitch, Robert S. Germain, Mark Mendell, Jed W. Pitera, Mike C. Pitman, Aleksandr Rayshubski, Yuk Sham, Frank Suits, William C. Swope, T. J. C. Ward, Yuriy Zhestkov and Ruhong Zhou. Blue Matter, An Application Framework for Molecular Simulation on Blue Gene. Journal of Parallel and Distributed Computing 63(7-8):759-73, July 2003.