Selected Publications and Presentations

  • 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.
  • Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, T.J. Christopher Ward, Mark Giampapa, Michael C. Pitman, and Robert S. Germain. Blue matter: Approaching the limits of concurrency for molecular dynamics. Research Report RC23956, IBM Research Division, April 2006.
  • 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)
  • 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-September2, 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)
  • 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, Robert S. Germain, and Scott Feller. Blue matter: Strong scaling of molecular dynamics on Blue Gene/L. Research Report RC23688, IBM Research Division, August 2005.
  • 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)
  • 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)
  • 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)
  • Maria Eleftheriou, Jose E. Moreira, Blake G. Fitch, and Robert S. Germain. A volumetric FFT for Blue Gene/L. In Timothy Mark Pinkston and Viktor K. Prasanna, editors, High Performance Computing - HiPC 2003, volume 2913 of Lecture Notes in Computer Science, pages 194–203. Springer, January 2003. (doi:10.1007/b94479)
  • 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)
  • 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)
  • 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)
  • Robert S. Germain, Andrea Califano, and Scott Colville. Fingerprint matching using transformation parameter clustering. IEEE Comput. Sci. Eng., 4(4):42–49, 1997. (doi:10.1109/99.641608)