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IBM Research Blue Gene Project Page
About IBM's Blue Gene Research Project
Blue Gene is an IBM Research project dedicated to exploring the
frontiers in supercomputing: in computer architecture, in the software
required to program and control massively parallel systems, and in the
use of computation to advance our understanding of important
biological processes such as protein folding.
The full Blue Gene/L machine is being built with the Department of
Energy's NNSA/Lawrence Livermore National Laboratory in California,
and will have a peak speed of 360 Teraflops. Blue Gene/L occupies the
#1 position in the TOP500
supercomputer list announced in November 2005 and IBM now offers a Blue
Gene Solution. IBM and its collaborators are currently exploring
a growing list of applications including hydrodynamics, quantum
chemistry, molecular dynamics, climate modeling and financial
modeling.
Photos of Blue Gene/L available at this link
Presentations, Preprints, and Publications
Blue Matter on Blue Gene/L: massively parallel computation for biomolecular simulation; Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis 2005; Jersey City, NJ, USA; September 19 - 21, 2005, pp 207 - 212
Performance Measurements of the 3D FFT on the Blue Gene/L Supercomputer; Lecture Notes in Computer Science, Volume 3648, Aug 2005, pp 795 - 803
Early Experience with Scientific Applications on the Blue Gene/L Supercomputer; Lecture Notes in Computer Science, Volume 3648, Aug 2005, pp 560 - 570
Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L; IBM Research Cyberdigest
Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers; The Journal of Chemical Physics 2005; 122(24) , 244715
Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers; The Journal of Chemical Physics 2005; 122(24) , 244714
IBM Journal of Research and Development, Vol. 49, No. 2/3, 2005; Special Issue on Blue Gene Supplementary Material
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 2005; 127(13) pp 4576 - 4577
Molecular-Level Organization of Saturated and Polyunsaturated Fatty Acids in a Phosphatidylcholine Bilayer Containing Cholesterol; Biochemistry 43(49); 2004; 15318-15328
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory; The Journal of Physical Chemistry B; 108(21); 2004; 6571-6581
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a beta-Hairpin Peptide; The Journal of Physical Chemistry B; 108(21); 2004; 6582-6594
Agenda and Presentations for Blue Gene Briefing Day--February 6, 2004
Design and Analysis of the BlueGene/L Torus Interconnection Network
A Volumetric FFT for Blue Gene/L, to appear in the Proceedings of HiPC2003
Blue Matter, An Application Framework for Molecular Simulation on Blue Gene, Journal of Parallel and Distributed Computing Volume 63, Issues 7-8 July-August 2003 , Pages 759-773
Understanding folding and design: Replica-exchange simulations of "Trp-cage" miniproteins, Proc. Natl. Acad. Sci. USA, Vol. 100, Issue 13, June 24, 2003, pp. 7587-7592
An overview of the BlueGene/L supercomputer, Supercomputing 2002 Technical Papers, November 2002
Can a continuum solvent model reproduce the free energy
landscape of a beta-hairpin folding in water?, Proc. Natl. Acad. Sci. USA, Vol. 99, Issue 20, October 1, 2002, pp. 12777-12782
The free energy landscape for beta-hairpin folding in explicit
water, Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 26, December 18, 2001, pp. 14931-14936
Blue Gene Project Update
Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular
systems, The Journal of Chemical Physics, Volume 115, Issue 5, 2001, pp. 2348-2358
Blue Gene: A vision for protein science using a petaflop supercomputer, IBM Systems Journal, Volume 40, Number 2, 2001, p. 310
Industry Links
Unraveling the Mystery of Protein Folding
Physicists Take on Challenge Of Showing How Proteins Fold, The Scientist
The Bridge from Genes to Proteins
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