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PPOPP
2006
ACM
14 years 1 months ago
Performance characterization of molecular dynamics techniques for biomolecular simulations
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
14 years 1 months ago
Anton, a special-purpose machine for molecular dynamics simulation
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the ...
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Je...
SC
2004
ACM
14 years 27 days ago
Analysis and Performance Results of a Molecular Modeling Application on Merrimac
The Merrimac supercomputer uses stream processors and a highradix network to achieve high performance at low cost and low power. The stream architecture matches the capabilities o...
Mattan Erez, Jung Ho Ahn, Ankit Garg, William J. D...
BMCBI
2010
175views more  BMCBI 2010»
13 years 7 months ago
Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspe
Background: RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly ...
S. P. T. Krishnan, Sim Sze Liang, Bharadwaj Veerav...
HPCC
2005
Springer
14 years 1 months ago
High Performance Subgraph Mining in Molecular Compounds
Structured data represented in the form of graphs arises in several fields of the science and the growing amount of available data makes distributed graph mining techniques partic...
Giuseppe Di Fatta, Michael R. Berthold