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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...
IPPS
2006
IEEE
14 years 1 months ago
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L
The Replica Exchange method is a popular approach for studying the folding thermodynamics of small to modest size proteins in explicit solvent, since it is easily parallelized. Ho...
Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. P...
FCCM
2004
IEEE
143views VLSI» more  FCCM 2004»
13 years 11 months ago
Reconfigurable Molecular Dynamics Simulator
Current high-performance applications are typically implemented on large-scale general-purpose distributed or multiprocessing systems often based on commodity microprocessors. Fie...
Navid Azizi, Ian Kuon, Aaron Egier, Ahmad Darabiha...
FGCS
2006
135views more  FGCS 2006»
13 years 7 months ago
Scaling applications to massively parallel machines using Projections performance analysis tool
Some of the most challenging applications to parallelize scalably are the ones that present a relatively small amount of computation per iteration. Multiple interacting performanc...
Laxmikant V. Kalé, Gengbin Zheng, Chee Wai ...
BMCBI
2006
127views more  BMCBI 2006»
13 years 7 months ago
On the attenuation and amplification of molecular noise in genetic regulatory networks
Background: Noise has many important roles in cellular genetic regulatory functions at the nanomolar scale. At present, no good theory exists for identifying all possible mechanis...
Bor-Sen Chen, Yu-Chao Wang