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» Programming in Biomolecular Computation
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CODES
2005
IEEE
14 years 2 months ago
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
This paper provides an overview of the Blue Matter application development effort within the Blue Gene project that supports our scientific simulation efforts in the areas of pro...
Robert S. Germain, Blake G. Fitch, Aleksandr Raysh...
FPL
2008
Springer
180views Hardware» more  FPL 2008»
13 years 10 months ago
Compiled hardware acceleration of Molecular Dynamics code
The objective of Molecular Dynamics (MD) simulations is to determine the shape of a molecule in a given biomolecular environment. These simulations are very demanding computationa...
Jason R. Villarreal, Walid A. Najjar
SC
1995
ACM
13 years 12 months ago
I/O Limitations in Parallel Molecular Dynamics
Abstract We discuss data production rates and their impact on the performance of scientific applications using parallel computers. On one hand, too high rates of data production c...
Terry W. Clark, L. Ridgway Scott, Stanislaw Wloked...
IPPS
2007
IEEE
14 years 2 months ago
Biomolecular Path Sampling Enabled by Processing in Network Storage
Computationally complex and data intensive atomic scale biomolecular simulation is enabled via Processing in Network Storage (PINS): a novel distributed system framework to overco...
Paul Brenner, Justin M. Wozniak, Douglas Thain, Aa...
BIRTHDAY
2004
Springer
14 years 4 days ago
An Algorithm for Testing Structure Freeness of Biomolecular Sequences
Satoshi Kobayashi, Takashi Yokomori, Yasubumi Saka...