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» Reconfigurable Molecular Dynamics Simulator
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BMCBI
2006
145views more  BMCBI 2006»
13 years 10 months ago
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Background: Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling appro...
Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yo...
IPPS
2007
IEEE
14 years 4 months ago
Modeling of NAMD's Network Input/Output on Large PC Clusters
This study examined the interplay among processor speed, cluster interconnect and file I/O, using parallel applications to quantify interactions. We focused on a common case wher...
Nancy Tran, Daniel A. Reed
ERSA
2007
142views Hardware» more  ERSA 2007»
13 years 11 months ago
An FPGA Implementation of Reciprocal Sums for SPME
Molecular Dynamics simulations have become an interesting target for acceleration using Field-Programmable Gate Arrays (FPGA). Still to be attempted completely in FPGA hardware is...
Sam Lee, Paul Chow
CPHYSICS
2007
82views more  CPHYSICS 2007»
13 years 9 months ago
Charge transfer mechanism in a PolydGpdCp fiber and in wet DNA
Recently there has been great interest in the conducting properties of DNA because of their potential applications to nanotechnology and their role in protecting the molecule from...
Francesco Luigi Gervasio
JCC
2002
79views more  JCC 2002»
13 years 9 months ago
Distance and exposure dependent effective dielectric function
: In an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (Deff) for a large ...
Buddhadeb Mallik, Artëm Masunov, Themis Lazar...