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FPL
2007
Springer
150views Hardware» more  FPL 2007»
13 years 11 months ago
Discrete Event Simulation of Molecular Dynamics with Configurable Logic
: Molecular dynamics simulation based on discrete event simulation (DMD) is emerging as an alternative to time-step driven molecular dynamics (MD). DMD uses simplified discretized ...
Josh Model, Martin C. Herbordt
VIS
2004
IEEE
148views Visualization» more  VIS 2004»
14 years 9 months ago
Detection and Visualization of Anomalous Structures in Molecular Dynamics Simulation Data
In this article we explore techniques to detect and visualize features in data from molecular dynamics (MD) simulations. Although the techniques proposed are general, we focus on ...
John Wilkins, Kaden Hazzard, Raghu Machiraju, Same...
ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
14 years 2 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...
JCC
2008
114views more  JCC 2008»
13 years 8 months ago
Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter tr
Abstract: Molecular dynamics simulations of the RN24 peptide, which includes a diverse set of structurally heterogeneous states, are carried out in explicit solvent. Two approaches...
Luca Monticelli, Eric J. Sorin, D. Peter Tieleman,...
EGH
2003
Springer
14 years 1 months ago
A multigrid solver for boundary value problems using programmable graphics hardware
—We present a method for using programmable graphics hardware to solve a variety of boundary value problems. The time-evolution of such problems is frequently governed by partial...
Nolan Goodnight, Cliff Woolley, Gregory Lewin, Dav...