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» Multiple grid methods for classical molecular dynamics
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ICASSP
2010
IEEE
13 years 5 months ago
Sparse Bayesian step-filtering for high-throughput analysis of molecular machine dynamics
Nature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-...
Max A. Little, Nick S. Jones
GRID
2007
Springer
13 years 11 months ago
Integrating multi-level molecular simulations across heterogeneous resources
— Biomolecular simulations play a key role in the study of complex biological processes at microscopic levels in which macromolecules such as proteins are involved. The simulatio...
Yudong Sun, Steve McKeever, Kia Balali-Mood, Mark ...
ICPP
2006
IEEE
13 years 11 months ago
Scalable Time-Parallelization of Molecular Dynamics Simulations in Nano Mechanics
— Molecular Dynamics (MD) is an important atomistic simulation technique, with widespread use in computational chemistry, biology, and materials. An important limitation of MD is...
Yanan Yu, Ashok Srinivasan, Namas Chandra
ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
13 years 11 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...
CPHYSICS
2008
121views more  CPHYSICS 2008»
13 years 5 months ago
A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations
A scalable parallel algorithm has been designed to perform multimillion-atom molecular dynamics (MD) simulations, in which first principlesbased reactive force fields (ReaxFF) des...
Ken-ichi Nomura, Rajiv K. Kalia, Aiichiro Nakano, ...