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ICPP
2006
IEEE
15 years 3 months ago
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications
— This paper presents Salsa, a novel, decentralized and asynchronous realization of the “replica exchange” algorithm for simulating the structure, function, folding, and dyna...
Li Zhang, Manish Parashar, Emilio Gallicchio, Rona...
FPL
2008
Springer
180views Hardware» more  FPL 2008»
14 years 11 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
ICS
2009
Tsinghua U.
15 years 4 months ago
Dynamic topology aware load balancing algorithms for molecular dynamics applications
Molecular Dynamics applications enhance our understanding of biological phenomena through bio-molecular simulations. Large-scale parallelization of MD simulations is challenging b...
Abhinav Bhatele, Laxmikant V. Kalé, Sameer ...
ESCIENCE
2006
IEEE
15 years 3 months ago
Using Lambda Networks to Enhance Performance of Interactive Large Simulations
— The ability to use a visualisation tool to steer large simulations provides innovative and novel usage scenarios, eg the ability to use new algorithms for the computation of fr...
Matt J. Harvey, Shantenu Jha, Mary-Ann Thyveetil, ...
VRML
1999
ACM
15 years 1 months ago
VRML Molecular Dynamics Trajectories
One application of VRML is visualisation of scientific data. Using VRML results of simulations and other scientific endeavours can be published on the web with all the advantage...
Geoff Leach, James Gilbert