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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
ICS
2009
Tsinghua U.
14 years 3 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 ...
SAC
2003
ACM
14 years 1 months ago
Real-Time Monitoring of Large Scientific Simulations
We present a distributed framework that enables real-time streaming and visualization of data generated by large remote simulations. We address issues arising from distributed cli...
Valerio Pascucci, Daniel E. Laney, Ray J. Frank, F...
CPHYSICS
2008
106views more  CPHYSICS 2008»
13 years 8 months ago
A space-time-ensemble parallel nudged elastic band algorithm for molecular kinetics simulation
A scalable parallel algorithm has been designed to study long-time dynamics of many-atom systems based on the nudged elastic band method, which performs mutually constrained molec...
Aiichiro Nakano
CPHYSICS
2004
54views more  CPHYSICS 2004»
13 years 8 months ago
Self-gravitational collapse of a magnetized cloud core: high resolution simulations with three-dimensional MHD nested grid
We investigate self-gravitational collapse of magnetized molecular cloud cores and formation of the outflow. We employ a nested grid in order to resolve fine structures of protost...
Tomoaki Matsumoto, Masahiro N. Machida, Kohji Tomi...