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» Programming an interpreter using molecular dynamics
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2000
ACM
13 years 10 months ago
Scalable Molecular Dynamics for Large Biomolecular Systems
We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program N...
Robert Brunner, James C. Phillips, Laxmikant V. Ka...
IANDC
2010
125views more  IANDC 2010»
13 years 3 months ago
A thread calculus with molecular dynamics
In a previous paper, we developed an algebraic theory of threads, interleaving of threads, and interaction between threads and services. In the current paper, we extend that theory...
Jan A. Bergstra, C. A. Middelburg
IPPS
2007
IEEE
14 years 2 days ago
Porting the GROMACS Molecular Dynamics Code to the Cell Processor
The Cell processor offers substantial computational power which can be effectively utilized only if application design and implementation are tuned to the Cell architecture. In th...
Stephen Olivier, Jan Prins, Jeff Derby, Ken V. Vu
IPPS
1999
IEEE
13 years 10 months ago
Application Performance of a Linux Cluster Using Converse
Abstract. Clusters of PCs are an attractive platform for parallel applications because of their cost effectiveness. We have implemented an interoperable runtime system called Conve...
Laxmikant V. Kalé, Robert Brunner, James C....
BMCBI
2008
163views more  BMCBI 2008»
13 years 5 months ago
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Background: High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpre...
Frédéric Chalmel, Michael Primig