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» Reconfigurable Molecular Dynamics Simulator
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ARC
2007
Springer
140views Hardware» more  ARC 2007»
14 years 3 months ago
Reconfigurable Computing for Accelerating Protein Folding Simulations
Abstract. This paper presents a methodology for the design of a reconfigurable computing system applied to a complex problem in molecular Biology: the protein folding problem. An e...
Nilton B. Armstrong, Heitor S. Lopes, Carlos R. Er...
ICS
2009
Tsinghua U.
14 years 5 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 ...
CPHYSICS
2008
106views more  CPHYSICS 2008»
13 years 11 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 10 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...
EH
1999
IEEE
122views Hardware» more  EH 1999»
14 years 3 months ago
The MorphoSys Dynamically Reconfigurable System-on-Chip
MorphoSys is a system-on-chip which combines a RISC processor with an array of reconfigurable cells. The important features of MorphoSys are coarse-grain granularity, dynamic reco...
Guangming Lu, Hartej Singh, Ming-Hau Lee, Nader Ba...