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SC
2000
ACM
14 years 1 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...
ICCS
2007
Springer
14 years 3 months ago
A General Long-Time Molecular Dynamics Scheme in Atomistic Systems: Hyperdynamics in Entropy Dominated Systems
Abstract. We extend the hyperdynamics method developed for lowdimensional energy-dominated systems, to simulate slow dynamics in more general atomistic systems. We show that a few ...
Xin Zhou, Yi Jiang
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 ...
EH
1999
IEEE
122views Hardware» more  EH 1999»
14 years 1 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...
HIPC
2003
Springer
14 years 2 months ago
Performance Analysis of Blue Gene/L Using Parallel Discrete Event Simulation
High performance computers currently under construction, such as IBM’s Blue Gene/L, consisting of large numbers (64K) of low cost processing elements with relatively small local...
Ed Upchurch, Paul L. Springer, Maciej Brodowicz, S...