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ICASSP
2010
IEEE
13 years 5 months ago
Sparse Bayesian step-filtering for high-throughput analysis of molecular machine dynamics
Nature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-...
Max A. Little, Nick S. Jones
ICS
2009
Tsinghua U.
14 years 2 days 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 ...
ESANN
2007
13 years 6 months ago
The Intrinsic Recurrent Support Vector Machine
In this work, we present a new model for a Recurrent Support Vector Machine. We call it intrinsic because the complete recurrence is directly incorporated within the considered opt...
Daniel Schneegaß, Anton Maximilian Schä...
IPPS
2008
IEEE
13 years 11 months ago
Overcoming scaling challenges in biomolecular simulations across multiple platforms
NAMD† is a portable parallel application for biomolecular simulations. NAMD pioneered the use of hybrid spatial and force decomposition, a technique now used by most scalable pr...
Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. ...
IEEEPACT
2009
IEEE
13 years 12 months ago
Quantifying the Potential of Program Analysis Peripherals
Abstract—As programmers are asked to manage more complicated parallel machines, it is likely that they will become increasingly dependent on tools such as multi-threaded data rac...
Mohit Tiwari, Shashidhar Mysore, Timothy Sherwood