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CSC
2010
11 years 8 days ago
Performance Modeling, Analysis, and Optimization of Cell-List Based Molecular Dynamics
- We have developed a performance prediction model for non-bonded interaction computations in molecular dynamics simulations, thereby predicting the optimal cell dimension in a lin...
Manaschai Kunaseth, Rajiv K. Kalia, Aiichiro Nakan...
PR
2007
107views more  PR 2007»
11 years 4 months ago
Newtonian clustering: An approach based on molecular dynamics and global optimization
Given a data set, a dynamical procedure is applied to the data points in order to shrink and separate, possibly overlapping clusters. Namely, Newton’s equations of motion are em...
Konstantinos Blekas, Isaac E. Lagaris
COMPLIFE
2006
Springer
11 years 9 months ago
Set-Oriented Dimension Reduction: Localizing Principal Component Analysis Via Hidden Markov Models
We present a method for simultaneous dimension reduction and metastability analysis of high dimensional time series. The approach is based on the combination of hidden Markov model...
Illia Horenko, Johannes Schmidt-Ehrenberg, Christo...
ASAP
2009
IEEE
142views Hardware» more  ASAP 2009»
12 years 2 months ago
Parallel Discrete Event Simulation of Molecular Dynamics Through Event-Based Decomposition
—Molecular dynamics simulation based on discrete event simulation (DMD) is emerging as an alternative to time-step driven molecular dynamics (MD). DMD uses simplified discretize...
Martin C. Herbordt, Md. Ashfaquzzaman Khan, Tony D...
WSC
1998
11 years 6 months ago
Parallel Implementation of a Molecular Dynamics Simulation Program
We have taken a NIST molecular dynamics simulation program (md3), which was configured as a single sequential process running on a CRAY C90 vector supercomputer, and parallelized ...
Alan Mink, Christophe Bailly
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