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MMAS
2010
Springer
13 years 2 months ago
Global Energy Matching Method for Atomistic-to-Continuum Modeling of Self-Assembling Biopolymer Aggregates
This paper studies mathematical models of biopolymer supramolecular aggregates that are formed by the self-assembly of single monomers. We develop a new multiscale numerical appro...
Lei Zhang, Leonid Berlyand, Maxim V. Fedorov, Houm...
ARC
2007
Springer
140views Hardware» more  ARC 2007»
13 years 11 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...
BIBE
2005
IEEE
116views Bioinformatics» more  BIBE 2005»
14 years 1 months ago
Stochastic Model of Protease-Ligand Reactions
Prediction of protein tertiary structure based on amino acid sequence is one of the most challenging open questions in computational molecular biology. The two most common experim...
Paul E. Anderson, Douglas W. Raiford, Deacon J. Sw...
BMCBI
2010
259views more  BMCBI 2010»
13 years 2 months ago
Rule-based spatial modeling with diffusing, geometrically constrained molecules
Background: We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our appro...
Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Ma...
PC
2012
223views Management» more  PC 2012»
12 years 3 months ago
Using shared arrays in message-driven parallel programs
This paper describes a safe and efficient combination of the object-based message-driven execution and shared array parallel programming models. In particular, we demonstrate how ...
Phil Miller, Aaron Becker, Laxmikant V. Kalé...