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» Scalable Molecular Dynamics for Large Biomolecular Systems
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WABI
2009
Springer
162views Bioinformatics» more  WABI 2009»
14 years 1 months ago
Aligning Biomolecular Networks Using Modular Graph Kernels
Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the stru...
Fadi Towfic, M. Heather West Greenlee, Vasant Hona...
ENTCS
2006
155views more  ENTCS 2006»
13 years 7 months ago
Biomolecular Agents as Multi-behavioural Concurrent Objects
In recent years, there has been increasing interest in computational models of biological systems based on various calculi of communicating processes, such as the stochastic pi-ca...
Denys Duchier, Céline Kuttler
NAR
2006
98views more  NAR 2006»
13 years 7 months ago
oGNM: online computation of structural dynamics using the Gaussian Network Model
An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperativefluctuationsaccessibleundernativestate conditions, is a first step towar...
Lee-Wei Yang, A. J. Rader, Xiong Liu, Christopher ...
IPPS
2006
IEEE
14 years 1 months ago
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L
The Replica Exchange method is a popular approach for studying the folding thermodynamics of small to modest size proteins in explicit solvent, since it is easily parallelized. Ho...
Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. P...
HPDC
2005
IEEE
14 years 19 days ago
Generosity and gluttony in GEMS: grid enabled molecular simulations
Biomolecular simulations produce more output data than can be managed effectively by traditional computing systems. Researchers need distributed systems that allow the pooling of...
Justin M. Wozniak, Paul Brenner, Douglas Thain, Aa...