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» Experiences of Using Cassandra for Molecular Dynamics Simula...
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CPHYSICS
2007
113views more  CPHYSICS 2007»
14 years 9 months ago
Atomic-level simulation of non-equilibrium surface chemical reactions under plasma-wall interaction
Molecular dynamics (MD) simulations are used for the study of non-thermal-equilibrium reactions that take place on the substrate surface during plasma etching processes. In MD sim...
Satoshi Hamaguchi, Masashi Yamashiro, Hideaki Yama...
BMCBI
2010
175views more  BMCBI 2010»
14 years 9 months ago
Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspe
Background: RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly ...
S. P. T. Krishnan, Sim Sze Liang, Bharadwaj Veerav...
BMCBI
2006
239views more  BMCBI 2006»
14 years 9 months ago
Applying dynamic Bayesian networks to perturbed gene expression data
Background: A central goal of molecular biology is to understand the regulatory mechanisms of gene transcription and protein synthesis. Because of their solid basis in statistics,...
Norbert Dojer, Anna Gambin, Andrzej Mizera, Bartek...
MMAS
2010
Springer
14 years 4 months ago
Simplified Modelling of a Thermal Bath, with Application to a Fluid Vortex System
Based on the thermodynamic concept of a reservoir, we investigate a computational model for interaction with unresolved degrees of freedom (a thermal bath). We assume that a finite...
Svetlana Dubinkina, Jason Frank, Ben Leimkuhler
HPCC
2005
Springer
15 years 3 months ago
A Multi-scale Computational Approach for Nanoparticle Growth in Combustion Environments
In this paper a new and powerful computer simulation capability for the characterization of carbonaceous nanoparticle assemblies across multiple, connected scales, starting from th...
Angela Violi, Gregory A. Voth