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» A Framework for Modeling DNA Based Molecular Systems
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ICPP
2009
IEEE
15 years 4 months ago
Load Balance in the Phylogenetic Likelihood Kernel
—Recent advances in DNA sequencing techniques have led to an unprecedented accumulation and availability of molecular sequence data that needs to be analyzed. This data explosion...
Alexandros Stamatakis, Michael Ott
75
Voted
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
CPHYSICS
2008
106views more  CPHYSICS 2008»
14 years 9 months ago
A space-time-ensemble parallel nudged elastic band algorithm for molecular kinetics simulation
A scalable parallel algorithm has been designed to study long-time dynamics of many-atom systems based on the nudged elastic band method, which performs mutually constrained molec...
Aiichiro Nakano
CIBCB
2007
IEEE
15 years 3 months ago
Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes
Abstract— This paper presents a parametric model to estimate the DNA-protein binding time using the DNA and protein structures and details of the binding site. To understand the ...
Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. ...
UC
2005
Springer
15 years 2 months ago
On Model-Checking of P Systems
Abstract. Membrane computing is a branch of molecular computing that aims to develop models and paradigms that are biologically motivated. It identifies an unconventional computin...
Zhe Dang, Oscar H. Ibarra, Cheng Li, Gaoyan Xie