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RECOMB
2007
Springer
14 years 10 months ago
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions
Abstract. Given the substantial computational requirements of stochastic simulation, approximation is essential for efficient analysis of any realistic biochemical system. This pap...
Hiroyuki Kuwahara, Chris J. Myers
ICCAD
2008
IEEE
133views Hardware» more  ICCAD 2008»
14 years 6 months ago
Module locking in biochemical synthesis
—We are developing a framework for computation with biochemical reactions with a focus on synthesizing specific logical functionality, a task analogous to technology-independent...
Brian Fett, Marc D. Riedel
ICCMS
2009
118views more  ICCMS 2009»
13 years 7 months ago
Optimized Parallel Implementation of Gillespie's First Reaction Method on Graphics Processing Units
The simulation of chemical reacting systems is one of the most challenging topics in Systems Biology, due to their complexity and inherent randomness. The Gillespie's Stochas...
Cristian Dittamo, Davide Cangelosi
BMCBI
2004
323views more  BMCBI 2004»
13 years 9 months ago
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true ...
David Adalsteinsson, David McMillen, Timothy C. El...
BIRD
2008
Springer
158views Bioinformatics» more  BIRD 2008»
13 years 11 months ago
A Computational Method for Reconstructing Gapless Metabolic Networks
Abstract. We propose a computational method for reconstructing metabolic networks. The method utilizes optimization techniques and graph traversal algorithms to discover a set of b...
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko ...