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» Stochastic Model of Protease-Ligand Reactions
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BIOCOMP
2010
13 years 2 months ago
A Model Reduction Technique for Stochastic Biochemical Kinetics
Abstract-- Modeling the intermolecular reactions in a single cell is a critical problem in computational biology. Biochemical reaction systems often involve species in both low and...
Silvana Ilie, Ekaterina Kudashkina
TCSB
2010
13 years 3 months ago
Rule-Based Modeling of Transcriptional Attenuation at the Tryptophan Operon
Transcriptional attenuation at E.coli’s tryptophan operon is a prime example of RNA-mediated gene regulation. In this paper, we present a discrete stochastic model for this pheno...
Céline Kuttler, Cédric Lhoussaine, M...
AROBOTS
2011
12 years 12 months ago
Setpoint regulation for stochastically interacting robots
— We present an integral feedback controller that regulates the average copy number of a particular assembly in a system of stochastically interacting robots. The mathematical mo...
Nils Napp, Samuel Burden, Eric Klavins
BMCBI
2010
149views more  BMCBI 2010»
13 years 5 months ago
RuleMonkey: software for stochastic simulation of rule-based models
Background: The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be...
Joshua Colvin, Michael I. Monine, Ryan N. Gutenkun...
ICCMS
2009
118views more  ICCMS 2009»
13 years 2 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