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Mathematical and Computer Modelling: An International Journal
Implementation of a discrete event simulator for biological self-assembly systems
WSC '05 Proceedings of the 37th conference on Winter simulation
Strong approximations of stochastic differential equations with jumps
Journal of Computational and Applied Mathematics
Modelling of Biochemical Reactions by Stochastic Automata Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
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Computers & Mathematics with Applications
Stochastic simulation of chemical reactions in spatially complex media
Computers & Mathematics with Applications
Brief Communication: Discrete-time stochastic modeling and simulation of biochemical networks
Computational Biology and Chemistry
Computational Probability for Systems Biology
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Chemical Master Equation and Langevin regimes for a gene transcription model
Theoretical Computer Science
Approximation of Event Probabilities in Noisy Cellular Processes
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Formalisms for Specifying Markovian Population Models
RP '09 Proceedings of the 3rd International Workshop on Reachability Problems
Developing Itô stochastic differential equation models for neuronal signal transduction pathways
Computational Biology and Chemistry
Computational Biology and Chemistry
Chemical master equation and Langevin Regimes for a gene transcription model
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Simultaneous stochastic simulation of multiple perturbations in biological network models
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Mean square exponential stability of stochastic genetic regulatory networks with time-varying delays
Information Sciences: an International Journal
Performance analysis of stochastic Process algebra models using stochastic simulation
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Modeling Proteolysis from Mass Spectrometry Proteomic Data
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
BioSimWare: a software for the modeling, simulation and analysis of biological systems
CMC'10 Proceedings of the 11th international conference on Membrane computing
Approximation of event probabilities in noisy cellular processes
Theoretical Computer Science
International Journal of Robotics Research
Computers & Mathematics with Applications
Grid computing for sensitivity analysis of stochastic biological models
PaCT'11 Proceedings of the 11th international conference on Parallel computing technologies
Towards a hybrid metabolic algorithm
WMC'06 Proceedings of the 7th international conference on Membrane Computing
Tau leaping stochastic simulation method in p systems
WMC'06 Proceedings of the 7th international conference on Membrane Computing
An evolution hypothesis of bacterial populations
WIRN'05 Proceedings of the 16th Italian conference on Neural Nets
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Automated abstraction methodology for genetic regulatory networks
Transactions on Computational Systems Biology VI
A framework for modeling DNA based molecular systems
DNA'06 Proceedings of the 12th international conference on DNA Computing
Online learning in a chemical perceptron
Artificial Life
A Bayesian hierarchical model for maximizing the vascular adhesion of nanoparticles
Computational Mechanics
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In recent years, stochastic modelling has emerged as a physically more realistic alternative for modelling in vivo reactions. There are numerous stochastic approaches available in the literature; most of these assume that observed random fluctuations are a consequence of the small number of reacting molecules. We review some important developments of the stochastic approach and consider its suitability for modelling intracellular reactions. We then describe recent efforts to include the fluctuation effects caused by the structural organisation of the cytoplasm and the limited diffusion of molecules due to macromolecular crowding.