An adaptive algorithm for simulation of stochastic reaction-diffusion processes
Journal of Computational Physics
Flexible single molecule simulation of reaction-diffusion processes
Journal of Computational Physics
A cultural algorithm for the representation of mitochondrial population
Advances in Artificial Intelligence - Special issue on Artificial Intelligence Applications in Biomedicine
A First-Passage Kinetic Monte Carlo method for reaction-drift-diffusion processes
Journal of Computational Physics
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Motivation: We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli. Results: In the regime where the number of molecules is small and reactions are diffusion-limited predicted fluctuations in the product number vary between the methods, while the average is the same. Computational approaches at the level of the reaction-diffusion master equation compute the same fluctuations as the reference result obtained from the particle-based method if the size of the sub-volumes is comparable to the diameter of reactants. Using numerical simulations of reversible binding of a pair of molecules we argue that the disagreement in predicted fluctuations is due to different modeling of inter-arrival times between reaction events. Simulations for a more complex biological study show that the different approaches lead to different results due to modeling issues. Finally, we present the physical assumptions behind the mesoscopic models for the reaction-diffusion systems. Availability: Input files for the simulations and the source code of GMP can be found under the following address: http://www.cwi.nl/projects/sic/bioinformatics2007/ Contact: m.dobrzynski@cwi.nl Supplementary information: Supplementary data are available at Bioinformatics online.