Simulation of stochastic reaction-diffusion processes on unstructured meshes
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Publication:3567005
DOI10.1137/080721388zbMATH Open1190.65015arXiv0804.3288OpenAlexW3103754732WikidataQ63407448 ScholiaQ63407448MaRDI QIDQ3567005FDOQ3567005
Lars Ferm, Stefan Engblom, Andreas Hellander, Per Lötstedt
Publication date: 10 June 2010
Published in: SIAM Journal on Scientific Computing (Search for Journal in Brave)
Abstract: Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic level, the master equation for a well stirred chemical system is combined with Brownian motion in space to obtain the reaction-diffusion master equation. The space is covered by an unstructured mesh and the diffusion coefficients on the mesoscale are obtained from a finite element discretization of the Laplace operator on the macroscale. The resulting method is a flexible hybrid algorithm in that the diffusion can be handled either on the meso- or on the macroscale level. The accuracy and the efficiency of the method are illustrated in three numerical examples inspired by molecular biology.
Full work available at URL: https://arxiv.org/abs/0804.3288
hybrid algorithmnumerical examplesBrownian motiondiffusionfinite element methodhybrid methodmaster equationunstructured meshmolecular biologyreaction rate equationschemical system
Stochastic partial differential equations (aspects of stochastic analysis) (60H15) Biochemistry, molecular biology (92C40) Reaction-diffusion equations (35K57) PDEs with randomness, stochastic partial differential equations (35R60) Computational methods for stochastic equations (aspects of stochastic analysis) (60H35)
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