MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit | Zendy

David Fange | Zendy; Anel Mahmutovic | Zendy; Johan Elf | Zendy

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MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit

Author(s) -

David Fange,

Anel Mahmutovic,

Johan Elf

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts584

Subject(s) - reaction–diffusion system , discretization , markup language , computer science , diffusion , scale (ratio) , master equation , license , documentation , limit (mathematics) , statistical physics , mathematics , programming language , physics , thermodynamics , mathematical analysis , world wide web , xml , operating system , quantum mechanics , quantum

MesoRD is a tool for simulating stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with additions to define compartment geometries. MesoRD 1.0 supports scale-dependent reaction rate constants and reactions between reactants in neighbouring subvolumes. These new features make it possible to construct physically consistent models of diffusion-controlled reactions also at fine spatial discretization.

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