Stochastic reaction-diffusion processes with embedded lower-dimensional structures

DOI10.1007/S11538-013-9910-XMaRDI QIDQ458698zbMATH OpenOpenAlexWikidataFDO

Authors Johan Elf, Stefan Hellander, Siyang Wang, Per Lötstedt

Publication date 8 October 2014

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s11538-013-9910-x

zbMATH Keywords

diffusionstochastic simulationchemical reactionmesoscalemicroscale

Mathematics Subject Classification ID

Systems biology, networks (92C42) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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Cites work

• scientific article; zbMATH DE number 3220189 (Why is no real title available?)
• A comparison of bimolecular reaction models for stochastic reaction-diffusion systems
• A first-passage kinetic Monte Carlo algorithm for complex diffusion-reaction systems
• A first-passage kinetic Monte Carlo method for reaction-drift-diffusion processes
• A stochastic immersed boundary method for fluid-structure dynamics at microscopic length scales
• Coupled mesoscopic and microscopic simulation of stochastic reaction-diffusion processes in mixed dimensions
• Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
• Flexible single molecule simulation of reaction-diffusion processes
• Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations
• Random Walks on Lattices. III. Calculation of First-Passage Times with Application to Exciton Trapping on Photosynthetic Units
• Random walks on lattices. II
• Simulation of stochastic reaction-diffusion processes on unstructured meshes
• Stochastic reaction-diffusion kinetics in the microscopic limit
• The reaction-diffusion master equation as an asymptotic approximation of diffusion to a small target
• Using gene expression noise to understand gene regulation

Cited in

(4)

• Editorial: Special issue on stochastic modelling of reaction-diffusion processes in biology
• Multiscale stochastic reaction-diffusion modeling: application to actin dynamics in filopodia
• Hybrid stochastic simulation of rule-based polymerization models
• Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations

Describes a project that uses

Uses Software

• Smoldyn
• MesoRD
• STEPS
• URDME

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