Efficient Green's function reaction dynamics (GFRD) simulations for diffusion-limited, reversible reactions

DOI10.1016/j.jcp.2017.12.025zbMath1382.65027OpenAlexW2781436866MaRDI QIDQ1699460

Zahedeh Bashardanesh, Per Loetstedt

Publication date: 23 February 2018

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcp.2017.12.025

zbMATH Keywords

simulationGreen's functionreaction-diffusion equationbiochemical networkSmoluchowski formalism

Mathematics Subject Classification ID

Reaction-diffusion equations (35K57) Classical flows, reactions, etc. in chemistry (92E20) Stochastic particle methods (65C35)

Uses Software

• ReaDDy

Cites Work

• Unnamed Item
• A first-passage kinetic Monte Carlo method for reaction-drift-diffusion processes
• Flexible single molecule simulation of reaction-diffusion processes
• A first-passage kinetic Monte Carlo algorithm for complex diffusion-reaction systems
• Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
• Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes
• Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
• Multiscale Simulation of Stochastic Reaction-Diffusion Networks

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