An unstructured mesh convergent reaction-diffusion master equation for reversible reactions

DOI10.1016/j.jcp.2018.07.036zbMath1416.35304arXiv1711.04220OpenAlexW2769021112WikidataQ60140958 ScholiaQ60140958MaRDI QIDQ2312155

Samuel A. Isaacson, Ying Zhang

Publication date: 4 July 2019

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

Full work available at URL: https://arxiv.org/abs/1711.04220

zbMATH Keywords

stochastic chemical kineticsDoi modelreaction-diffusion master equationstochastic reaction-diffusion equationvolume reactivity model

Mathematics Subject Classification ID

Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Stochastic partial differential equations (aspects of stochastic analysis) (60H15) PDEs with randomness, stochastic partial differential equations (35R60) Finite volume methods for initial value and initial-boundary value problems involving PDEs (65M08) Probabilistic methods, particle methods, etc. for initial value and initial-boundary value problems involving PDEs (65M75)

Related Items (4)

A probabilistic framework for particle-based reaction-diffusion dynamics using classical Fock space representations ⋮ Fluctuation analysis for particle-based stochastic reaction-diffusion models ⋮ How Reaction-Diffusion PDEs Approximate the Large-Population Limit of Stochastic Particle Models ⋮ Mean Field Limits of Particle-Based Stochastic Reaction-Diffusion Models

Uses Software

• CGAL
• Gmsh
• URDME
• na14
• ReaDDy
• STEPS

Cites Work

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• A first-passage kinetic Monte Carlo algorithm for complex diffusion-reaction systems
• Hybrid framework for the simulation of stochastic chemical kinetics
• Remarks around 50 lines of Matlab: short finite element implementation
• A robust numerical algorithm for studying biomolecular transport processes
• Exact calculation of the overlap volume of spheres and mesh elements
• The influence of spatial variation in chromatin density determined by X-ray tomograms on the time to find DNA binding sites
• Incorporating Active Transport of Cellular Cargo in Stochastic Mesoscopic Models of Living Cells
• Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
• Analysis and Design of Jump Coefficients in Discrete Stochastic Diffusion Models
• Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes
• Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
• Gmsh: A 3-D finite element mesh generator with built-in pre- and post-processing facilities
• Deterministic limit of the stochastic model of chemical reactions with diffusion
• Stochastic reaction-diffusion kinetics in the microscopic limit
• The computational geometry algorithms library CGAL
• The Reaction-Diffusion Master Equation as an Asymptotic Approximation of Diffusion to a Small Target
• Stochastic Analysis of Biochemical Systems
• Relationship between the reaction–diffusion master equation and particle tracking models
• Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations
• Handbook of stochastic methods for physics, chemistry and natural sciences.

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