A comparison of bimolecular reaction models for stochastic reaction-diffusion systems

DOI10.1007/S11538-013-9833-6zbMATH Open1297.92029arXiv1301.0547OpenAlexW2027820689WikidataQ51072824 ScholiaQ51072824MaRDI QIDQ458707FDOQ458707

Ikemefuna C. Agbanusi, Samuel A. Isaacson

Publication date: 8 October 2014

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

Abstract: Stochastic reaction-diffusion models have become an important tool in studying how both noise in the chemical reaction process and the spatial movement of molecules influences the behavior of biological systems. There are two primary spatially-continuous models that have been used in recent studies: the diffusion limited reaction model of Smoluchowski, and a second approach popularized by Doi. Both models treat molecules as points undergoing Brownian motion. The former represents chemical reactions between two reactants through the use of reactive boundary conditions, with two molecules reacting instantly upon reaching a fixed separation (called the reaction-radius). The Doi model uses reaction potentials, whereby two molecules react with a fixed probability per unit time, $lambda$, when separated by less than the reaction radius. In this work we study the rigorous relationship between the two models. For the special case of a protein diffusing to a fixed DNA binding site, we prove that the solution to the Doi model converges to the solution of the Smoluchowski model as $lambdaoinfty$, with a rigorous $O(lambd{a}^{-1/2+epsilon})$ error bound (for any fixed $epsilon>0$). We investigate by numerical simulation, for biologically relevant parameter values, the difference between the solutions and associated reaction time statistics of the two models. As the reaction-radius is decreased, for sufficiently large but fixed values of $lambda$, these differences are found to increase like the inverse of the binding radius.

Full work available at URL: https://arxiv.org/abs/1301.0547

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zbMATH Keywords

stochastic reaction-diffusiondiffusion limited reaction

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

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Cited In (14)

• Quantitative Propagation of Chaos in a Bimolecular Chemical Reaction-Diffusion Model
• Stochastic reaction networks within interacting compartments
• Accurate Particle-Based Reaction Algorithms for Fixed Timestep Simulators
• Galerkin finite element method for time-fractional stochastic diffusion equations
• Multiscale Simulation of Stochastic Reaction-Diffusion Networks
• Title not available (Why is that?)
• Reactive boundary conditions as limits of interaction potentials for Brownian and Langevin dynamics
• Editorial: Special issue on stochastic modelling of reaction-diffusion processes in biology
• Stochastic reaction-diffusion processes with embedded lower-dimensional structures
• Stochastic analysis of reaction-diffusion processes
• A semi-continuous extended kinetic model for bimolecular chemical reactions
• Comparison of stochastic and deterministic models of a linear chemical reaction with diffusion
• Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling
• Spatial stochastic intracellular kinetics: a review of modelling approaches

Uses Software

• URDME
• STEPS
• MesoRD

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