A discrete stochastic formulation for reversible bimolecular reactions via diffusion encounter

DOI10.4310/CMS.2016.V14.N6.A13zbMATH Open1352.92070arXiv1511.08798MaRDI QIDQ344396FDOQ344396

Authors: Mauricio J. Del Razo, Hong Qian 

Publication date: 22 November 2016

Published in: Communications in Mathematical Sciences (Search for Journal in Brave)

Abstract: The classical models for irreversible diffusion-influenced reactions can be derived by introducing absorbing boundary conditions to over-damped continuous Brownian motion (BM) theory. As there is a clear corresponding stochastic process, the mathematical description takes both Kolmogorov forward equation for the evolution of the probability distribution function and the stochastic sample trajectories. This dual description is a fundamental characteristic of stochastic processes and allows simple particle based simulations to accurately match the expected statistical behavior. However, in the traditional theory using the back-reaction boundary condition to model reversible reactions with geminate recombinations, several subtleties arise: it is unclear what the underlying stochastic process is, which causes complications in producing accurate simulations; and it is non-trivial how to perform an appropriate discretization for numerical computations. In this work, we derive a discrete stochastic model that recovers the classical models and their boundary conditions in the continuous limit. In the case of reversible reactions, we recover the back-reaction boundary condition, unifying the back-reaction approach with those of current simulation packages. Furthermore, all the complications encountered in the continuous models become trivial in the discrete model. Our formulation brings to attention the question: With computations in mind, can we develop a discrete reaction kinetics model that is more fundamental than its continuous counterpart?

Full work available at URL: https://arxiv.org/abs/1511.08798

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zbMATH Keywords

Markov chainBrownian motionchemical kineticsabsorption boundaryback-reaction boundarydiscrete stochastic reaction-diffusion model

Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Biochemistry, molecular biology (92C40) Boundary theory for Markov processes (60J50) Stochastic particle methods (65C35) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Cited In (6)

• Chemical diffusion master equation: Formulations of reaction–diffusion processes on the molecular level
• Reversible Doi and Smoluchowski kinetics for high-order reactions
• Title not available (Why is that?)
• A probabilistic framework for particle-based reaction-diffusion dynamics using classical Fock space representations
• Coupling particle-based reaction-diffusion simulations with reservoirs mediated by reaction-diffusion PDEs
• Analysis of Brownian dynamics simulations of reversible bimolecular reactions

Uses Software

• E-CELL
• URDME
• ReaDDy
• STEPS
• MesoRD

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