Chemical diffusion master equation: formulations of reaction--diffusion processes on the molecular level

DOI10.1063/5.0129620zbMATH Open1511.81142arXiv2210.02268MaRDI QIDQ6412975FDOQ6412975

Authors: Mauricio J. Del Razo, Stefanie Winkelmann, Rupert Klein, Felix Höfling 

Publication date: 5 October 2022

Abstract: The chemical diffusion master equation (CDME) describes the probabilistic dynamics of reaction--diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112:49, 2022]; it can be considered the master equation for reaction--diffusion processes. The CDME consists of an infinite ordered family of Fokker--Planck equations, where each level of the ordered family corresponds to a certain number of particles and each particle represents a molecule. The equations at each level describe the spatial diffusion of the corresponding set of particles, and they are coupled to each other via reaction operators --linear operators representing chemical reactions. These operators change the number of particles in the system, and thus transport probability between different levels in the family. In this work, we present three approaches to formulate the CDME and show the relations between them. We further deduce the non-trivial combinatorial factors contained in the reaction operators, and we elucidate the relation to the original formulation of the CDME, which is based on creation and annihilation operators acting on many-particle probability density functions. Finally we discuss applications to multiscale simulations of biochemical systems among other future prospects.

Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Biochemistry, molecular biology (92C40) Reaction-diffusion equations (35K57) Molecular physics (81V55) Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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