Paper detail

A probabilistic framework for particle-based reaction-diffusion dynamics using classical Fock space representations

The modeling and simulation of stochastic reaction-diffusion processes is a topic of steady interest that is approached with a wide range of methods. \rev{At the level of particle-resolved descriptions, where chemical reactions are coupled to the spatial diffusion of individual particles, there exist comprehensive numerical simulation schemes, while the corresponding mathematical formalization is relatively underdeveloped. The aim of this paper is to provide a framework to systematically formulate the probabilistic evolution equation, termed chemical diffusion master equation (CDME), that governs particle-based stochastic reaction-diffusion processes. To account for the non-conserved and unbounded particle number of this type of open systems, we employ a classical analogue of the quantum mechanical Fock space that contains the symmetrized probability densities of the many-particle configurations in space. Following field-theoretical ideas of second quantization, we introduce creation and annihilation operators that act on single-particle densities and provide natural representations of symmetrized probability densities as well as of reaction and diffusion operators. These operators allow us to consistently and systematically formulate the CDME for arbitrary reaction schemes. The resulting form of the CDME further serves as the foundation to derive more coarse-grained descriptions of reaction-diffusion dynamics. In this regard, we show that a discretization of the evolution equation by projection onto a Fock subspace generated by a finite set of single-particle densities leads to a generalized form of the well-known reaction-diffusion master equation, which supports non-local reactions between grid cells and which converges properly in the continuum limit.