title: The pseudo-compartment method for coupling partial differential equation and compartment-based models of diffusion.
abstract: Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs), which assumes there are sufficient densities of particles that a continuum approximation is valid. However, owing to recent advances in computational power, the simulation and therefore postulation, of computationally intensive individual-based models has become a popular way to investigate the effects of noise in reaction-diffusion systems in which regions of low copy numbers exist. The specific stochastic models with which we shall be concerned in this manuscript are referred to as 'compartment-based' or 'on-lattice'. These models are characterized by a discretization of the computational domain into a grid/lattice of 'compartments'. Within each compartment, particles are assumed to be well mixed and are permitted to react with other particles within their compartment or to transfer between neighbouring compartments. Stochastic models provide accuracy, but at the cost of significant computational resources. For models that have regions of both low and high concentrations, it is often desirable, for reasons of efficiency, to employ coupled multi-scale modelling paradigms. In this work, we develop two hybrid algorithms in which a PDE in one region of the domain is coupled to a compartment-based model in the other. Rather than attempting to balance average fluxes, our algorithms answer a more fundamental question: 'how are individual particles transported between the vastly different model descriptions?' First, we present an algorithm derived by carefully redefining the continuous PDE concentration as a probability distribution. While this first algorithm shows very strong convergence to analytical solutions of test problems, it can be cumbersome to simulate. Our second algorithm is a simplified and more efficient implementation of the first, it is derived in the continuum limit over the PDE region alone. We test our hybrid methods for functionality and accuracy in a variety of different scenarios by comparing the averaged simulations with analytical solutions of PDEs for mean concentrations.
authors.affiliation: Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK c.yates@bath.ac.uk.
authors.forename: Christian A
authors.identifier: http://orcid.org/0000-0003-0461-7297
authors.initials: CA
authors.lastname: Yates
authors.affiliation: School of Mathematical Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.
authors.forename: Mark B
authors.initials: MB
authors.lastname: Flegg
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004058:Diffusion; D005246:Feedback; D046911:Macromolecular Substances / Q000737:chemistry*; D044085:Microfluidics / Q000379:methods; D008956:Models, Chemical; D015233:Models, Statistical; D012997:Solvents / Q000737:chemistry*
chemical_list: D046911:Macromolecular Substances; D012997:Solvents
keywords: hybrid modelling; multiscale modelling; pseudo-compartment; stochastic reaction–diffusion