title: Solving the advection-diffusion equations in biological contexts using the cellular Potts model.
abstract: The cellular Potts model (CPM) is a robust, cell-level methodology for simulation of biological tissues and morphogenesis. Both tissue physiology and morphogenesis depend on diffusion of chemical morphogens in the extra-cellular fluid or matrix (ECM). Standard diffusion solvers applied to the cellular potts model use finite difference methods on the underlying CPM lattice. However, these methods produce a diffusing field tied to the underlying lattice, which is inaccurate in many biological situations in which cell or ECM movement causes advection rapid compared to diffusion. Finite difference schemes suffer numerical instabilities solving the resulting advection-diffusion equations. To circumvent these problems we simulate advection diffusion within the framework of the CPM using off-lattice finite-difference methods. We define a set of generalized fluid particles which detach advection and diffusion from the lattice. Diffusion occurs between neighboring fluid particles by local averaging rules which approximate the Laplacian. Directed spin flips in the CPM handle the advective movement of the fluid particles. A constraint on relative velocities in the fluid explicitly accounts for fluid viscosity. We use the CPM to solve various diffusion examples including multiple instantaneous sources, continuous sources, moving sources, and different boundary geometries and conditions to validate our approximation against analytical and established numerical solutions. We also verify the CPM results for Poiseuille flow and Taylor-Aris dispersion.
authors.affiliation: Biocomplexity Institute and Department of Physics, Indiana University, 727 E. 3rd Street, Swain Hall West 159, Bloomington, Indiana 47405-7105, USA. ddan@indiana.edu
authors.forename: Debasis
authors.initials: D
authors.lastname: Dan
authors.forename: Chris
authors.initials: C
authors.lastname: Mueller
authors.forename: Kun
authors.initials: K
authors.lastname: Chen
authors.forename: James A
authors.initials: JA
authors.lastname: Glazier
mesh_terms: D000465:Algorithms; D000818:Animals; D001692:Biological Transport; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D004058:Diffusion; D005109:Extracellular Matrix / Q000737:chemistry* / Q000502:physiology*; D016326:Extracellular Matrix Proteins / Q000737:chemistry* / Q000502:physiology*; D006133:Growth Substances / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008954:Models, Biological; D008956:Models, Chemical; D009024:Morphogenesis / Q000502:physiology*
chemical_list: D016326:Extracellular Matrix Proteins; D006133:Growth Substances