title: A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection.
abstract: This paper describes a method for incorporating a diffusion field modeling oxygen usage and dispersion in a multi-scale model of Mycobacterium tuberculosis (Mtb) infection mediated granuloma formation. We implemented this method over a floating-point field to model oxygen dynamics in host tissue during chronic phase response and Mtb persistence. The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step. Instead, diffusion is modeled by a matrix-based, steady state approximate solution to the diffusion equation. Presented in figure 1 is the evolution of the diffusion profiles of a containment granuloma over time.
authors.forename: Cheryl L
authors.initials: CL
authors.lastname: Sershen
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Plimpton
authors.forename: Elebeoba E
authors.initials: EE
authors.lastname: May
mesh_terms: D004058:Diffusion; D006099:Granuloma / Q000378:metabolism / Q000382:microbiology*; D054884:Host-Pathogen Interactions; D006801:Humans; D008954:Models, Biological; D009169:Mycobacterium tuberculosis / Q000502:physiology*; D010100:Oxygen / Q000378:metabolism*; D049490:Systems Biology; D014376:Tuberculosis / Q000378:metabolism / Q000382:microbiology*
chemical_list: D010100:Oxygen