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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. Moreover, presented in figure 1 is the evolution of the diffusion profiles of a containment granuloma over time.

Authors:
 [1];  [1];  [1]
  1. Univ. of Houston, Houston, TX (United States)
Publication Date:
Research Org.:
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1237360
Report Number(s):
SAND-2015-0080J
Journal ID: ISSN 1557-170X; 558360
Grant/Contract Number:
AC04-94AL85000
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
IEEE Engineering in Medicine and Biology. Annual Conference
Additional Journal Information:
Journal Volume: 2014; Conference: Engineering in Medicince and Biology Society (EMBC), 2014 36th Annual Conference, Chicago, IL (United States), 26-30 Aug 2014; Journal ID: ISSN 1557-170X
Publisher:
IEEE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Plimpton, Steven J., Sershen, Cheryl L., and May, Elebeoba E. A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection. United States: N. p., 2015. Web. doi:10.1109/EMBC.2014.6943590.
Plimpton, Steven J., Sershen, Cheryl L., & May, Elebeoba E. A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection. United States. doi:10.1109/EMBC.2014.6943590.
Plimpton, Steven J., Sershen, Cheryl L., and May, Elebeoba E. Thu . "A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection". United States. doi:10.1109/EMBC.2014.6943590. https://www.osti.gov/servlets/purl/1237360.
@article{osti_1237360,
title = {A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection},
author = {Plimpton, Steven J. and Sershen, Cheryl L. and May, Elebeoba E.},
abstractNote = {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. Moreover, presented in figure 1 is the evolution of the diffusion profiles of a containment granuloma over time.},
doi = {10.1109/EMBC.2014.6943590},
journal = {IEEE Engineering in Medicine and Biology. Annual Conference},
number = ,
volume = 2014,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2015},
month = {Thu Jan 01 00:00:00 EST 2015}
}

Journal Article:
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