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:
-
- 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:
- 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. https://doi.org/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. https://doi.org/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}
}
Works referencing / citing this record:
Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach
journal, February 2016
- Sershen, Cheryl L.; Plimpton, Steven J.; May, Elebeoba E.
- Frontiers in Cellular and Infection Microbiology, Vol. 6