A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection

Plimpton, Steven J.; Sershen, Cheryl L.; May, Elebeoba E.

doi:10.1109/EMBC.2014.6943590

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:

Plimpton, Steven J. ^[1]; Sershen, Cheryl L. ^[1]; May, Elebeoba E. ^[1]

Univ. of Houston, Houston, TX (United States)

Publication Date:: Thu Jan 01 00:00:00 EST 2015

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.

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                    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

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                    Plimpton, Steven J., Sershen, Cheryl L., and May, Elebeoba E. 2015.  
        "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.

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@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},

  url          = {https://www.osti.gov/biblio/1237360},
  journal      = {IEEE Engineering in Medicine and Biology. Annual Conference},

  issn         = {1557-170X},

  number       = ,

  volume       = 2014,

  place        = {United States},

  year         = {Thu Jan 01 00:00:00 EST 2015},

  month        = {Thu Jan 01 00:00:00 EST 2015}

}

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Journal Article:

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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
https://doi.org/10.3389/fcimb.2016.00006

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Title: A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection

Abstract

Citation Formats

Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach journal, February 2016

Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach
journal, February 2016