Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

Matthew B Biggs and Jason A Papin

PLOS ONE, 2013, vol. 8, issue 10, 1-

Abstract: Multiscale modeling is used to represent biological systems with increasing frequency and success. Multiscale models are often hybrids of different modeling frameworks and programming languages. We present the MATLAB-NetLogo extension (MatNet) as a novel tool for multiscale modeling. We demonstrate the utility of the tool with a multiscale model of Pseudomonas aeruginosa biofilm formation that incorporates both an agent-based model (ABM) and constraint-based metabolic modeling. The hybrid model correctly recapitulates oxygen-limited biofilm metabolic activity and predicts increased growth rate via anaerobic respiration with the addition of nitrate to the growth media. In addition, a genome-wide survey of metabolic mutants and biofilm formation exemplifies the powerful analyses that are enabled by this computational modeling tool.

Date: 2013
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0078011

DOI: 10.1371/journal.pone.0078011

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