title: Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation.
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.
authors.affiliation: Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Biggs
authors.forename: Jason A
authors.initials: JA
authors.lastname: Papin
mesh_terms: D018441:Biofilms / Q000254:growth & development*; D003198:Computer Simulation; D011550:Pseudomonas aeruginosa / Q000254:growth & development*