A multiscale agent-based model for the investigation of E. coli K12 metabolic response during biofilm formation

DOI10.1007/S11538-018-0494-3MaRDI QIDQ1617094zbMATH OpenOpenAlexWikidataFDO

Authors Majid jun. Latif, Elebeoba E. May

Publication date 7 November 2018

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s11538-018-0494-3

zbMATH Keywords

agent-based modelingbiofilmEscherichia coli K12quorum sensingsystems biology

Mathematics Subject Classification ID

Cell movement (chemotaxis, etc.) (92C17) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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Cites work

• A methodology for performing global uncertainty and sensitivity analysis in systems biology
• Complexity reduction preserving dynamical behavior of biochemical networks
• Identifying control mechanisms of granuloma formation during \textit{M. tuberculosis} infection using an agent-based model
• Mathematical description of microbial biofilms
• Monod's bacterial growth model revisited

Cited in

(5)

• Microcolony and biofilm formation as a survival strategy for bacteria
• A hybrid agent-based approach for modeling microbiological systems
• Influence of nutrient availability and quorum sensing on the formation of metabolically inactive microcolonies within structurally heterogeneous bacterial biofilms: an individual-based 3D cellular automata model
• Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates
• Reaction-diffusion modeling of \textit{E. coli} colony growth based on nutrient distribution and agar dehydration

Describes a project that uses

Uses Software

• KEGG
• Matlab
• DAKOTA
• iDynoR
• DFBAlab
• COBRA Toolbox
• FiPy
• COMSTAT

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