Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment

  • Received: 01 April 2007 Accepted: 29 June 2018 Published: 01 March 2008
  • MSC : Primary: 92-08, 92C15; Secondary: 65C05, 68U20.

  • The CompuCell3D modeling environment provides a convenient platform for biofilm simulations using the Glazier-Graner-Hogeweg (GGH) model, a cell-oriented framework designed to simulate growth and pattern formation due to biological cells' behaviors. We show how to develop such a simulation, based on the hybrid (continuum-discrete) model of Picioreanu, van Loosdrecht, and Heijnen (PLH), simulate the growth of a single-species bacterial biofilm, and study the roles of cell-cell and cell-field interactions in determining biofilm morphology. In our simulations, which generalize the PLH model by treating cells as spatially extended, deformable bodies, differential adhesion between cells, and their competition for a substrate (nutrient), suffice to produce a fingering instability that generates the finger shapes of biofilms. Our results agree with most features of the PLH model, although our inclu- sion of cell adhesion, which is difficult to implement using other modeling approaches, results in slightly different patterns. Our simulations thus pro- vide the groundwork for simulations of medically and industrially important multispecies biofilms.

    Citation: Nikodem J. Poplawski, Abbas Shirinifard, Maciej Swat, James A. Glazier. Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment[J]. Mathematical Biosciences and Engineering, 2008, 5(2): 355-388. doi: 10.3934/mbe.2008.5.355

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  • The CompuCell3D modeling environment provides a convenient platform for biofilm simulations using the Glazier-Graner-Hogeweg (GGH) model, a cell-oriented framework designed to simulate growth and pattern formation due to biological cells' behaviors. We show how to develop such a simulation, based on the hybrid (continuum-discrete) model of Picioreanu, van Loosdrecht, and Heijnen (PLH), simulate the growth of a single-species bacterial biofilm, and study the roles of cell-cell and cell-field interactions in determining biofilm morphology. In our simulations, which generalize the PLH model by treating cells as spatially extended, deformable bodies, differential adhesion between cells, and their competition for a substrate (nutrient), suffice to produce a fingering instability that generates the finger shapes of biofilms. Our results agree with most features of the PLH model, although our inclu- sion of cell adhesion, which is difficult to implement using other modeling approaches, results in slightly different patterns. Our simulations thus pro- vide the groundwork for simulations of medically and industrially important multispecies biofilms.
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    © 2008 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
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