American Institute of Mathematical Sciences

Advanced
2008, 5(2): 355-388. doi: 10.3934/mbe.2008.5.355

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

Nikodem J. Poplawski 1, , Abbas Shirinifard 1, , Maciej Swat 1, and  James A. Glazier 1,

1. 

Biocomplexity Institute and Department of Physics, Indiana University, Swain Hall West, 727 East Third Street, Bloomington, IN 47405-7105, United States, United States, United States, United States

Received  April 2007 Revised  December 2007 Published  March 2008

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.
Keywords: cellular Potts model, CompuCell3D., computational biology, Biofilms, bacterial growth, Glazier-Graner-Hogeweg model.
Mathematics Subject Classification: Primary: 92-08, 92C15; Secondary: 65C05, 68U2.
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. Mathematical Biosciences & Engineering, 2008, 5 (2) : 355-388. doi: 10.3934/mbe.2008.5.355
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