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CompuCell3D

swMATH ID: 34248
Software Authors: Popławski, Nikodem J.; Shirinifard, Abbas; Swat, Maciej; Glazier, James A.
Description: Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Ho-ge-weg model and the CompuCell3D modeling environment. 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.
Homepage: https://compucell3d.org
Keywords: biofilms; Glazier-Graner-Hogeweg model; cellular Potts model; bacterial growth; computational biology; CompuCell3D
Related Software: PhysiCell; Chaste; EmbryoMaker; ParaView; CellSys; Microvessel Chaste; Morpheus; VirtualLeaf; Biocellion; CellML; MiniSom; GitHub; Matlab; MASON; NetLogo; Trilinos; deal.ii; SuperLU; Qhull; ABAQUS
Referenced in: 24 Publications
Further Publications: https://compucell3d.org/Publications

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