Simulation of single-species bacterial-biofilm growth using the glazier-graner-hogeweg model and the compucell3d modeling environment. Export

@article{citeulike:3451702, abstract = {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.}, author = {Poplawski, N. J. and Shirinifard, A. and Swat, M. and Glazier, J. A.}, citeulike-article-id = {3451702}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/18613738}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=18613738}, day = {1}, issn = {1547-1063}, journal = {Mathematical biosciences and engineering : MBE}, keywords = {cpm}, month = {April}, number = {2}, pages = {355--388}, posted-at = {2008-10-26 19:10:54}, priority = {3}, title = {Simulation of single-species bacterial-biofilm growth using the glazier-graner-hogeweg model and the compucell3d modeling environment.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/18613738}, volume = {5}, year = {2008} }

TY - JOUR ID - citeulike:3451702 L3 - citeulike-article-id:3451702 N2 - 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. IS - 2 JF - Mathematical biosciences and engineering : MBE SN - 1547-1063 EP - 388 TI - Simulation of single-species bacterial-biofilm growth using the glazier-graner-hogeweg model and the compucell3d modeling environment. VL - 5 SP - 355 KW - cpm AU - Poplawski, NJ AU - Shirinifard, A AU - Swat, M AU - Glazier, JA PY - 2008/04/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/18613738 ER -