Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment
The CompuCell3D modeling environment provides a convenientplatform for biofilm simulations using the Glazier-Graner-Hogeweg (GGH)model, a cell-oriented framework designed to simulate growth and patternformation due to biological cells' behaviors. We show how to develop sucha simulation, based o...
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| Format: | Article |
| Language: | English |
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AIMS Press
2008-02-01
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| Series: | Mathematical Biosciences and Engineering |
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| Online Access: | https://www.aimspress.com/article/doi/10.3934/mbe.2008.5.355 |
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| author | Nikodem J. Poplawski Abbas Shirinifard Maciej Swat James A. Glazier |
| author_facet | Nikodem J. Poplawski Abbas Shirinifard Maciej Swat James A. Glazier |
| author_sort | Nikodem J. Poplawski |
| collection | DOAJ |
| description | The CompuCell3D modeling environment provides a convenientplatform for biofilm simulations using the Glazier-Graner-Hogeweg (GGH)model, a cell-oriented framework designed to simulate growth and patternformation due to biological cells' behaviors. We show how to develop sucha simulation, based on the hybrid (continuum-discrete) model of Picioreanu,van Loosdrecht, and Heijnen (PLH), simulate the growth of a single-speciesbacterial biofilm, and study the roles of cell-cell and cell-field interactions indetermining biofilm morphology. In our simulations, which generalize the PLHmodel by treating cells as spatially extended, deformable bodies, differentialadhesion between cells, and their competition for a substrate (nutrient), sufficeto 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 modelingapproaches, results in slightly different patterns. Our simulations thus pro-vide the groundwork for simulations of medically and industrially importantmultispecies biofilms. |
| format | Article |
| id | doaj-art-3744f9c492644b1681fcab41b131b6cc |
| institution | Kabale University |
| issn | 1551-0018 |
| language | English |
| publishDate | 2008-02-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | Mathematical Biosciences and Engineering |
| spelling | doaj-art-3744f9c492644b1681fcab41b131b6cc2025-01-24T01:58:10ZengAIMS PressMathematical Biosciences and Engineering1551-00182008-02-015235538810.3934/mbe.2008.5.355Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environmentNikodem J. Poplawski0Abbas Shirinifard1Maciej Swat2James A. Glazier3Biocomplexity Institute and Department of Physics, Indiana University, Swain Hall West, 727 East Third Street, Bloomington, IN 47405-7105Biocomplexity Institute and Department of Physics, Indiana University, Swain Hall West, 727 East Third Street, Bloomington, IN 47405-7105Biocomplexity Institute and Department of Physics, Indiana University, Swain Hall West, 727 East Third Street, Bloomington, IN 47405-7105Biocomplexity Institute and Department of Physics, Indiana University, Swain Hall West, 727 East Third Street, Bloomington, IN 47405-7105The CompuCell3D modeling environment provides a convenientplatform for biofilm simulations using the Glazier-Graner-Hogeweg (GGH)model, a cell-oriented framework designed to simulate growth and patternformation due to biological cells' behaviors. We show how to develop sucha simulation, based on the hybrid (continuum-discrete) model of Picioreanu,van Loosdrecht, and Heijnen (PLH), simulate the growth of a single-speciesbacterial biofilm, and study the roles of cell-cell and cell-field interactions indetermining biofilm morphology. In our simulations, which generalize the PLHmodel by treating cells as spatially extended, deformable bodies, differentialadhesion between cells, and their competition for a substrate (nutrient), sufficeto 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 modelingapproaches, results in slightly different patterns. Our simulations thus pro-vide the groundwork for simulations of medically and industrially importantmultispecies biofilms.https://www.aimspress.com/article/doi/10.3934/mbe.2008.5.355cellular potts modelcompucell3d.computational biologybiofilmsbacterial growthglazier-graner-hogeweg model |
| spellingShingle | 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 and Engineering cellular potts model compucell3d. computational biology biofilms bacterial growth glazier-graner-hogeweg model |
| title | Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment |
| title_full | Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment |
| title_fullStr | Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment |
| title_full_unstemmed | Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment |
| title_short | Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment |
| title_sort | simulation of single species bacterial biofilm growth using the glazier graner hogeweg model and the compucell3d modeling environment |
| topic | cellular potts model compucell3d. computational biology biofilms bacterial growth glazier-graner-hogeweg model |
| url | https://www.aimspress.com/article/doi/10.3934/mbe.2008.5.355 |
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