ArticleMathematical biosciences and engineering : MBE2008
Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment.
Article in Mathematical biosciences and engineering : MBE, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Rheological transition driven by matrix makes cancer spheroids resilient under confinement.Life science alliance · 2025Article
- Competing mechanisms in bacterial invasion of human colon mucus probed with agent-based modeling.Biophysical journal · 2024Article
- A framework for multi-scale intervention modeling: virtual cohorts, virtual clinical trials, and model-to-model comparisons.Frontiers in systems biology · 2023Article
- Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action.Royal Society open science · 2022Article
- The Antimicrobial Effect ofFrontiers in microbiology · 2022Article
- Biofilm viscoelasticity and nutrient source location control biofilm growth rate, migration rate, and morphology in shear flow.Scientific reports · 2021Article
- Article
- Mesoscopic Energy Minimization Drives Pseudomonas aeruginosa Biofilm Morphologies and Consequent Stratification of Antibiotic Activity Based on Cell Metabolism.Antimicrobial agents and chemotherapy · 2018Article
- Virtual-tissue computer simulations define the roles of cell adhesion and proliferation in the onset of kidney cystic disease.Molecular biology of the cell · 2016Article
- Variable cell morphology approach for individual-based modeling of microbial communities.Biophysical journal · 2014Article
- Adhesion failures determine the pattern of choroidal neovascularization in the eye: a computer simulation study.PLoS computational biology · 2012Article
- Study on multicellular systems using a phase field model.PloS one · 2012Article
- Multi-scale modeling of tissues using CompuCell3D.Methods in cell biology · 2012Article
- Article
- A multi-cell, multi-scale model of vertebrate segmentation and somite formation.PLoS computational biology · 2011Review
- Article
- 3D multi-cell simulation of tumor growth and angiogenesis.PloS one · 2009Article
- Stochastic collective movement of cells and fingering morphology: no maverick cells.Biophysical journal · 2009Article
- Front instabilities and invasiveness of simulated avascular tumors.Bulletin of mathematical biology · 2009Article
- Multicell simulations of development and disease using the CompuCell3D simulation environment.Methods in molecular biology (Clifton, N.J.) · 2009Article
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4 authors.
Funding
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 inclusion of cell adhesion, which is difficult to implement using other modeling approaches, results in slightly different patterns. Our simulations thus provide the groundwork for simulations of medically and industrially important multispecies biofilms.
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