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

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 cellcell 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.

Biofilm growth on rugose surfaces

“…When only growth processes are taken into account, vertical fingers are formed if the growth dynamics is constrained by the limiting concentration (see Refs. [24,25]). If a large enough concentration reaches most cells, biofilms tend to be flatter.…”

“…In static flows, the distance between fingers is shown to increase as the availability of nutrients diminishes in Ref. [24]. Additionally, the erosion mechanism can generate, suppress, or modify patterns.…”

“…Experimental measurements of some parameters (unavailable at present) should be required to attempt quantitative comparisons. Fitting model parameters to practical setups seems to be a general problem with models for biofilms due to a lack of adequate experimental data [15,24].…”

“…Hybrid variants include the EPS matrix as an incompressible viscous flow, which embeds the discrete microbial cells [23]. Hybrid models combine discrete descriptions of the cells with continuous descriptions of other relevant fields [24,25]. A hybrid model trying to account for the effect of the flow is proposed in Ref.…”

Differential growth of wrinkled biofilms

“…Different modeling frameworks characterize individual bacteria in different ways. Cellular automata [31][32][33], cellular Potts [34], and individual-based [22,25,35] representations have been proposed for biofilms in flows. We will comment on the general approaches in Sec.…”