ChemChaste: A hybrid continuum-discrete modelling software suite for simulating bacterial communities

Bacterial communities, such as those contained within biofilms, are found in a wide range of industrial and clinical scenarios. They can be composed of multiple cell types which complicate the task of tackling film build up, such as in infections or marine biofouling. We seek to understand the biofilm wide dynamics through developing a hybrid continuum-discrete software library to complement experimentation and improve data informed biological modelling. By extending the widely used multi-scale simulation package Chaste, our open sourced software ChemChaste provides the means to simulate general reaction-diffusion PDEs coupled to individual cell models. Each cell within ChemChaste contains metabolic pathways, a personal cell cycle model, and membranous transport to enable the simulation of the complex chemical interactions within heterogeneous communities. Using ChemChaste we look to infer the role of environment-metabolic feedback on the community structure and consider how utilising multiple different cell types may protect a spatially distributed community from external stress or attack. Our results provide insights which may further our understanding of bacterial biofilms found in both industrial, and clinical, scenarios.