ChemChaste: Modelling chemical dynamics in spatially distributed bio-films

Biofilms are ubiquitous in medical settings. Biofilms can contain multiple distinct bacterial strains which complicate the task of tackling infections. Mathematical modelling can help us improve our understanding of, and design better-informed experiments to probe, the dynamics of such systems. We seek to understand the biofilm wide dynamics through developing a hybrid continuum-discrete software library, ChemChaste. Building upon the multi-scale simulation package Chaste, ChemChaste introduces the means to simulate general reaction-diffusion PDEs coupled to individual based cell cycle models. Each cell within the simulation contains its own metabolic pathways, cell cycle model, and membranous transport to enable the simulation of complex chemical interactions between heterogeneous communities. The emergence of structure within the communities is simulated through the segregation of cell types driven by the chemical signaling and external reaction systems. This combination of cell based and external domain reactions enables ChemChaste to simulate chemical dynamics occurring within biofilms. From this we probe the role of microenvironment-metabolism feedback on the community structure and infer how the distribution of cell types may protect the community from external stress. Our results provide insights which may further our understanding of bacterial infections in clinical practice.