Bioform: an in-silico tool for the 3D modelling of bacterial populations, from design to simulation and analysis

by Jonny Naylor

16:00 (40 min) in CT 7.01

My project involves developing a software tool for simulating bacterial populations in 3D, as well as using this tool to pursue case studies with experimental collaborators. In my presentation I will discuss the current state of the art regarding this type of modelling, the software I am developing in its current form, alongside case study preliminary results. In addition, I will discuss current obstacles and potential solutions concerning the modelling of bacterial populations.

Bacterial communities such as biofilms exhibit complex adaptive behaviours, with population level coordination emerging from local interactions. Their dynamics are not fully understood and are typically species and environment dependent, however common underlying principles and mechanisms are well established. Statistical models offer insights into population trends, but cannot elaborate on the details of sub-relations and the specific circumstances which lead to community self-organisation, such as bacterial differentiation and biofilm morphology. We propose a spatially-explicit 3D modelling platform which allows for the design, simulation and analysis of bacterial populations. We aim to produce a flexible, extendable and high-performance tool which unifies existing modelling and analysis techniques into a common platform, as well as providing novel features to allow for the simulation of physical, chemical and biological factors.