Simbiotics: A multiscale integrative platform for 3D modelling of bacterial populations

by Jonathan Naylor

16:00 (40 min) in USB 2.022

For my PhD I have been developing a 3D simulation platform for modelling bacterial populations. Due to the complex self-organising nature of bacteria and the wide range of existing bacterial behaviours, the platform is not specific to a particular bacterial species (it provides a generic framework). Bacteria are represented as geometric entities which may move around a domain filled with chemical gradients. Bacteria may interact with each other and with the extracellular chemicals. Each bacteria can be defined to have its own individual biological activity. This form of "bottom-up" modelling allows for the study of emergent population dynamics, offering insights into existing bacterial systems, but also as a CAD tool for synthetic biologists who are designing populations of synthetic bacteria. This generalised tool is flexible and extendable, and requires minimal programming experience to use, allowing for experimentalists and theorists to integrate the tool into their workflow, and for the tool to still be applicable as scientific knowledge progresses.

I will present the Simbiotics simulation platform, followed by a description of the systems we modelled during the development of the software. We pursued two case studies, focusing the physical aspects of these systems to verify these components of the simulator. The first case study is in collaboration with the School of Dental Sciences and Newcastle University, looking at bacterial coaggregation in saliva. The second study was in collaboration with the Department of Chemical and Biological Engineering, looking at how cell-surface charge may effect biofilm architecture. I will also discuss the new case studies being pursued with the tool.