Simulate Bacterial Movement through Chemotaxis

Abstract

This thesis describes the development of an agent-based simulation of E. coli chemotaxis in C# and the Unity game engine. The agents use a mathematical model of the chemical pathway underlying chemotaxis to produce either forward-motion (running) or rotation (tumbling), in response to the concentration of ligand in their immediate environment. This model consists of a system of ODEs from Edgington and Tindall [1] and elements of survival analysis. A tool for analysing data from these simulations was also developed, and used to make quantitative comparisons between simulations. This is used to compare our model to a simplified model of chemotaxis, designed to always display chemotactic behaviour. It is concluded that both models display chemotactic movement, with the simplified model being more effective at finding the ligand source, but the ODE-based model being more adaptive.