In order to model the chemotactic motion of the engineered bacteria, a simulation program was designed and produced. The simulation models the motion of a population of bacteria in a small environment composed of two chemoattractants. This page provides an overview of the simulator followed by an in-depth discussion of the mathematical model used [1,2]. The inputs to the model and the possible outputs are highlighted. An analysis of the assumptions made in development, and resulting shortcomings of the tool is also conducted.

Overview

The simulation tool, as shown in the alongside figure, models the chemotactic motion of a population of bacteria in a small environment (a petri dish). As in the project setup, two chemoattractants (shown in red and green) are present in the environment and influence the motile action of the bacteria. The representative bacteria take the colour of the chemical towards which they are attracted, and move about the environment according to a movement algorithm. Various options are available to the user of the tool to specify the experiment setup (see later) and the panel on the left allows for this.

The tool may be viewed at this link. It is necessary to install the

As may be seen from the above figure, the initial chemical concentration does indeed have an effect on the rate at which bacteria successfully navigate to the attractant. The chosen arbitrary reference concentration sees an almost 10 fold increase of the number of bacteria in the toggled state over the chosen 2 minutes of simulation time. Even at half of the reference concentration, a six fold increase over pure random motion was obtained. Concentration increases above 10 times the reference concentration had increasingly minimal impact on the chemotaxis of the bacteria. This is due to the overall underlying stochastic nature of the movement and physical distance between where the bacteria are initially located and the chemoattractant.