Modelling

Modelling took a large place in the project. We used modelling for the characterization of KillerRed and the Voigt plasmids and also needed it for the control of the bacterial population. With our device, we cannot control a population of living cells with a simple closed-loop transfer function. The first reason is that optical measurements (OD at 600 nm or fluorescence) originate from all cells, whether they are alive or not. As a consequence, it is not easy to reconstruct the size of a population of living cells from a fluorescent intensity or an $OD_{600}$ reading. Second, there is a large delay between an action and its effect: there are about one or two hours between the onset of illumination and a decrease in fluorescence growth rate. In those conditions, a simple closed-loop transfer function is predictably unstable, and a predictive model is needed to stabilize the population of living cells.

Come, sit, and listen to the story of the model's construction! You will hear about the journey of this model, from its genesis to its completion ! Going through the reasons that drove it to consider the time of maturation of KillerRed or the resilience of bacteria.

Here, you traveler, you will read about the way the parameters were chosen to best fit the experiments, and thus make the model properly predict the evolution of the bacterial concentration. You will see how a genetic algorithm can be used to understand a genetic network. And of course you will appreciate the final results.

At last, you will discover the power and the impact that light has on our system. Then you will be introduced to a crafty way to master it and control a bacterial population with its help. You will be shown how it is supposed to be done.