The Dry Lab used computational simulations to explore the different properties of the Biofabricator. Our activities are summarized on this page. To find out more please visit the Dry Lab Hub.
We have developed a simple model for the growth of B. subtilis where the rate of growth is related to the amount of nutrients available. To this purpose we have exploited the ideas put forward by last year's Imperial College iGEM team for their modelling of F2620 in a cell-free system.
We have also built mathematical models for the time evolution of the basic genetic circuits that comprise our device. We have verified which model best describe the behaviour of the circuit better by using laboratory data.
Finally, we have carried out a detailed analysis of the swimming motility of B. subtilis, which led us, among other things, to develop a simple mechanical model for the swimming motility of B. subtilis. Using manual tracking, we were able to extract x,y coordinate data from the cell trajectory. This has allowed us to fit experimental data with our model. The data suggest that flagellar force of B. subtilis is Exponentially distributed.
All model simulations and motility data analysis were carried out with MATLAB. Cell tracking was done with ImageJ via the Manual Tracking Plugin. All our MATLAB files can be found in the Appendices section.