A game-of-life like simulator for design-oriented modeling of BioBricks in synthetic biology

This paper deals with the development of a new simulator that will be very helpful to establish new accurate and predictive design-oriented models for the BioBricks used in synthetic biology. The simulator uses the principle of the game-of-life: molecules can move on a grid and, at every iteration, binding and dissociation rules are applied when two molecules are on same node. The principle is elementary but it can highlight interesting biological phenomenon. Those can be modeled by mathematical equations to achieve design-oriented models. In this case, the simulator also helps to make to link between mathematical parameters and the microscopic parameters. A first version of the software has been implemented in MATLAB. It permits to retrieve very interesting results, such as the Hill's equation and the properties of Hill's coefficient.