Modeling

The modelling sub-team aims to predict the main features of our project to understand how stable, standard and orthogonal engineered systems are. In order to accomplish this goal, two different approaches have been taken into account: mRNA and protein expression levels prediction tools and plasmid dynamics. These two approaches may give insight of the presented problem.

In order to predict accurately the mRNA and protein expression levels, we propose a model considering both intrinsic (metabolic burden) and extrinsic (pH or temperature) characteristics of our system. Using this model, we aim to describe the bacterial response to different kind of stresses (e.g. temperature, pH, UV radiation).

A second approach tries to predict the behaviour of two different plasmids sharing the same origin of replication in a single cell. As they share the same mechanism of regulation, they may behave in a non-orthogonal way. The model is based in stochastic dynamics (how perturbations may become a relevant feature of the system) using both simulation and analysis tools.

While both models are different, we want to create a framework to gain knowledge in engineered molecular biological systems, explaining our experimental results and proposing new hypothesis, to design more reliable and predictable biological machines.