This thesis will focus on the evolution of bacterial metabolic pathways, combining modeling and simulation methods.

We will focus on questions related to :

(a) the selection pressures acting on genome evolution and organization induced by biochemicals constraints related to metabolism (robustness and stability of expression despite stochastic fluctuations), and (b) the population dynamics resulting from between-individuals interactions (exchange of metabolites) and the resulting eco-evolutionary phenomena (diversification and specialization).

This will be tackled by combining three types of modeling and simulation approaches :
1. Modeling bacterial metabolism with Flux Balance Analysis and related methods
2. Ecological modeling and simulation of between-individuals interactions (transforming the previous model into multi-scale modeling)
3. Modeling and simulation of the genome organization, using artificial life models.