Towards Predictable Computer-Aided Designs for Synthetic Gene Circuits: Application to Gene-Metabolic Oscillator in Bacteria

Advances in molecular biology and the reduced costs in genetic modifications promoted the emergence of systems and synthetic biology over the last decade. In principle, these approaches can be applied on system level design for specific biological behavior through rewiring natural connectivity in the regulatory network. However, reality suggests otherwise: even for simple gene circuits, design and implementation of nonlinear dynamics such as bistability or oscillation has been proven to be extremely difficult. Most designs strategies are ad hoc, rather than systematic or strategic. In addition, physicochemical models can only qualitatively describe, rather than predict gene circuit behaviors. My interest is to develop approaches to improve the predictability of physicochemical models in designing gene circuit to exhibit specific desirable behaviors. Ultimately, these approaches shall enable system level design of large scale in vivo biological regulatory networks.