Synthetic Gene Circuit Analysis and Optimization

Synthetic biology aims to engineer synthetic circuits with predefined target functions. From a systems (model-based) perspective, two problems are of central importance: (i) given a model of a biomolecular circuit, determining whether it is capable of exhibiting a specific behavior or functionality; and (ii) starting from a predefined required functionality and a library of biological parts, identifying the biomolecular circuit that, when constructed as a combination of such parts, achieves the desired behavior. These two problems, which can be framed, respectively, as nonlinear analysis and automated design problems, are addressed here using efficient optimization methods. In this chapter, we specifically focus on deterministic frameworks, in which the effect of intrinsic molecular noise on the dynamics is not significant. We illustrate these methods through case studies focused on the analysis and design of biocircuits capable of bistability (bistable switches). Bistability is of particular interest in systems and synthetic biology because it endows cells with the capacity to make decisions.