Designing a new biological function in synthetic biology

Abstract

Synthetic biology is a science resulting from the connection between biotechnology and engineering sciences. It aims to design and build new biological systems and functions. In this paper, models of biologic gates using different abstraction levels have been presented. For each kind of model, its advantages and drawbacks were discussed. The high-level model will be used during the first step of the design to validate the concept. It allows fast simulation, even for big systems, and can be completed by mathematical tools in order to automatism the process. An intermediate model, using templates (like in microelectronics), gives some indications about concentration and timing which allows to validate a system in a worst- case situation without complex simulations. Finally, the low- level model, which uses biological ODEs, can be used to predict accurately the time-dependent evolution of protein concentration in the cell. Two types of low-level model are presented: the signal flow model, which consists in explicit ODEs and the conservative model which is based on implicate ODEs coming from matter conservation principle. For the latter, we developed a formalism that permits to represent a biological mechanism by an electronic circuit using voltage and current sources, resistances and capacities. © 2011 Springer-Verlag Berlin Heidelberg.