Modelling and Stochastic Simulation of Synthetic Biological Boolean Gates

Synthetic Biology aspires to design, compose and engineer biological systems that implement specified behaviour. When designing such systems, hypothesis testing via computational modelling and simulation is vital in order to reduce the need of costly wet lab experiments. As a case study, we discuss the use of computational modelling and stochastic simulation for engineered genetic circuits that implement Boolean AND and OR gates that have been reported in the literature. We present performance analysis results for nine different state-of-the-art stochastic simulation algorithms and analyse the dynamic behaviour of the proposed gates. Stochastic simulations verify the desired functioning of the proposed gate designs.

I. Introduction

Synthetic Biology is a relatively new discipline that aspires to design and compose biological systems that implement designer specified behaviour [1]. Synthetic Biology allows scientists to engineer biochemical systems that perform tasks that otherwise would not exist in nature, by harnessing mechanisms that have successfully proliferated all forms of life.