Design and implementation of feedback control systems for synthetic biology

Synthetic biology is a growing field at the interface of the engineering and biological sciences which aims to apply rational engineering design principles in biological contexts. It has many applications ranging from healthcare and the environment to industrial chemical synthesis and computation. When researchers attempt to apply synthetic biological tools to tackle these problems, they often follow a similar design-build-test cycle to that employed in traditional engineering disciplines. However, there are major challenges at each step in this cycle due to the variability inherent in biological systems, and our limited ability to understand and measure their behaviour. This thesis addresses select problems in each step of the design-build-test cycle as applied to synthetic biology, from a control-theoretic perspective. To aid the design process of synthetic biological circuits I begin by using traditional control-theoretic analysis to derive structural requirements that biological systems must satisfy if they are to achieve behaviours such as disturbance rejection. I demonstrate how these requirements can be used to inform the biological design process, and highlight the challenges that must be overcome for effective noise attenuation in such circuits. To refine the build/creation process for synthetic biological systems, I describe the experimental implementation and subsequent analysis of new synthetic biological feedback controllers built from two classes of components; short RNA and Recombinase proteins. Our results demonstrate how these circuits can be used to tune (or create) feedback loops, and reduce the influence of cellular noise on the performance of our synthetic circuits. This work thus has the double benefit of demonstrating new approaches to the engineering of biological systems, as well as creating well-characterised biological circuits that can be applied directly to a range of applications. Finally, to improve the testing/characterisation process for synthetic biological systems I develop a novel biological approach to measuring cell-to-cell variability, as well as a new automated experimental platform: The Turbidostat. This device provides many of the important measurement and actuation capabilities required for synthetic biological research in a cheap and easy-to-use robotic platform. It can thus be used to automate a diverse range of characterisation experiments that would otherwise be highly laborious and prone to variability/noise. I perform several validation experiments, demonstrating this device’s broad range of capabilities.