Computational Synthetic Biology for Molecular Communications

Bacteria-based synthetic biology systems have been proposed in the past twenty years as solutions for biotechnology and the design of novel therapeutics. In parallel to the field of synthetic biology, a new field has emerged where engineers can characterize and design communications systems through the exchange of molecules. This field is known as molecular communications, and has taken the paradigm from conventional communication networks and applied it to biological systems. This paradigm shift has numerous challenges, and in particular due to the characteristics of the molecular signal propagation behaviour that is very different from electromagnetic signals. Since the birth of this new field, numerous research works have concentrated on characterizing the communication channels and developing theoretical models to lay the groundwork for novel applications. Both Synthetic Biology and Molecular Communications fields have evolved since then, and the current challenges reside in the ability to combine these two fields together to create novel applications. The aim of integrating these two fields is to enable implementation of complex synthetic circuits that are able to autonomously operate in the long-term with high accuracy levels and reliability. In this PhD thesis, synthetic biology and molecular communications systems are integrated through computational methods for a number of applications that utilizes bacteria as the main cell lines to be programmed. This novel combination can provide novel biotechnology solutions such as biofilm prevention, bio-sensor synthetic gates, as well as synthetic logic circuits. This synergistic integration was proven in this PhD thesis, and can provide a new direction for the molecular communications community.