My research uses computer engineering principles of abstraction, composition, and interface specifications to build programmable bio-organisms with sensors and actuators precisely controlled by logic circuitry. Here, recombinant DNA-binding proteins represent signals, and recombinant genes perform the computation by regulating protein expression. To demonstrate basic cellular computation and intercellular communication, I have constructed and tested biochemical gates in Escherichia coli that implement the AND, NOT and IMPLIES logic operations. After measuring and modifying the ``device physics'' of these gates, I combined matching gates to implement several small circuits. To aid in this biocircuit design process I implemented BioSpice, a prototype genetic circuit simulation and verification tool.

Finally, I defined the Microbial Colony Language (MCL), a simple programming paradigm that could be instantiated in-vivo with small circuits and intercellular communications. This intermediate-level programming language is used to explore how to achieve globally coordinated behavior (e.g. pattern formation) from a large number of unreliable computing elements such as programmed cells that are constrained to communicate locally.

My contributions so far: