DREAMY

Recent advances in the design of genetically engineered synthetic bacteria have high potential impact on new solutions towards biological computing by bacteria such as bio-sensing applications, bio-production, and intelligent drugs. This research project proposes innovative solutions to the problem of building distributed circuits in bacteria from an algorithmic, theoretical perspective that contributes to real-world implementable solutions. We envision the following expected outcomes: New robust algorithms and improved understanding of design decisions: The mathematical analysis of distributed algorithms serves two main purposes: it establishes correctness and performance bounds and allows one to systematically assess algorithmic design decisions. Since biological implementations and their environment are inherently noise- and fault-prone, robustness to these effects is key for the distributed algorithms. Concrete requirements are robustness to variations of model parameters (e.g., due to the variability among bacterial cells) and to a fraction of the bacteria not following the algorithm (e.g., due to loss-of-function mutations). New building blocks: Any algorithm crucially relies on available primitives/building blocks. For distributed algorithms communication primitives are central. We will design, implement, and experimentally verify a new phage-based system to transfer DNA from one bacterium to another.