Design and analysis of DNA circuits for molecular computing

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. In the first part of my talk, I will introduce how, with colleagues at University of Washington, we have programmed DNA to perform computations, by implementing the formalism of chemical reaction networks in low-level DNA interactions. We have implemented several building-block reaction types and combined them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents. In the second part, I will introduce how we have been using probabilistic model checking to analyse the stochastic dynamics of localised DNA circuits. DNA-based computing executed via local interactions has potential advantages of speed, sharper switching behaviour, higher precision, parallelism and modularity and scalability. We analyse designs of localised DNA circuitry using software tools developed at Microsoft Research that have recently been extended to facilitate probabilistic analyses. Our method relies on numerical integration of the chemical master equation using standard methods for initial value problems, which turns out to be rather more efficient than previously thought.