Speaker:Michael Gerten

Software Engineering for Molecular Programs

The use of non-traditional computing mechanisms is a rapidly growing field of study. One paradigm uses chemical reaction networks (CRNs) to perform computations via chemical inter-actions. CRNs are used to develop molecular devices at the nanoscale, such as intelligent drug therapeutics. In practice, these programs are written and simulated in environments like MATLAB and later compiled into physical molecules such as DNA strands. However, techniques for testing the correctness of CRNs are lacking. Current methods of validating CRNs include using model checking and theorem proving, but these techniques are limited in scalability. We introduce new techniques including a testing framework for evaluating CRNs, an automated test generation technique using program invariants, and an automated program repair technique. Continuing this work, we propose to develop a fault localization method that works with the challenges of CRNs, a method of test prioritization, and extend the automated program repair work with new CRN models and repair operators.

Committee: Myra Cohen (co-major professor), James Lathrop (co-major professor), Samik Basu, Robyn Lutz, and Jonathan Smith