Challenges in automated verification and synthesis for molecular programming

Molecular programming is concerned with building synthetic nanoscale devices from molecules, which can be programmed to autonomously perform a specific task. Several artifacts have been demonstrated experimentally, including DNA circuits that can compute a logic formula and molecular robots that can transport cargo. In view of their natural interface to biological components, many potential applications are envisaged, e.g. point-of-care diagnostics and targeted delivery of drugs. However, the inherent complexity of the resulting biochemical systems makes the manual process of designing such devices error-prone, requiring automated design support methodologies, analogous to design automation tools for digital systems. This paper gives an overview of the role that probabilistic modelling and verification techniques can play in designing, analysing, debugging and synthesising programmable molecular devices, and outlines the challenges in achieving automated verification and synthesis software technologies in this setting.