Publications associated with Self-assembled structures and devices

Automated design and verification of localized DNA computation circuits

DNA 2015: DNA Computing and Molecular Programming Springer International Publishing Switzerland 9211 (2015) 168-180

M Boemo, AJ Turberfield, L Cardelli

Simple computations can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it.

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