[LPC+12] Matthew Lakin, David Parker, Luca Cardelli, Marta Kwiatkowska and Andrew Phillips. Design and Analysis of DNA Strand Displacement Devices using Probabilistic Model Checking. Journal of the Royal Society Interface, 9(72), pages 1470-1485, The Royal Society. July 2012. [pdf] [bib] [Analyses correctness, reliability and performance of DNA computing designs using PRISM and DSD.]
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Notes: Supplementary material (files to be used with the software tools Visual DSD and PRISM to reproduce the results presented in the paper) can be found here.
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Abstract. Designing correct, robust DNA devices is difficult because of the many possibilities for unwanted interference between molecules in the system. DNA strand displacement has been proposed as a design paradigm for DNA devices, and the DSD programming language has been developed as a means of formally programming and analysing these devices to check for unwanted interference. We demonstrate, for the first time, the use of probabilistic verification techniques to analyse the correctness, reliability and performance of DNA devices during the design phase. We use the probabilistic model checker PRISM, in combination with the DSD language, to design and debug DNA strand displacement components and to investigate their kinetics. We show how our techniques can be used to identify design flaws and to evaluate the merits of contrasting design decisions, even on devices comprising relatively few inputs. We then demonstrate the use of these components to construct a DNA strand displacement device for approximate majority voting. Finally, we discuss some of the challenges and possible directions for applying these methods to more complex designs.