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Modelling, simulating and verifying DNA strand displacement systems

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DNA strand displacement has been used to implement a broad range of information processing devices using nucleic acids: from logic gates, to chemical reaction networks, to architectures for universal computation. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. In this talk I will present a methodology for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. Device designs can be programmed using a common syntax and then analysed at varying levels of detail, with or without interference. I will also discuss simulation and verification techniques for strand displacement systems which may produce unbounded numbers of species and reactions.

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