Abstract
We demonstrate how the DSD programming language can be used to design a DNA stack machine and to analyse its behaviour. Stack machines are of interest because they can efficiently simulate a Turing machine. We extend the semantics of the DSD language to support operations on DNA polymers and use our stack machine design to implement a non-trivial example: a ripple carry adder which can sum two binary numbers of arbitrary size. We use model checking to verify that the ripple carry adder executes correctly on a range of inputs. This provides the first opportunity to assess the correctness and kinetic properties of DNA strand displacement systems performing Turing-powerful symbolic computation.
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Lakin, M.R., Phillips, A. (2011). Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems. In: Cardelli, L., Shih, W. (eds) DNA Computing and Molecular Programming. DNA 2011. Lecture Notes in Computer Science, vol 6937. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23638-9_12
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DOI: https://doi.org/10.1007/978-3-642-23638-9_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-23637-2
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