Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems

  • Matthew R. Lakin
  • Andrew Phillips
Conference paper

DOI: 10.1007/978-3-642-23638-9_12

Volume 6937 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
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

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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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Matthew R. Lakin
    • 1
  • Andrew Phillips
    • 1
  1. 1.Microsoft ResearchCambridgeUK