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Functional Analysis of Large-Scale DNA Strand Displacement Circuits

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DNA Computing and Molecular Programming (DNA 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8141))

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Abstract

We present a method for the analysis of functional properties of large-scale DNA strand displacement (DSD) circuits based on Satisfiability Modulo Theories that enables us to prove the functional correctness of DNA circuit designs for arbitrary inputs, and provides significantly improved scalability and expressivity over existing methods. We implement this method as an extension to the Visual DSD tool, and use it to formalize the behavior of a 4-bit square root circuit, together with the components used for its construction. We show that our method successfully verifies that certain designs function as required and identifies erroneous computations in others, even when millions of copies of a circuit are interacting with each other in parallel. Our method is also applicable in the verification of properties for more general chemical reaction networks.

The original version of this chapter was revised: The copyright line was incorrect. This has been corrected. The Erratum to this chapter is available at DOI: 10.1007/978-3-319-01928-4_15

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Author information

Authors and Affiliations

  1. Microsoft Research, Cambridge, UK

    Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Andrew Phillips & Hillel Kugler

Authors
  1. Boyan Yordanov
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  2. Christoph M. Wintersteiger
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  3. Youssef Hamadi
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  4. Andrew Phillips
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  5. Hillel Kugler
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Editors and Affiliations

  1. Center for Systems and Synthetic Biology, University of California, 1700 4th Street, San Francisco, 94158, CA, USA

    David Soloveichik

  2. Materials Science and Engineering Department, Boise State University, 1910 University Drive, 83725, Boise, ID, USA

    Bernard Yurke

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Yordanov, B., Wintersteiger, C.M., Hamadi, Y., Phillips, A., Kugler, H. (2013). Functional Analysis of Large-Scale DNA Strand Displacement Circuits. In: Soloveichik, D., Yurke, B. (eds) DNA Computing and Molecular Programming. DNA 2013. Lecture Notes in Computer Science, vol 8141. Springer, Cham. https://doi.org/10.1007/978-3-319-01928-4_14

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  • DOI: https://doi.org/10.1007/978-3-319-01928-4_14

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-01927-7

  • Online ISBN: 978-3-319-01928-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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