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Towards Temporal Logic Computation Using DNA Strand Displacement Reactions

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Unconventional Computation and Natural Computation (UCNC 2017)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10240))

Abstract

Time-varying signals are ubiquitous throughout science, and studying the high-level temporal structure of such processes is of significant practical importance. In this context, techniques from computer science such as temporal logic are a powerful tool. Temporal logic allows one to describe temporal properties of time-varying processes, e.g., the order in which particular events occur. In this paper, we show that DNA strand displacement reaction networks can be used to implement computations that check certain temporal relationships within time-varying input signals. A key aspect of this work is the development of DNA circuits that incorporate a primitive memory, so that their behavior is influenced not just by the current observed chemical environment, but also by environments observed in the past. We formalize our circuit designs in the DSD programming language and use simulation results to confirm that they function as intended. This work opens up the possibility of developing DNA circuits capable of long-term monitoring of processes such as cellular function, and points to possible designs of future DNA circuits that can decide more sophisticated temporal logics.

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Notes

  1. 1.

    See the Supporting Information (available from the first author’s web page) for full DSD code listings for each system simulated in this paper, including full definitions of the modules.

  2. 2.

    See the Supporting Information (available from the first author’s web page) for full DSD code listings for each system simulated in this paper, including full definitions of the modules.

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Acknowledgments

This material is based upon work supported by the National Science Foundation under grants 1525553, 1518861, and 1318833.

Author information

Authors and Affiliations

  1. Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, USA

    Matthew R. Lakin

  2. Department of Computer Science, University of New Mexico, Albuquerque, NM, USA

    Matthew R. Lakin & Darko Stefanovic

  3. Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, USA

    Matthew R. Lakin & Darko Stefanovic

Authors
  1. Matthew R. Lakin
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  2. Darko Stefanovic
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Corresponding author

Correspondence to Matthew R. Lakin .

Editor information

Editors and Affiliations

  1. University of Arkansas, Fayetteville, Arkansas, USA

    Matthew J. Patitz

  2. University of Sheffield, Sheffield, United Kingdom

    Mike Stannett

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Lakin, M.R., Stefanovic, D. (2017). Towards Temporal Logic Computation Using DNA Strand Displacement Reactions. In: Patitz, M., Stannett, M. (eds) Unconventional Computation and Natural Computation. UCNC 2017. Lecture Notes in Computer Science(), vol 10240. Springer, Cham. https://doi.org/10.1007/978-3-319-58187-3_4

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  • DOI: https://doi.org/10.1007/978-3-319-58187-3_4

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-58186-6

  • Online ISBN: 978-3-319-58187-3

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