Chemical reaction network designs for asynchronous logic circuits View Full Text


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Article Info

DATE

2017-12-22

AUTHORS

Luca Cardelli, Marta Kwiatkowska, Max Whitby

ABSTRACT

Chemical reaction networks (CRNs) are a versatile language for describing the dynamical behaviour of chemical kinetics, capable of modelling a variety of digital and analogue processes. While CRN designs for synchronous sequential logic circuits have been proposed and their implementation in DNA demonstrated, a physical realisation of these devices is difficult because of their reliance on a clock. Asynchronous sequential logic, on the other hand, does not require a clock, and instead relies on handshaking protocols to ensure the temporal ordering of different phases of the computation. This paper provides novel CRN designs for the construction of asynchronous logic, arithmetic and control flow elements based on a bi-molecular reaction motif with catalytic reactions and uniform reaction rates. We model and validate the designs for the deterministic and stochastic semantics using Microsoft's GEC tool and the probabilistic model checker PRISM, demonstrating their ability to emulate the function of asynchronous components under low molecular count. More... »

PAGES

109-130

References to SciGraph publications

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  • 2013-09-03. Deterministic function computation with chemical reaction networks in NATURAL COMPUTING
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  • 2009-08-13. Programmability of Chemical Reaction Networks in ALGORITHMIC BIOPROCESSES
  • 2008-03-26. A simple population protocol for fast robust approximate majority in DISTRIBUTED COMPUTING
  • 2015-06-04. On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets in APPLICATION AND THEORY OF PETRI NETS AND CONCURRENCY
  • 2016-08-14. Chemical Reaction Network Designs for Asynchronous Logic Circuits in DNA COMPUTING AND MOLECULAR PROGRAMMING
  • 2015-09-02. Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation in COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY
  • 2012-09-13. The Cell Cycle Switch Computes Approximate Majority in SCIENTIFIC REPORTS
  • 2014-06-07. DNA walker circuits: computational potential, design, and verification in NATURAL COMPUTING
  • 2013-09-29. Programmable chemical controllers made from DNA in NATURE NANOTECHNOLOGY
  • 2011. PRISM 4.0: Verification of Probabilistic Real-Time Systems in COMPUTER AIDED VERIFICATION
  • 2008-02-02. Computation with finite stochastic chemical reaction networks in NATURAL COMPUTING
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s11047-017-9665-7

    DOI

    http://dx.doi.org/10.1007/s11047-017-9665-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1099923748

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29576757


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