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On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets

  • Benoît Barbot
  • Marta Kwiatkowska
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9115)

Abstract

Molecular programming is an emerging field concerned with building synthetic biomolecular computing devices at the nanoscale, for example from DNA or RNA molecules. Many promising applications have been proposed, ranging from diagnostic biosensors and nanorobots to synthetic biology, but prohibitive complexity and imprecision of experimental observations makes reliability of molecular programs difficult to achieve. This paper advocates the development of design automation methodologies for molecular programming, highlighting the role of quantitative verification in this context. We focus on DNA ‘walker’ circuits, in which molecules can be programmed to traverse tracks placed on a DNA origami tile, taking appropriate decisions at junctions and reporting the outcome when reaching the end of the track. The behaviour of molecular walkers is inherently probabilistic and thus probabilistic model checking methods are needed for their analysis. We demonstrate how DNA walkers can be modelled using stochastic Petri nets, and apply statistical model checking using the tool Cosmos to analyse the reliability and performance characteristics of the designs. The results are compared and contrasted with those obtained for the PRISM model checker. The paper ends by summarising future research challenges in the field.

Keywords

Model Check Temporal Logic Atomic Proposition Chemical Master Equation Statistical Model Check 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Department of Computer ScienceUniversity of OxfordOxfordUK

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