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Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking

Authors: Bowen Li, Neil Mackenzie, Ben Shirt-Ediss, Natalio Krasnogor, and Paolo Zuliani

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract

A DNA stack nano-device is a bio-computing system that can read and write molecular signals based on DNA-DNA hybridisation and strand displacement. In vitro implementation of the DNA stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the DNA stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? The results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield.

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Bowen Li, Neil Mackenzie, Ben Shirt-Ediss, Natalio Krasnogor, and Paolo Zuliani. Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{li_et_al:LIPIcs.DNA.28.5,
  author =	{Li, Bowen and Mackenzie, Neil and Shirt-Ediss, Ben and Krasnogor, Natalio and Zuliani, Paolo},
  title =	{{Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.5},
  URN =		{urn:nbn:de:0030-drops-167904},
  doi =		{10.4230/LIPIcs.DNA.28.5},
  annote =	{Keywords: probabilistic model checking, CTMC, DNA computing, DNA stack}
}

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Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking

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