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Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.DNA.28.5
URN: urn:nbn:de:0030-drops-167904
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2022/16790/
Li, Bowen ;
Mackenzie, Neil ;
Shirt-Ediss, Ben ;
Krasnogor, Natalio ;
Zuliani, Paolo
Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking
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.
BibTeX - Entry
@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/opus/volltexte/2022/16790},
URN = {urn:nbn:de:0030-drops-167904},
doi = {10.4230/LIPIcs.DNA.28.5},
annote = {Keywords: probabilistic model checking, CTMC, DNA computing, DNA stack}
}
