2026-08-10T11:21:35Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:16790 2024-03-06T10:58:13Z ddc:004 open_access

Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking Li, Bowen Mackenzie, Neil Shirt-Ediss, Ben Krasnogor, Natalio Zuliani, Paolo probabilistic model checking CTMC DNA computing DNA stack 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. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Bowen Li and Neil Mackenzie and Ben Shirt-Ediss and Natalio Krasnogor and Paolo Zuliani 2022 Is Part Of LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.DNA.28.5 urn:nbn:de:0030-drops-167904 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.5 eng https://creativecommons.org/licenses/by/4.0/legalcode