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Petri-net-based 2D design of DNA walker circuits
We consider localised DNA computation, where a DNA strand walks along a binary decision graph to compute a binary function. One of the challenges for the design of reliable walker circuits consists in leakage transitions, which occur when a walker jumps into another branch of the decision graph. We...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Netherlands
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5856876/ https://www.ncbi.nlm.nih.gov/pubmed/29576759 http://dx.doi.org/10.1007/s11047-018-9671-4 |
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author | Gilbert, David Heiner, Monika Rohr, Christian |
author_facet | Gilbert, David Heiner, Monika Rohr, Christian |
author_sort | Gilbert, David |
collection | PubMed |
description | We consider localised DNA computation, where a DNA strand walks along a binary decision graph to compute a binary function. One of the challenges for the design of reliable walker circuits consists in leakage transitions, which occur when a walker jumps into another branch of the decision graph. We automatically identify leakage transitions, which allows for a detailed qualitative and quantitative assessment of circuit designs, design comparison, and design optimisation. The ability to identify leakage transitions is an important step in the process of optimising DNA circuit layouts where the aim is to minimise the computational error inherent in a circuit while minimising the area of the circuit. Our 2D modelling approach of DNA walker circuits relies on coloured stochastic Petri nets which enable functionality, topology and dimensionality all to be integrated in one two-dimensional model. Our modelling and analysis approach can be easily extended to 3-dimensional walker systems. |
format | Online Article Text |
id | pubmed-5856876 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Springer Netherlands |
record_format | MEDLINE/PubMed |
spelling | pubmed-58568762018-03-21 Petri-net-based 2D design of DNA walker circuits Gilbert, David Heiner, Monika Rohr, Christian Nat Comput Article We consider localised DNA computation, where a DNA strand walks along a binary decision graph to compute a binary function. One of the challenges for the design of reliable walker circuits consists in leakage transitions, which occur when a walker jumps into another branch of the decision graph. We automatically identify leakage transitions, which allows for a detailed qualitative and quantitative assessment of circuit designs, design comparison, and design optimisation. The ability to identify leakage transitions is an important step in the process of optimising DNA circuit layouts where the aim is to minimise the computational error inherent in a circuit while minimising the area of the circuit. Our 2D modelling approach of DNA walker circuits relies on coloured stochastic Petri nets which enable functionality, topology and dimensionality all to be integrated in one two-dimensional model. Our modelling and analysis approach can be easily extended to 3-dimensional walker systems. Springer Netherlands 2018-02-28 2018 /pmc/articles/PMC5856876/ /pubmed/29576759 http://dx.doi.org/10.1007/s11047-018-9671-4 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Article Gilbert, David Heiner, Monika Rohr, Christian Petri-net-based 2D design of DNA walker circuits |
title | Petri-net-based 2D design of DNA walker circuits |
title_full | Petri-net-based 2D design of DNA walker circuits |
title_fullStr | Petri-net-based 2D design of DNA walker circuits |
title_full_unstemmed | Petri-net-based 2D design of DNA walker circuits |
title_short | Petri-net-based 2D design of DNA walker circuits |
title_sort | petri-net-based 2d design of dna walker circuits |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5856876/ https://www.ncbi.nlm.nih.gov/pubmed/29576759 http://dx.doi.org/10.1007/s11047-018-9671-4 |
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