On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets
Molecular programming is an emerging field concerned with building synthetic biomolecular computing devices at 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 com...
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| Other Authors: | |
| Format: | Conference item |
| Language: | English |
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2015
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| _version_ | 1826259853830520832 |
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| author | Barbot, B Kwiatkowska, M |
| author2 | Devillers, R |
| author_facet | Devillers, R Barbot, B Kwiatkowska, M |
| author_sort | Barbot, B |
| collection | OXFORD |
| description | Molecular programming is an emerging field concerned with building synthetic biomolecular computing devices at 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. |
| first_indexed | 2024-03-06T18:56:22Z |
| format | Conference item |
| id | oxford-uuid:11fa6c2d-f088-4033-ab59-680e2f49ca5b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T18:56:22Z |
| publishDate | 2015 |
| record_format | dspace |
| spelling | oxford-uuid:11fa6c2d-f088-4033-ab59-680e2f49ca5b2022-03-26T10:05:17ZOn Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri NetsConference itemhttp://purl.org/coar/resource_type/c_5794uuid:11fa6c2d-f088-4033-ab59-680e2f49ca5bEnglishOxford University Research Archive - Valet2015Barbot, BKwiatkowska, MDevillers, RMolecular programming is an emerging field concerned with building synthetic biomolecular computing devices at 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. |
| spellingShingle | Barbot, B Kwiatkowska, M On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets |
| title | On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets |
| title_full | On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets |
| title_fullStr | On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets |
| title_full_unstemmed | On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets |
| title_short | On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets |
| title_sort | on quantitative modelling and verification of dna walker circuits using stochastic petri nets |
| work_keys_str_mv | AT barbotb onquantitativemodellingandverificationofdnawalkercircuitsusingstochasticpetrinets AT kwiatkowskam onquantitativemodellingandverificationofdnawalkercircuitsusingstochasticpetrinets |