Automated design and verification of localized DNA computation circuits
Simple computations can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show h...
| Main Authors: | , , |
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| Format: | Conference item |
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Springer International Publishing Switzerland
2015
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| _version_ | 1797086404185948160 |
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| author | Boemo, M Turberfield, A Cardelli, L |
| author2 | Phillips, A |
| author_facet | Phillips, A Boemo, M Turberfield, A Cardelli, L |
| author_sort | Boemo, M |
| collection | OXFORD |
| description | Simple computations can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it. |
| first_indexed | 2024-03-07T02:21:34Z |
| format | Conference item |
| id | oxford-uuid:a4196188-c941-45aa-afe7-01692bba7813 |
| institution | University of Oxford |
| last_indexed | 2024-03-07T02:21:34Z |
| publishDate | 2015 |
| publisher | Springer International Publishing Switzerland |
| record_format | dspace |
| spelling | oxford-uuid:a4196188-c941-45aa-afe7-01692bba78132022-03-27T02:31:33ZAutomated design and verification of localized DNA computation circuitsConference itemhttp://purl.org/coar/resource_type/c_5794uuid:a4196188-c941-45aa-afe7-01692bba7813Symplectic Elements at OxfordSpringer International Publishing Switzerland2015Boemo, MTurberfield, ACardelli, LPhillips, AYin, PSimple computations can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it. |
| spellingShingle | Boemo, M Turberfield, A Cardelli, L Automated design and verification of localized DNA computation circuits |
| title | Automated design and verification of localized DNA computation circuits |
| title_full | Automated design and verification of localized DNA computation circuits |
| title_fullStr | Automated design and verification of localized DNA computation circuits |
| title_full_unstemmed | Automated design and verification of localized DNA computation circuits |
| title_short | Automated design and verification of localized DNA computation circuits |
| title_sort | automated design and verification of localized dna computation circuits |
| work_keys_str_mv | AT boemom automateddesignandverificationoflocalizeddnacomputationcircuits AT turberfielda automateddesignandverificationoflocalizeddnacomputationcircuits AT cardellil automateddesignandverificationoflocalizeddnacomputationcircuits |