Conference item

Automated design and verification of localized DNA computation circuits

Abstract:: 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.

Publication status:: Published

Peer review status:: Peer reviewed

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APA Style

Boemo, M., Turberfield, A., & Cardelli, L. (2015). Automated design and verification of localized DNA computation circuits. In A. Phillips & P. Yin (Eds.), DNA 2015: DNA Computing and Molecular Programming (Vol. 9211, pp. 168–180). Springer International Publishing Switzerland.

MLA Style

Boemo, M., et al. “Automated Design and Verification of Localized DNA Computation Circuits.” DNA 2015: DNA Computing and Molecular Programming, edited by A Phillips and P Yin, vol. 9211, Springer International Publishing Switzerland, 2015, pp. 168–80.

Chicago Style

Boemo, M, A Turberfield, and L Cardelli. 2015. “Automated Design and Verification of Localized DNA Computation Circuits.” In DNA 2015: DNA Computing and Molecular Programming, edited by A Phillips and P Yin, 9211:168–80. Springer International Publishing Switzerland.
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Publisher copy:: 10.1007/978-3-319-21999-8_11

Authors

+ Boemo, M More by this author

Institution:: University of Oxford
Division:: MPLS
Department:: Physics
Sub department:: Condensed Matter Physics
Role:: Author

+ Turberfield, A More by this author

Role:: Author

+ Cardelli, L More by this author

Role:: Author

Contributors

Role:: Editor

Role:: Editor

Publisher:: Springer International Publishing Switzerland
Host title:: DNA 2015: DNA Computing and Molecular Programming
Journal:: DNA Computing and Molecular Programming More from this journal
Volume:: 9211
Pages:: 168-180
Publication date:: 2015-01-01
DOI:: 10.1007/978-3-319-21999-8_11
EISSN:: 1611-3349
ISSN:: 0302-9743
ISBN:: 9783319219981

Keywords:: SBTMR
Pubs id:: pubs:578321
UUID:: uuid:a4196188-c941-45aa-afe7-01692bba7813
Local pid:: pubs:578321
Source identifiers:: 578321
Deposit date:: 2016-05-17

Terms of use

Copyright holder:: Springer International Publishing Switzerland
Copyright date:: 2015

Licence:: Terms and Conditions of Use for Oxford University Research Archive

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