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Documents authored by Ouldridge, Thomas E.

Document
Complete Volume
DOI: 10.4230/LIPIcs.DNA.28
LIPIcs, Volume 238, DNA 28, Complete Volume

Authors: Thomas E. Ouldridge and Shelley F. J. Wickham

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
LIPIcs, Volume 238, DNA 28, Complete Volume
Cite as

28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 1-198, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@Proceedings{ouldridge_et_al:LIPIcs.DNA.28,
  title =	{{LIPIcs, Volume 238, DNA 28, Complete Volume}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{1--198},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28},
  URN =		{urn:nbn:de:0030-drops-167843},
  doi =		{10.4230/LIPIcs.DNA.28},
  annote =	{Keywords: LIPIcs, Volume 238, DNA 28, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.DNA.28.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Thomas E. Ouldridge and Shelley F. J. Wickham

Published in: LIPIcs, Volume 238, 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (2022)

Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as

28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{ouldridge_et_al:LIPIcs.DNA.28.0,
  author =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
  pages =	{0:i--0:xvi},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-253-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{238},
  editor =	{Ouldridge, Thomas E. and Wickham, Shelley F. J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.28.0},
  URN =		{urn:nbn:de:0030-drops-167857},
  doi =		{10.4230/LIPIcs.DNA.28.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.DNA.2020.7
Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts

Authors: Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge

Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)

Abstract
DNA strand displacement (DSD) reactions have been used to construct chemical reaction networks in which species act catalytically at the level of the overall stoichiometry of reactions. These effective catalytic reactions are typically realised through one or more of the following: many-stranded gate complexes to coordinate the catalysis, indirect interaction between the catalyst and its substrate, and the recovery of a distinct "catalyst" strand from the one that triggered the reaction. These facts make emulation of the out-of-equilibrium catalytic circuitry of living cells more difficult. Here, we propose a new framework for constructing catalytic DSD networks: Active Circuits of Duplex Catalysts (ACDC). ACDC components are all double-stranded complexes, with reactions occurring through 4-way strand exchange. Catalysts directly bind to their substrates, and the "identity" strand of the catalyst recovered at the end of a reaction is the same molecule as the one that initiated it. We analyse the capability of the framework to implement catalytic circuits analogous to phosphorylation networks in living cells. We also propose two methods of systematically introducing mismatches within DNA strands to avoid leak reactions and introduce driving through net base pair formation. We then combine these results into a compiler to automate the process of designing DNA strands that realise any catalytic network allowed by our framework.
Cite as

Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge. Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 7:1-7:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{lankinen_et_al:LIPIcs.DNA.2020.7,
  author =	{Lankinen, Antti and Mullor Ruiz, Ismael and Ouldridge, Thomas E.},
  title =	{{Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts}},
  booktitle =	{26th International Conference on DNA Computing and Molecular Programming (DNA 26)},
  pages =	{7:1--7:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-163-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{174},
  editor =	{Geary, Cody and Patitz, Matthew J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.7},
  URN =		{urn:nbn:de:0030-drops-129602},
  doi =		{10.4230/LIPIcs.DNA.2020.7},
  annote =	{Keywords: DNA strand displacement, Catalysis, Information-processing networks}
}
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