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Documents authored by Lakin, Matthew R.

Document
DOI: 10.4230/LIPIcs.DNA.30.1
Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks

Authors: Matthew R. Lakin and Sarika Kumar

Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)

Abstract
Localized molecular devices are a powerful tool for engineering complex information-processing circuits and molecular robots. Their practical advantages include speed and scalability of interactions between components tethered near to each other on an underlying nanostructure, and the ability to restrict interactions between more distant components. The latter is a critical feature that must be factored into computational tools for the design and simulation of localized molecular devices: unlike in solution-phase systems, the geometries of molecular interactions must be accounted for when attempting to determine the network of possible reactions in a tethered molecular system. This work aims to address that challenge by integrating, for the first time, automated approaches to analysis of molecular geometry with reaction enumeration algorithms for DNA strand displacement reaction networks that can be applied to tethered molecular systems. By adapting a simple approach to solving the biophysical constraints inherent in molecular interactions to be applicable to tethered systems, we produce a localized reaction enumeration system that enhances previous approaches to reaction enumeration in tethered system by not requiring users to explicitly specify the subsets of components that are capable of interacting. This greatly simplifies the user’s task and could also be used as the basis of future systems for automated placement or routing of signal-transmission and logical processing in molecular devices. We apply this system to several published example systems from the literature, including both tethered molecular logic systems and molecular robots.
Cite as

Matthew R. Lakin and Sarika Kumar. Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 1:1-1:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{lakin_et_al:LIPIcs.DNA.30.1,
  author =	{Lakin, Matthew R. and Kumar, Sarika},
  title =	{{Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks}},
  booktitle =	{30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
  pages =	{1:1--1:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-344-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{314},
  editor =	{Seki, Shinnosuke and Stewart, Jaimie Marie},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.1},
  URN =		{urn:nbn:de:0030-drops-209294},
  doi =		{10.4230/LIPIcs.DNA.30.1},
  annote =	{Keywords: Localized circuits, reaction enumeration, DNA strand displacement, geometry, molecular computing}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.DNA.27
LIPIcs, Volume 205, DNA 27, Complete Volume

Authors: Matthew R. Lakin and Petr Šulc

Published in: LIPIcs, Volume 205, 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021)

Abstract
LIPIcs, Volume 205, DNA 27, Complete Volume
Cite as

27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 1-240, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@Proceedings{lakin_et_al:LIPIcs.DNA.27,
  title =	{{LIPIcs, Volume 205, DNA 27, Complete Volume}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{1--240},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-205-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{205},
  editor =	{Lakin, Matthew R. and \v{S}ulc, Petr},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27},
  URN =		{urn:nbn:de:0030-drops-146669},
  doi =		{10.4230/LIPIcs.DNA.27},
  annote =	{Keywords: LIPIcs, Volume 205, DNA 27, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.DNA.27.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Matthew R. Lakin and Petr Šulc

Published in: LIPIcs, Volume 205, 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021)

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

27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{lakin_et_al:LIPIcs.DNA.27.0,
  author =	{Lakin, Matthew R. and \v{S}ulc, Petr},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{0:i--0:xiv},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-205-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{205},
  editor =	{Lakin, Matthew R. and \v{S}ulc, Petr},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27.0},
  URN =		{urn:nbn:de:0030-drops-146679},
  doi =		{10.4230/LIPIcs.DNA.27.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
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