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Documents authored by Lakin, Matthew R.

Artifact
Software
DOI: 10.4230/artifacts.27484
LocalizedEnumeratorOptimization

Authors: Matthew R. Lakin

Abstract
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@misc{dagpub-supp--paper-25457-urlgithub.com-matthewlakin-LocalizedEnumeratorOptimization,
   title = {{LocalizedEnumeratorOptimization}}, 
   author = {Lakin, Matthew R.},
   note = {Software, swhId: \href{https://archive.softwareheritage.org/swh:1:dir:095f551c8228cf74f1548237675d8391b3963452;origin=https://github.com/matthewlakin/LocalizedEnumeratorOptimization;visit=swh:1:snp:0dd546eb08d02d7763e89ab566b95e59b3f08a51;anchor=swh:1:rev:a71a192a507f94738e58a41f6ae52afbe541d61a}{\texttt{swh:1:dir:095f551c8228cf74f1548237675d8391b3963452}} (visited on 2026-07-27)},
   url = {https://github.com/matthewlakin/LocalizedEnumeratorOptimization},
}
Document
DOI: 10.4230/LIPIcs.DNA.32.5
Geometric Constraint Optimization for Localized Strand Displacement Reactions

Authors: Matthew R. Lakin

Published in: LIPIcs, Volume 387, 32nd International Conference on DNA Computing and Molecular Programming (DNA 32) (2026)

Abstract
Localized molecular circuits offer practical advantages over those implemented using components freely diffusing in bulk solution, such as computation speed and component reuse. A common framework for implementing such circuits uses DNA strand displacement reactions with components localized via tethering to a DNA origami tile. While a number of papers have demonstrated the capability of such circuits, design tools for enumerating localized reactions and analyzing their behavior are relatively scarce. The key difficulty in modeling such circuits is that the geometric constraints imposed by the tethering of specific components at specific points on the tile surface are critical in determining whether or not a particular reaction may occur. In previous work, we deployed simple techniques based on random sampling of the structure space in an attempt to find geometric structures for candidate reaction products that satisfy all of the geometric constraints. In this paper, we show that this approach can be enhanced by using an optimization algorithm that takes initial guessed structures that fail to satisfy certain constraints and attempts to refine them into structures that do satisfy all of the constraints. We illustrate this approach on simple example reactions as well as a strand displacement-based signal transmission example from the literature. This work thus advances the state of the art in modeling tools for localized molecular circuits.
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Matthew R. Lakin. Geometric Constraint Optimization for Localized Strand Displacement Reactions. In 32nd International Conference on DNA Computing and Molecular Programming (DNA 32). Leibniz International Proceedings in Informatics (LIPIcs), Volume 387, pp. 5:1-5:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{lakin:LIPIcs.DNA.32.5,
  author =	{Lakin, Matthew R.},
  title =	{{Geometric Constraint Optimization for Localized Strand Displacement Reactions}},
  booktitle =	{32nd International Conference on DNA Computing and Molecular Programming (DNA 32)},
  pages =	{5:1--5:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-444-4},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{387},
  editor =	{Scalise, Dominic and Schweller, Robert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.32.5},
  URN =		{urn:nbn:de:0030-drops-267756},
  doi =		{10.4230/LIPIcs.DNA.32.5},
  annote =	{Keywords: Localized circuits, reaction enumeration, DNA strand displacement, constraint solving, geometry, molecular computing}
}
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.
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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
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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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