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Molecular Machines from Topological Linkages

Authors: Keenan Breik, Austin Luchsinger, and David Soloveichik

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

Abstract

Life is built upon amazingly sophisticated molecular machines whose behavior combines mechanical and chemical action. Engineering of similarly complex nanoscale devices from first principles remains an as yet unrealized goal of bioengineering. In this paper we formalize a simple model of mechanical motion (mechanical linkages) combined with chemical bonding. The model has a natural implementation using DNA with double-stranded rigid links, and single-stranded flexible joints and binding sites. Surprisingly, we show that much of the complex behavior is preserved in an idealized topological model which considers solely the graph connectivity of the linkages. We show a number of artifacts including Boolean logic, catalysts, a fueled motor, and chemo-mechanical coupling, all of which can be understood and reasoned about in the topological model. The variety of achieved behaviors supports the use of topological chemical linkages in understanding and engineering complex molecular behaviors.

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Keenan Breik, Austin Luchsinger, and David Soloveichik. Molecular Machines from Topological Linkages. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 7:1-7:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{breik_et_al:LIPIcs.DNA.27.7,
  author =	{Breik, Keenan and Luchsinger, Austin and Soloveichik, David},
  title =	{{Molecular Machines from Topological Linkages}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{7:1--7:20},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27.7},
  URN =		{urn:nbn:de:0030-drops-146749},
  doi =		{10.4230/LIPIcs.DNA.27.7},
  annote =	{Keywords: chemical computation, mechanical computation, bioengineering, models of biochemistry, molecular machines, mechanical linkages, generic rigidity}
}

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Molecular Machines from Topological Linkages

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