Molecular Machines from Topological Linkages

Authors Keenan Breik, Austin Luchsinger, David Soloveichik

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Keenan Breik
  • The University of Texas at Austin, TX, USA
Austin Luchsinger
  • The University of Texas at Austin, TX, USA
David Soloveichik
  • The University of Texas at Austin, TX, USA


We thank Tosan Omabegho for introducing us to chemical linkages and for extensive discussions.

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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)


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.

Subject Classification

ACM Subject Classification
  • Theory of computation → Models of computation
  • Theory of computation → Computational geometry
  • chemical computation
  • mechanical computation
  • bioengineering
  • models of biochemistry
  • molecular machines
  • mechanical linkages
  • generic rigidity


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