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DOI: 10.4230/LIPIcs.SAND.2022.14

Simulating 3-Symbol Turing Machines with SIMD||DNA

Authors: David Doty and Aaron Ong

Published in: LIPIcs, Volume 221, 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)

Abstract

SIMD||DNA [Wang et al., 2019] is a model of DNA strand displacement allowing parallel in-memory computation on DNA storage. We show how to simulate an arbitrary 3-symbol space-bounded Turing machine with a SIMD||DNA program, giving a more direct and efficient route to general-purpose information manipulation on DNA storage than the Rule 110 simulation of Wang, Chalk, and Soloveichik [Wang et al., 2019]. We also develop software (https://github.com/UC-Davis-molecular-computing/simd-dna) that can simulate SIMD||DNA programs and produce SVG figures.

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David Doty and Aaron Ong. Simulating 3-Symbol Turing Machines with SIMD||DNA. In 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 221, pp. 14:1-14:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{doty_et_al:LIPIcs.SAND.2022.14,
  author =	{Doty, David and Ong, Aaron},
  title =	{{Simulating 3-Symbol Turing Machines with SIMD||DNA}},
  booktitle =	{1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)},
  pages =	{14:1--14:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-224-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{221},
  editor =	{Aspnes, James and Michail, Othon},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2022.14},
  URN =		{urn:nbn:de:0030-drops-159568},
  doi =		{10.4230/LIPIcs.SAND.2022.14},
  annote =	{Keywords: DNA storage, strand displacement, parallel computation}
}

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Simulating 3-Symbol Turing Machines with SIMD||DNA

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