LIPIcs.SAND.2022.14.pdf
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Simulating 3-Symbol Turing Machines with SIMD||DNA
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David Doty 
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1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)
Series: Leibniz International Proceedings in Informatics (LIPIcs)
Conference: Symposium on Algorithmic Foundations of Dynamic Networks (SAND) - License:
Creative Commons Attribution 4.0 International license
- Publication Date: 2022-04-29
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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)
https://doi.org/10.4230/LIPIcs.SAND.2022.14
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.
Subject Classification
ACM Subject Classification
- Theory of computation → Models of computation
Keywords
- DNA storage
- strand displacement
- parallel computation
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Supplementary Materials
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Software (Simulator Source Code)
https://github.com/UC-Davis-molecular-computing/simd-dna
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References
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