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Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching

Authors: Tonglin Chen, Arnav Solanki, and Marc Riedel

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

Abstract

Prior research has introduced the Single-Instruction-Multiple-Data paradigm for DNA computing (SIMD DNA). It offers the potential for storing information and performing in-memory computations on DNA, with massive parallelism. This paper introduces three new SIMD DNA operations: sorting, shifting, and searching. Each is a fundamental operation in computer science. Our implementations demonstrate the effectiveness of parallel pairwise operations with this new paradigm.

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Tonglin Chen, Arnav Solanki, and Marc Riedel. Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 11:1-11:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{chen_et_al:LIPIcs.DNA.27.11,
  author =	{Chen, Tonglin and Solanki, Arnav and Riedel, Marc},
  title =	{{Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{11:1--11:21},
  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.27.11},
  URN =		{urn:nbn:de:0030-drops-146780},
  doi =		{10.4230/LIPIcs.DNA.27.11},
  annote =	{Keywords: Molecular Computing, DNA Computing, DNA Storage, Parallel Computing, Strand Displacement}
}

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Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching

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