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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.

Cite as

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-dev.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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