Parallel pairwise operations on data stored in dna: Sorting, shifting, and searching

Tonglin Chen, Arnav Solanki, Marc Riedel

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

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.

Original languageEnglish (US)
Title of host publication27th International Conference on DNA Computing and Molecular Programming, DNA 2021
EditorsMatthew R. Lakin, Petr Sulc
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)9783959772051
DOIs
StatePublished - Sep 1 2021
Event27th International Conference on DNA Computing and Molecular Programming, DNA 2021 - Virtual, Oxford, United Kingdom
Duration: Sep 13 2021Sep 16 2021

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume205
ISSN (Print)1868-8969

Conference

Conference27th International Conference on DNA Computing and Molecular Programming, DNA 2021
Country/TerritoryUnited Kingdom
CityVirtual, Oxford
Period9/13/219/16/21

Bibliographical note

Funding Information:
Funding The authors are funded by DARPA grant #W911NF-18-2-0032.

Publisher Copyright:
© 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

Keywords

  • DNA Computing
  • DNA Storage
  • Molecular Computing
  • Parallel Computing
  • Strand Displacement

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