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

Tonglin Chen; Arnav Solanki; Marc Riedel

doi:10.4230/LIPIcs.DNA.27.11

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

Tonglin Chen
, Arnav Solanki
, Marc Riedel

Electrical and Computer Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

5 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 language	English (US)
Title of host publication	27th International Conference on DNA Computing and Molecular Programming, DNA 2021
Editors	Matthew R. Lakin, Petr Sulc
Publisher	Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)	9783959772051
DOIs	https://doi.org/10.4230/LIPIcs.DNA.27.11
State	Published - Sep 1 2021
Event	27th International Conference on DNA Computing and Molecular Programming, DNA 2021 - Virtual, Oxford, United Kingdom Duration: Sep 13 2021 → Sep 16 2021

Publication series

Name	Leibniz International Proceedings in Informatics, LIPIcs
Volume	205
ISSN (Print)	1868-8969

Conference

Conference	27th International Conference on DNA Computing and Molecular Programming, DNA 2021
Country/Territory	United Kingdom
City	Virtual, Oxford
Period	9/13/21 → 9/16/21

Bibliographical note

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

Publisher link

10.4230/LIPIcs.DNA.27.11

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Cite this

Chen, T., Solanki, A., & Riedel, M. (2021). Parallel pairwise operations on data stored in dna: Sorting, shifting, and searching. In M. R. Lakin, & P. Sulc (Eds.), 27th International Conference on DNA Computing and Molecular Programming, DNA 2021 Article 11 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 205). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.DNA.27.11

Parallel pairwise operations on data stored in dna: Sorting, shifting, and searching. / Chen, Tonglin; Solanki, Arnav; Riedel, Marc.
27th International Conference on DNA Computing and Molecular Programming, DNA 2021. ed. / Matthew R. Lakin; Petr Sulc. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2021. 11 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 205).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Chen, T, Solanki, A & Riedel, M 2021, Parallel pairwise operations on data stored in dna: Sorting, shifting, and searching. in MR Lakin & P Sulc (eds), 27th International Conference on DNA Computing and Molecular Programming, DNA 2021., 11, Leibniz International Proceedings in Informatics, LIPIcs, vol. 205, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 27th International Conference on DNA Computing and Molecular Programming, DNA 2021, Virtual, Oxford, United Kingdom, 9/13/21. https://doi.org/10.4230/LIPIcs.DNA.27.11

Chen T, Solanki A, Riedel M. Parallel pairwise operations on data stored in dna: Sorting, shifting, and searching. In Lakin MR, Sulc P, editors, 27th International Conference on DNA Computing and Molecular Programming, DNA 2021. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. 2021. 11. (Leibniz International Proceedings in Informatics, LIPIcs). doi: 10.4230/LIPIcs.DNA.27.11

Chen, Tonglin ; Solanki, Arnav ; Riedel, Marc. / Parallel pairwise operations on data stored in dna : Sorting, shifting, and searching. 27th International Conference on DNA Computing and Molecular Programming, DNA 2021. editor / Matthew R. Lakin ; Petr Sulc. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2021. (Leibniz International Proceedings in Informatics, LIPIcs).

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

Abstract

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Bibliographical note

Keywords

Publisher link

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