LIPIcs.DNA.27.11.pdf
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Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching
Authors
Arnav Solanki 
,
Marc Riedel
-
Part of:
Volume:
27th International Conference on DNA Computing and Molecular Programming (DNA 27)
Series: Leibniz International Proceedings in Informatics (LIPIcs)
Conference: International Conference on DNA Computing and Molecular Programming - License:
Creative Commons Attribution 4.0 International license
- Publication Date: 2021-09-08
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Author Details
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
Acknowledgements
We thank David Soloveichik, Olgica Milenkovic, Boya Wang, and Cameron Chalk.
Cite AsGet BibTex
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)
https://doi.org/10.4230/LIPIcs.DNA.27.11
https://doi.org/10.4230/LIPIcs.DNA.27.11
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.
Subject Classification
ACM Subject Classification
- Computing methodologies → Parallel computing methodologies
- Applied computing → Computational biology
Keywords
- Molecular Computing
- DNA Computing
- DNA Storage
- Parallel Computing
- Strand Displacement
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