research-article

DNA-based molecular architecture with spatially localized components

Authors:

Richard A. Muscat,

Georg SeeligAuthors Info & Claims

ISCA '13: Proceedings of the 40th Annual International Symposium on Computer Architecture

Pages 177 - 188

https://doi.org/10.1145/2485922.2485938

Published: 23 June 2013 Publication History

Abstract

Performing computation inside living cells offers life-changing applications, from improved medical diagnostics to better cancer therapy to intelligent drugs. Due to its bio-compatibility and ease of engineering, one promising approach for performing in-vivo computation is DNA strand displacement. This paper introduces computer architects to DNA strand displacement "circuits", discusses associated architectural challenges, and proposes a new organization that provides practical composability. In particular, prior approaches rely mostly on stochastic interaction of freely diffusing components. This paper proposes practical spatial isolation of components, leading to more easily designed DNA-based circuits. DNA nanotechnology is currently at a turning point, with many proposed applications being realized [20, 9]. We believe that it is time for the computer architecture community to take notice and contribute.

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Cited By

Lakin MSpaccasassi CPhillips A(2023)Computational Design of Nucleic Acid Circuits: Past, Present, and FutureVisions of DNA Nanotechnology at 40 for the Next 4010.1007/978-981-19-9891-1_18(311-346)Online publication date: 5-Jul-2023
https://doi.org/10.1007/978-981-19-9891-1_18
Kumar SWeisburd JLakin M(2021)Structure sampling for computational estimation of localized DNA interaction ratesScientific Reports10.1038/s41598-021-92145-811:1Online publication date: 16-Jun-2021
https://doi.org/10.1038/s41598-021-92145-8
Jamalzadeh EJahanian A(2020)High Accuracy Multi-input DNA Logic Gate Using The Spatially Localized DNA Structures2020 25th International Computer Conference, Computer Society of Iran (CSICC)10.1109/CSICC49403.2020.9050089(1-8)Online publication date: Jan-2020
https://doi.org/10.1109/CSICC49403.2020.9050089
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Index Terms

DNA-based molecular architecture with spatially localized components
1. Hardware

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cover image ACM Other conferences

ISCA '13: Proceedings of the 40th Annual International Symposium on Computer Architecture

June 2013

686 pages

ISBN:9781450320795

DOI:10.1145/2485922

General Chair:
Avi Mendelson
Technion

ACM SIGARCH Computer Architecture News Volume 41, Issue 3
ICSA '13
June 2013
666 pages
ISSN:0163-5964
DOI:10.1145/2508148
Issue’s Table of Contents

Copyright © 2013 ACM.

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Published: 23 June 2013

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ISCA'13: The 40th Annual International Symposium on Computer Architecture

June 23 - 27, 2013

Tel-Aviv, Israel

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ISCA '13 Paper Acceptance Rate 56 of 288 submissions, 19%;

Overall Acceptance Rate 543 of 3,203 submissions, 17%

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Cited By

Lakin MSpaccasassi CPhillips A(2023)Computational Design of Nucleic Acid Circuits: Past, Present, and FutureVisions of DNA Nanotechnology at 40 for the Next 4010.1007/978-981-19-9891-1_18(311-346)Online publication date: 5-Jul-2023
https://doi.org/10.1007/978-981-19-9891-1_18
Kumar SWeisburd JLakin M(2021)Structure sampling for computational estimation of localized DNA interaction ratesScientific Reports10.1038/s41598-021-92145-811:1Online publication date: 16-Jun-2021
https://doi.org/10.1038/s41598-021-92145-8
Jamalzadeh EJahanian A(2020)High Accuracy Multi-input DNA Logic Gate Using The Spatially Localized DNA Structures2020 25th International Computer Conference, Computer Society of Iran (CSICC)10.1109/CSICC49403.2020.9050089(1-8)Online publication date: Jan-2020
https://doi.org/10.1109/CSICC49403.2020.9050089
Engelen WWijnands SMerkx M(2018)Accelerating DNA-Based Computing on a Supramolecular PolymerJournal of the American Chemical Society10.1021/jacs.8b06146140:30(9758-9767)Online publication date: 10-Jul-2018
https://doi.org/10.1021/jacs.8b06146
Bui HShah SMokhtar RSong TGarg SReif J(2018)Localized DNA Hybridization Chain Reactions on DNA OrigamiACS Nano10.1021/acsnano.7b0669912:2(1146-1155)Online publication date: 25-Jan-2018
https://doi.org/10.1021/acsnano.7b06699
Lakin MPhillips A(2018)Automated analysis of tethered DNA nanostructures using constraint solvingNatural Computing: an international journal10.1007/s11047-018-9693-y17:4(709-722)Online publication date: 1-Dec-2018
https://dl.acm.org/doi/10.1007/s11047-018-9693-y
Bui HGarg SMiao VSong TMokhtar RReif J(2017)Design and analysis of linear cascade DNA hybridization chain reactions using DNA hairpinsNew Journal of Physics10.1088/1367-2630/aa53d019:1(015006)Online publication date: 12-Jan-2017
https://doi.org/10.1088/1367-2630/aa53d0
Lakin MPhillips A(2017)Automated, Constraint-Based Analysis of Tethered DNA NanostructuresDNA Computing and Molecular Programming10.1007/978-3-319-66799-7_1(1-16)Online publication date: 24-Aug-2017
https://doi.org/10.1007/978-3-319-66799-7_1
Bui HMiao VGarg SMokhtar RSong TReif J(2017)Design and Analysis of Localized DNA Hybridization Chain ReactionsSmall10.1002/smll.20160298313:12Online publication date: 16-Jan-2017
https://doi.org/10.1002/smll.201602983
Bornholt JLopez RCarmean DCeze LSeelig GStrauss K(2016)A DNA-Based Archival Storage SystemACM SIGARCH Computer Architecture News10.1145/2980024.287239744:2(637-649)Online publication date: 25-Mar-2016
https://dl.acm.org/doi/10.1145/2980024.2872397
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