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Proofreading tile sets: Error correction for algorithmic self-assembly

Winfree, Erik and Bekbolatov, Renat (2004) Proofreading tile sets: Error correction for algorithmic self-assembly. In: DNA Computing. Lecture Notes in Computer Science. No.2943. Springer , Berlin, pp. 126-144. ISBN 3-540-20930-1. https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203016

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Abstract

For robust molecular implementation of tile-based algorithmic self-assembly, methods for reducing errors must be developed. Previous studies suggested that by control of physical conditions, such as temperature and the concentration of tiles, errors (ε) can be reduced to an arbitrarily low rate - but at the cost of reduced speed (r) for the self-assembly process. For tile sets directly implementing blocked cellular automata, it was shown that r ≈ βε^2 was optimal. Here, we show that an improved construction, which we refer to as proofreading tile sets, can in principle exploit the cooperativity of tile assembly reactions to dramatically improve the scaling behavior to r ≈ βε and better. This suggests that existing DNA-based molecular tile approaches may be improved to produce macroscopic algorithmic crystals with few errors. Generalizations and limitations of the proofreading tile set construction are discussed.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1007/978-3-540-24628-2_13DOIArticle
https://rdcu.be/b555PPublisherFree ReadCube access
ORCID:
AuthorORCID
Winfree, Erik0000-0002-5899-7523
Additional Information:© 2004 Springer-Verlag Berlin Heidelberg. This work benefited from discussions with Leonard Adleman, Matthew Cook, Ashish Gael, Paul Rothemund, Rebecca Schulman, Georg Seelig, David Soloveichik, and Chris Umans. Thanks to John Reif for encouraging me to write this up and for sharing his unpublished manuscript. EW and RB were supported by NSF CAREER Grant No. 0093486, DARPA BioComputation Contract F30602-01-2-0561, NASA NRA2-37143, and GenTel. Simulation code and tile sets used in this paper, as well as MATLAB scripts for evaluating the kinetic trapping models, may be obtained from http://www .dna.caltech.edu/SupplementaryMaterial.
Funders:
Funding AgencyGrant Number
NSFCNS-0093486
Defense Advanced Research Projects Agency (DARPA)F30602-01-2-0561
NASANRA2-37143
GenTelUNSPECIFIED
Series Name:Lecture Notes in Computer Science
Issue or Number:2943
DOI:10.1007/978-3-540-24628-2_13
Record Number:CaltechAUTHORS:20110309-104203016
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203016
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:22768
Collection:CaltechAUTHORS
Deposited By: Lucinda Acosta
Deposited On:25 Oct 2011 22:44
Last Modified:09 Nov 2021 16:07

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