Self-correcting self-assembly

Growth models and the hammersley process

Yuliy Baryshnikov, Ed Coffman, Nadrian Seeman, Teddy Yimwadsana

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

Abstract

This paper extends the stochastic analysis of self assembly in DNA-based computation. The new analysis models an error-correcting technique called pulsing which is analogous to checkpointing in computer operation. The model is couched in terms of the well-known tiling models of DNA-based computation and focuses on the calculation of computation times, in particular the times to self assemble rectangular structures. Explicit asymptotic results are found for small error rates q, and exploit the connection between these times and the classical Hammersley process. Specifically, it is found that the expected number of pulsing stages needed to complete the self assembly of an N × N square lattice is asymptotically 2N √q as N → ∞ within a suitable scaling. Simulation studies are presented which yield performance under more general assumptions.

Original languageEnglish (US)
Title of host publicationDNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers
Pages1-11
Number of pages11
Volume3892 LNCS
DOIs
StatePublished - 2006
Event11th International Workshop on DNA Computing, DNA11 - London, ON, Canada
Duration: Jun 6 2005Jun 9 2005

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3892 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other11th International Workshop on DNA Computing, DNA11
CountryCanada
CityLondon, ON
Period6/6/056/9/05

Fingerprint

Self-assembly
Growth Model
Molecular Computers
Self assembly
Growth
Checkpointing
DNA
Stochastic Analysis
Computer operating procedures
Model Analysis
Tiling
Square Lattice
Error Rate
Simulation Study
Scaling
Model

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Baryshnikov, Y., Coffman, E., Seeman, N., & Yimwadsana, T. (2006). Self-correcting self-assembly: Growth models and the hammersley process. In DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers (Vol. 3892 LNCS, pp. 1-11). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3892 LNCS). https://doi.org/10.1007/11753681_1

Self-correcting self-assembly : Growth models and the hammersley process. / Baryshnikov, Yuliy; Coffman, Ed; Seeman, Nadrian; Yimwadsana, Teddy.

DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers. Vol. 3892 LNCS 2006. p. 1-11 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3892 LNCS).

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

Baryshnikov, Y, Coffman, E, Seeman, N & Yimwadsana, T 2006, Self-correcting self-assembly: Growth models and the hammersley process. in DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers. vol. 3892 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3892 LNCS, pp. 1-11, 11th International Workshop on DNA Computing, DNA11, London, ON, Canada, 6/6/05. https://doi.org/10.1007/11753681_1
Baryshnikov Y, Coffman E, Seeman N, Yimwadsana T. Self-correcting self-assembly: Growth models and the hammersley process. In DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers. Vol. 3892 LNCS. 2006. p. 1-11. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/11753681_1
Baryshnikov, Yuliy ; Coffman, Ed ; Seeman, Nadrian ; Yimwadsana, Teddy. / Self-correcting self-assembly : Growth models and the hammersley process. DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers. Vol. 3892 LNCS 2006. pp. 1-11 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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