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
Publication statusPublished - 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

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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