TY - GEN

T1 - Self-correcting self-assembly

T2 - 11th International Workshop on DNA Computing, DNA11

AU - Baryshnikov, Yuliy

AU - Coffman, Ed

AU - Seeman, Nadrian

AU - Yimwadsana, Teddy

PY - 2006/7/13

Y1 - 2006/7/13

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33745753535&partnerID=8YFLogxK

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U2 - 10.1007/11753681_1

DO - 10.1007/11753681_1

M3 - Conference contribution

AN - SCOPUS:33745753535

SN - 3540341617

SN - 9783540341611

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 1

EP - 11

BT - DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers

Y2 - 6 June 2005 through 9 June 2005

ER -