Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly

  • Erik Winfree
  • Renat Bekbolatov
Conference paper

DOI: 10.1007/978-3-540-24628-2_13

Volume 2943 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Winfree E., Bekbolatov R. (2004) Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly. In: Chen J., Reif J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg

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 rβε2 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 rβε 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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Erik Winfree
    • 1
  • Renat Bekbolatov
    • 1
  1. 1.Computer Science and Computation & Neural SystemsCalifornia Institute of TechnologyPasadenaUSA