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String tile models for DNA computing by self-assembly

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DNA Computing (DNA 2000)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2054))

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Abstract

This paper investigates computation by linear assemblies of complex DNA tiles, which we call string tiles. By keeping track of the strands as they weave back and forth through the assembly, we show that surprisingly sophisticated calculations can be performed using linear self-assembly. Examples range from generating an addition table to providing O(1) solutions to CNF-SAT and DHPP. We classify the families of languages that can be generated by various types of DNA molecules, and establish a correspondence to the existing classes ET0L ml and ET0L fin. Thus, linear self-assembly of string tiles can generate the output lan- guages of finite-visit Turing Machines.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Colorado at Boulder, Boulder, CO, 80309, USA

    Erik Winfree

  2. Depts. of Computer Science and CNS, California Institute of Technology, Pasadena, CA, 91125, USA

    Tony Eng

  3. Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

    Grzegorz Rozenberg

  4. Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands

    Grzegorz Rozenberg

Authors
  1. Erik Winfree
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  2. Tony Eng
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  3. Grzegorz Rozenberg
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of British Columbia, 201-2366 Main Mall, Vancouver, B.C., Canada, V6T 1Z4

    Anne Condon

  2. Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands

    Grzegorz Rozenberg

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© 2001 Springer-Verlag Berlin Heidelberg

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Winfree, E., Eng, T., Rozenberg, G. (2001). String tile models for DNA computing by self-assembly. In: Condon, A., Rozenberg, G. (eds) DNA Computing. DNA 2000. Lecture Notes in Computer Science, vol 2054. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44992-2_6

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  • DOI: https://doi.org/10.1007/3-540-44992-2_6

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42076-7

  • Online ISBN: 978-3-540-44992-8

  • eBook Packages: Springer Book Archive

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