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International Workshop on DNA-Based Computers

DNA 2012: DNA Computing and Molecular Programming pp 58–72Cite as

Synthesizing Minimal Tile Sets for Complex Patterns in the Framework of Patterned DNA Self-Assembly

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7433))

Abstract

Ma and Lombardi (2009) introduce and study the Pattern self-Assembly Tile set Synthesis (PATS) problem. In particular they show that the optimization version of the PATS problem is NP-hard. However, their NP-hardness proof turns out to be incorrect. Our main result is to give a correct NP-hardness proof via a reduction from the 3SAT. By definition, the PATS problem assumes that the assembly of a pattern starts always from an “L”-shaped seed structure, fixing the borders of the pattern. In this context, we study the assembly complexity of various pattern families and we show how to construct families of patterns which require a non-constant number of tiles to be assembled.

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Author information

Authors and Affiliations

  1. Department of Information and Computer Science, School of Science, Aalto University, P.O. Box 15400, FI-00076, Aalto, Finland

    Eugen Czeizler

  2. Department of Communications and Networking, School of Electrical Engineering, Aalto University, P.O. Box 15400, FI-00076, Aalto, Finland

    Alexandru Popa

Authors
  1. Eugen Czeizler
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  2. Alexandru Popa
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of New Mexico, MSC01 1130, 1 University of New Mexico, 87131, Albuquerque, NM, USA

    Darko Stefanovic

  2. Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, OX 1 3PU, Oxford, UK

    Andrew Turberfield

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© 2012 Springer-Verlag Berlin Heidelberg

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Czeizler, E., Popa, A. (2012). Synthesizing Minimal Tile Sets for Complex Patterns in the Framework of Patterned DNA Self-Assembly. In: Stefanovic, D., Turberfield, A. (eds) DNA Computing and Molecular Programming. DNA 2012. Lecture Notes in Computer Science, vol 7433. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32208-2_5

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  • DOI: https://doi.org/10.1007/978-3-642-32208-2_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-32207-5

  • Online ISBN: 978-3-642-32208-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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