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International Workshop on DNA-Based Computers

DNA 2010: DNA Computing and Molecular Programming pp 123–140Cite as

Efficient Turing-Universal Computation with DNA Polymers

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6518))

Abstract

Bennett’s proposed chemical Turing machine is one of the most important thought experiments in the study of the thermodynamics of computation. Yet the sophistication of molecular engineering required to physically construct Bennett’s hypothetical polymer substrate and enzymes has deterred experimental implementations. Here we propose a chemical implementation of stack machines — a Turing-universal model of computation similar to Turing machines — using DNA strand displacement cascades as the underlying chemical primitive. More specifically, the mechanism described herein is the addition and removal of monomers from the end of a DNA polymer, controlled by strand displacement logic. We capture the motivating feature of Bennett’s scheme: that physical reversibility corresponds to logically reversible computation, and arbitrarily little energy per computation step is required. Further, as a method of embedding logic control into chemical and biological systems, polymer-based chemical computation is significantly more efficient than geometry-free chemical reaction networks.

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Author information

Authors and Affiliations

  1. Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA

    Lulu Qian & Erik Winfree

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

    Erik Winfree

  3. Computation & Neural Systems, California Institute of Technology, Pasadena, CA, 91125, USA

    Erik Winfree

  4. Computer Science & Engineering, University of Washington, Seattle, WA, 98195, USA

    David Soloveichik

Authors
  1. Lulu Qian
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  2. David Soloveichik
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  3. Erik Winfree
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Editor information

Editors and Affiliations

  1. Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, 223-8522, Yokohama, Japan

    Yasubumi Sakakibara

  2. Department of Chemical Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China

    Yongli Mi

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© 2011 Springer-Verlag Berlin Heidelberg

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Qian, L., Soloveichik, D., Winfree, E. (2011). Efficient Turing-Universal Computation with DNA Polymers. In: Sakakibara, Y., Mi, Y. (eds) DNA Computing and Molecular Programming. DNA 2010. Lecture Notes in Computer Science, vol 6518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18305-8_12

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  • DOI: https://doi.org/10.1007/978-3-642-18305-8_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-18304-1

  • Online ISBN: 978-3-642-18305-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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