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Design of Autonomous DNA Cellular Automata

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DNA Computing (DNA 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3892))

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Abstract

Recent experimental progress in DNA lattice construction, DNA robotics, and DNA computing provides the basis for designing DNA cellular computing devices, i.e. autonomous nano-mechanical DNA computing devices embedded in DNA lattices. Once assembled, DNA cellular computing devices can serve as reusable, compact computing devices that perform (universal) computation, and programmable robotics devices that demonstrate complex motion. As a prototype of such devices, we recently reported the design of an Autonomous DNA Turing Machine, which is capable of universal sequential computation, and universal translational motion, i.e. the motion of the head of a single tape universal mechanical Turing machine. In this paper, we describe the design of an Autonomous DNA Cellular Automaton (ADCA), which can perform parallel universal computation by mimicking a one-dimensional (1D) universal cellular automaton. In the computation process, this device, embedded in a 1D DNA lattice, also demonstrates well coordinated parallel motion. The key technical innovation here is a molecular mechanism that synchronizes pipelined “molecular reaction waves” along a 1D track, and in doing so, realizes parallel computation. We first describe the design of ADCA on an abstract level, and then present detailed DNA sequence level implementation using commercially available protein enzymes. We also discuss how to extend the 1D design to 2D.

The work is supported by NSF ITR Grants EIA-0086015 and CCR-0326157, NSF QuBIC Grants EIA-0218376 and EIA-0218359, and DARPA/AFSOR Contract F30602-01-2-0561.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Duke University, Box 90129, Durham, NC, 27708-0129, USA

    Peng Yin, Sudheer Sahu & John H. Reif

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

    Andrew J. Turberfield

Authors
  1. Peng Yin
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  2. Sudheer Sahu
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  3. Andrew J. Turberfield
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  4. John H. Reif
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Université Pierre et Marie Curie, INSERM U511,, 91 Boulevard de L’Hôpital, 75013, Paris, France

    Alessandra Carbone

  2. California Institute of Technology, Applied and Computational Mathematics, Bioengineering,, MC 114-96, 91125, Pasadena, CA, USA

    Niles A. Pierce

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© 2006 Springer-Verlag Berlin Heidelberg

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Yin, P., Sahu, S., Turberfield, A.J., Reif, J.H. (2006). Design of Autonomous DNA Cellular Automata. In: Carbone, A., Pierce, N.A. (eds) DNA Computing. DNA 2005. Lecture Notes in Computer Science, vol 3892. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11753681_32

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  • DOI: https://doi.org/10.1007/11753681_32

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-34161-1

  • Online ISBN: 978-3-540-34165-9

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