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Design of Autonomous DNA Cellular Automata

Peng YinContact Information, Sudheer SahuContact Information, Andrew J. TurberfieldContact Information and John H. ReifContact Information

(1)  Department of Computer Science, Duke University, Box 90129, Durham, NC 27708-0129, USA
(2)  University of Oxford, Department of Physics, Clarendon Laboratory, Parks Road, Oxford OX 1 3PU, UK
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.

Contact Information Peng Yin
Email: py@cs.duke.edu

Contact Information Sudheer Sahu
Email: sudheer@cs.duke.edu

Contact Information Andrew J. Turberfield
Email: a.turberfield@physics.ox.ac.uk

Contact Information John H. Reif
Email: reif@cs.duke.edu
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Referenced by
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  1. Bath, Jonathan (2007) DNA nanomachines. Nature Nanotechnology 2(5)
    [CrossRef]
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