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Design of autonomous DNA cellular automata

Publication ,  Journal Article
Yin, P; Sahu, S; Turberfield, AJ; Reif, JH
Published in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
July 13, 2006

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 (ID) universal cellular automaton. In the computation process, this device, embedded in a ID 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 ID 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 ID design to 2D. © Springer-Verlag Berlin Heidelberg 2006.

Duke Scholars

Published In

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

DOI

EISSN

1611-3349

ISSN

0302-9743

Publication Date

July 13, 2006

Volume

3892 LNCS

Start / End Page

399 / 416

Related Subject Headings

  • Artificial Intelligence & Image Processing
  • 46 Information and computing sciences
 

Citation

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Yin, P., Sahu, S., Turberfield, A. J., & Reif, J. H. (2006). Design of autonomous DNA cellular automata. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 3892 LNCS, 399–416. https://doi.org/10.1007/11753681_32
Yin, P., S. Sahu, A. J. Turberfield, and J. H. Reif. “Design of autonomous DNA cellular automata.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 3892 LNCS (July 13, 2006): 399–416. https://doi.org/10.1007/11753681_32.
Yin P, Sahu S, Turberfield AJ, Reif JH. Design of autonomous DNA cellular automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2006 Jul 13;3892 LNCS:399–416.
Yin, P., et al. “Design of autonomous DNA cellular automata.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3892 LNCS, July 2006, pp. 399–416. Scopus, doi:10.1007/11753681_32.
Yin P, Sahu S, Turberfield AJ, Reif JH. Design of autonomous DNA cellular automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2006 Jul 13;3892 LNCS:399–416.

Published In

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

DOI

EISSN

1611-3349

ISSN

0302-9743

Publication Date

July 13, 2006

Volume

3892 LNCS

Start / End Page

399 / 416

Related Subject Headings

  • Artificial Intelligence & Image Processing
  • 46 Information and computing sciences