Simulating Boolean circuits on a DNA computer

Mitsunori Ogihara, Animesh Ray

Research output: Chapter in Book/Report/Conference proceedingConference contribution

22 Citations (Scopus)

Abstract

We demonstrate that DNA computers can simulate Boolean circuits with a small overhead. Boolean circuits embody the notion of massively parallel signal processing and are frequently encountered in many parallel algorithms. Many important problems such as sorting, integer arithmetic, and matrix multiplication are known to be computable by small size Boolean circuits much faster than by ordinary sequential digital computers. This paper shows that DNA chemistry allows one to simulate large semi-unbounded fan-in Boolean circuits with a logarithmic slowdown in computation time. Also, for the class NC, the slowdown can be reduced to a constant. In this algorithm we have encoded the inputs, the Boolean AND gates, and the OR gates to DNA oligonucleotide sequences. We operate on the gates and the inputs by standard molecular techniques of sequence-specific annealing, ligation, separation by size, amplification, sequence-specific cleavage, and detection by size. Additional steps of amplification are not necessary for NC circuits. Preliminary biochemical experiments on a small test circuit have produced encouraging results. Further confirmatory experiments are in progress.

Original languageEnglish (US)
Title of host publicationProceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB
PublisherACM
Pages226-231
Number of pages6
StatePublished - 1997
Externally publishedYes
EventProceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB - Santa Fe, NM, USA
Duration: Jan 20 1997Jan 23 1997

Other

OtherProceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB
CitySanta Fe, NM, USA
Period1/20/971/23/97

Fingerprint

DNA
Networks (circuits)
Amplification
Oligonucleotides
Digital computers
Sorting
Parallel algorithms
Signal processing
Experiments
Annealing

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Ogihara, M., & Ray, A. (1997). Simulating Boolean circuits on a DNA computer. In Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB (pp. 226-231). ACM.

Simulating Boolean circuits on a DNA computer. / Ogihara, Mitsunori; Ray, Animesh.

Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB. ACM, 1997. p. 226-231.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ogihara, M & Ray, A 1997, Simulating Boolean circuits on a DNA computer. in Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB. ACM, pp. 226-231, Proceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB, Santa Fe, NM, USA, 1/20/97.
Ogihara M, Ray A. Simulating Boolean circuits on a DNA computer. In Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB. ACM. 1997. p. 226-231
Ogihara, Mitsunori ; Ray, Animesh. / Simulating Boolean circuits on a DNA computer. Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB. ACM, 1997. pp. 226-231
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