Simulating Boolean circuits on a DNA computer

Mitsunori Ogihara, Animesh Ray

Research output: Contribution to conferencePaper

22 Scopus citations

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)
Pages226-231
Number of pages6
DOIs
StatePublished - 1997
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

ASJC Scopus subject areas

  • Engineering(all)

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    Ogihara, M., & Ray, A. (1997). Simulating Boolean circuits on a DNA computer. 226-231. Paper presented at Proceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB, Santa Fe, NM, USA, . https://doi.org/10.1145/267521.267759