Simulating Boolean circuits on a DNA computer

M. Ogihara, A. Ray

Research output: Contribution to journalArticlepeer-review

39 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 NC1, 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 NC1 circuits. The feasibility of the DNA algorithm has been successfully tested on a small circuit by actual biochemical experiments.

Original languageEnglish (US)
Pages (from-to)239-250
Number of pages12
JournalAlgorithmica (New York)
Volume25
Issue number2-3
DOIs
StatePublished - Jan 1 1999
Externally publishedYes

Keywords

  • Boolean circuits
  • DNA computation
  • Parallel computation

ASJC Scopus subject areas

  • Computer Science(all)
  • Computer Science Applications
  • Applied Mathematics

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