Simulating Boolean circuits on a DNA computer

Research output: Contribution to journalArticle

36 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 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
StatePublished - 1999
Externally publishedYes

Fingerprint

Boolean Circuits
DNA
Networks (circuits)
Amplification
Matrix multiplication
Parallel Processing
Annealing
Sorting
DNA Sequence
Parallel Algorithms
Chemistry
Signal Processing
Logarithmic
Oligonucleotides
Digital computers
Parallel algorithms
Integer
Necessary
Signal processing
Demonstrate

Keywords

  • Boolean circuits
  • DNA computation
  • Parallel computation

ASJC Scopus subject areas

  • Computer Graphics and Computer-Aided Design
  • Software
  • Safety, Risk, Reliability and Quality
  • Applied Mathematics

Cite this

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

In: Algorithmica (New York), Vol. 25, No. 2-3, 1999, p. 239-250.

Research output: Contribution to journalArticle

Ogihara, M & Ray, A 1999, 'Simulating Boolean circuits on a DNA computer', Algorithmica (New York), vol. 25, no. 2-3, pp. 239-250.
Ogihara, Mitsunori ; Ray, A. / Simulating Boolean circuits on a DNA computer. In: Algorithmica (New York). 1999 ; Vol. 25, No. 2-3. pp. 239-250.
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