Simulating Boolean circuits on a DNA computer
- Univ. of Rochester, NY (United States)
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{sup 1}, 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{sup 1} circuits. Preliminary biochemical experiments on a small test circuit have produced encouraging results. Further confirmatory experiments are in progress. 19 refs., 3 figs., 1 tab.
- Research Organization:
- Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
- OSTI ID:
- 549018
- Report Number(s):
- CONF-970137--; CNN: Grant MCB-9630402
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
BASIC STUDIES
99 GENERAL AND MISCELLANEOUS
ALGORITHMS
ANNEALING
AUTOMATION
BIOLOGICAL MODELS
CHEMISTRY
CLEAVAGE
COMPUTERIZED SIMULATION
COMPUTERS
DESIGN
DNA SEQUENCING
ELECTRONIC CIRCUITS
FUNCTIONAL MODELS
MATHEMATICAL MODELS
MOLECULAR BIOLOGY
OLIGONUCLEOTIDES
PARALLEL PROCESSING
POLYMERASE CHAIN REACTION
RECOMBINANT DNA
SIZE
SORTING