Topics in the theory of DNA computing
Theoretical Computer Science - Natural computing
Processing DNA Tokens in Parallel Computing
IPDPS '01 Proceedings of the 15th International Parallel & Distributed Processing Symposium
DNA-based Parallel Computation of Simple Arithmetic
DNA 7 Revised Papers from the 7th International Workshop on DNA-Based Computers: DNA Computing
Binary Arithmetic for DNA Computers
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Another Logical Molecular NAND Gate System
MICRONEURO '99 Proceedings of the 7th International Conference on Microelectronics for Neural, Fuzzy and Bio-Inspired Systems
Reversible P Systems to Simulate Fredkin Circuits
Fundamenta Informaticae - SPECIAL ISSUE MCU2004
Universal families of reversible p systems
MCU'04 Proceedings of the 4th international conference on Machines, Computations, and Universality
Reversible P Systems to Simulate Fredkin Circuits
Fundamenta Informaticae - SPECIAL ISSUE MCU2004
Fundamenta Informaticae
DNA-algorithm for timetable problem
International Journal of Bioinformatics Research and Applications
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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$^1$, 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, limited amplification, sequence-specific cleavage, and detection by size. Preliminary biochemical experiments on a small test circuit have produced encouraging results. Further confirmatory experiments are in progress.