DNA-based parallel computation by "counting"

The potential of DNA as a truly parallel computing device is enormous. Solution-phase DNA chemistry, though not unlimited, provides the only currently-available experimental system. Its practical feasibility, however, is controversial. We have sought to extend the feasibility and generality of DNA computing by a novel application of the theory of counting . The biochemically equivalent operation for DNA counting is well known. We propose a DNA algorithm that employs this new operation. We also present an implementation of this algorithm by a novel DNA-chemical method. Preliminary computer simulations suggest that the algorithm can signi cantly reduce the DNA space complexity (i.e., the maximum number of DNA molecules that must be present in the test tube during computation) for solving 3SAT to O(20:4n). If the observation is correct, our algorithm can solve 3SAT instances of size up to or exceeding 120 variables.