A DNA based implementation of an evolutionary search for good encodings for DNA computation

Computation based on manipulation of DNA molecules has the potential to solve problems with massive parallelism. DNA computation, however, is implemented with chemical reactions between the nucleotide bases, and therefore, the results can be error-prone. Application of DNA based computation to traditional computing paradigms requires error-free computation, which the DNA chemistry is unable to support. Careful encoding of the nucleotide sequences can alleviate the production of errors, but these good encodings are difficult to find. In this paper, an algorithm for evolutionary computation with DNA is sketched. Evolutionary computation does not require error-free DNA chemistry, and in fact, takes advantage of errors to produce change and variation in the population. An application of the DNA based evolution program to a search for good DNA encodings is sketched.