Watson-Crick walks and roads on DOL graphs

Abstract

Apart from the massive parallelism of DNA strands, the phenomenon known as Watson-Crick complementarity, is basic both in the experiments and theory of DNA computing. The parallelism makes exhaustive searches possible, whereas the complementarity is a powerful computational tool. This paper investigates complementarity as a language-theoretic operation: "bad" words obtained through a generative process are replaced by their complementary ones. While this idea is applicable to any generative process, it seems particularly suitable for Lindenmayer systems. DOL systems augmented with a specific complementarity transition, "Watson-Crick DOL systems", are investigated in this paper. Many issues involved are conveniently expressed in terms of certain paths, "Watson- Crick walks", in an associated digraph