Horn Clause Computation by Self-assembly of DNA Molecules

Abstract

Kobayashi proposed Horn clause computation by DNA molecules, which is more suitable for expressing complex algorithms than other models for DNA computing. This paper describes a new implementation of Horn clause computation by DNA. It employs branching DNA molecules for representing Horn clauses. As derivations are realized by self-assembly of such molecules, the implementation requires only a constant number of laboratory operations. Furthermore, it deals with first-order Horn clauses with some restrictions. In order to realize first-order logic, we implement variable substitutions by string tiling proposed by Winfree, et al. As we show the computational power of a Horn clause program in our model, we give another proof that a polynomial number of operations using self-assembly of DNA molecules can compute any problem in NP.KeywordsHorn ClauseDeductive InferenceFact MoleculeQuery MoleculeBody TileThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.