Doubler and linearizer: An approach toward a unified theory for molecular computing based on DNA complementarity

Kaoru Onodera, Takashi Yokomori

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    Abstract

    Two specific mappings called doubler f d and linearizer f e are introduced to bridge between two kinds of languages. Specifically, f d maps string languages into (double-stranded) molecular languages, while f e performs the opposite mapping. Using these mappings, we obtain new characterizations for the families of sticker languages and of Watson-Crick languages, which lead to not only a unified view of the two families of languages but also provide a helpful view on the computational capability of DNA complementarity. Furthermore, we introduce a special type of a projection f pr which is composed of f d and a projection in the usual sense. We show that any recursively enumerable language L can be expressed as f pr(L m) for a minimal linear language L m. This result can be strengthened to L = f p(L s), for a specific form of minimal linear language L s, which provides a simple morphic characterization for the family of recursively enumerable languages.

    Original languageEnglish
    Pages (from-to)125-143
    Number of pages19
    JournalNatural Computing
    Volume7
    Issue number1
    DOIs
    Publication statusPublished - 2008 Mar

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    Keywords

    • Mapping
    • Molecular language
    • Recursively enumerable language
    • Sticker system
    • Watson-Crick finite automaton

    ASJC Scopus subject areas

    • Computer Science(all)

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