Iterated hairpin completions of non-crossing words

Authors:
Lila Kari;Steffen Kopecki;Shinnosuke Seki
Affiliations:
Department of Computer Science, University of Western Ontario, London, Canada;Department of Computer Science, University of Western Ontario, London, Canada;Department of Systems Biosciences for Drug Discovery Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
Venue:
SOFSEM'12 Proceedings of the 38th international conference on Current Trends in Theory and Practice of Computer Science
Year:
2012

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Abstract

Iterated hairpin completion is an operation on formal languages that is inspired by the hairpin formation in DNA biochemistry. Iterated hairpin completion of a word (or more precisely a singleton language) is always a context-sensitive language and for some words it is known to be non-context-free. However, it is unknown whether regularity of iterated hairpin completion of a given word is decidable. Also the question whether iterated hairpin completion of a word can be context-free but not regular was asked in literature. In this paper we investigate iterated hairpin completions of non-crossing words and, within this setting, we are able to answer both questions. For non-crossing words we prove that the regularity of iterated hairpin completions is decidable and that if iterated hairpin completion of a non-crossing word is not regular, then it is not context-free either.