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Language Forbidding-Enforcing Systems Defining DNA Codewords

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The Nature of Computation. Logic, Algorithms, Applications (CiE 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7921))

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Abstract

DNA code word design is an interesting and important area of research in DNA computing and generating a large set of DNA strands that satisfy a given set of constraints is a difficult and important problem. On the other hand, forbidding and enforcing systems (fe-systems) are a molecularly inspired model of computation that defines structures based on constraints. This paper reinforces the connection between fe-systems and DNA codes by using the single language model of fe-systems to characterize a variety of DNA codes that avoid certain types of cross hybridizations. Some known methods of generating good DNA code words which have been tested experimentally are generalized by fe-systems. Finally, it is shown how the theoretical definitions by fe-systems can be used as a computational tool and also to model laboratory experiments.

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Authors and Affiliations

  1. Department of Mathematics and Statistics, University of North Florida, Jacksonville, FL, 32224, U.S.A.

    Daniela Genova

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  1. Daniela Genova
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Editors and Affiliations

  1. Dipartimento die Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Piazza dell’Ateneo Nuovo 1, 20126, Milan, Italy

    Paola Bonizzoni

  2. Institute for Theoretical Computer Science, Mathematics and Operations Research, Faculty of Computer Science, Universität der Bundeswehr München, Werner-Heisenberg-Weg 39, 85577, Neubiberg, Germany

    Vasco Brattka

  3. Institute for Logic, Language and Computation, University of Amsterdam, Postbus 94242, 1090 GE, Amsterdam, The Netherlands

    Benedikt Löwe

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Genova, D. (2013). Language Forbidding-Enforcing Systems Defining DNA Codewords. In: Bonizzoni, P., Brattka, V., Löwe, B. (eds) The Nature of Computation. Logic, Algorithms, Applications. CiE 2013. Lecture Notes in Computer Science, vol 7921. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39053-1_25

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  • DOI: https://doi.org/10.1007/978-3-642-39053-1_25

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-39052-4

  • Online ISBN: 978-3-642-39053-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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