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Generating DNA Code Words Using Forbidding and Enforcing Systems

  • Daniela Genova
  • Kalpana Mahalingam
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7505)

Abstract

Research in DNA computing was initiated by Leonard Adleman in 1994 when he solved an instance of an NP-complete problem solely by molecules. DNA code words arose in the attempt to avoid unwanted hybridizations of DNA strands for DNA based computations. Given a set of constraints, generating a large set of DNA strands that satisfy the constraints is an important problem in DNA computing. On the other hand, motivated by the non-determinism of molecular reactions, A. Ehrenfeucht and G. Rozenberg introduced forbidding and enforcing systems (fe-systems) as a model of computation that defines classes of languages based on two sets of constraints. We attempt to establish a connection between these two areas of research in natural computing by characterizing a variety of DNA codes that avoid certain types of cross hybridizations by fe-systems. We show that one fe-system can generate the entire class of DNA codes of a certain property, for example θ-k-codes, and confirm some properties of DNA codes through fe-systems. We generalize by fe-systems some known methods of generating good DNA code words which have been tested experimentally.

Keywords

fe-systems fe-families Biomolecular computing Watson-Crick involution Hybridization DNA codes 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Daniela Genova
    • 1
  • Kalpana Mahalingam
    • 2
  1. 1.Department of Mathematics and StatisticsUniversity of North FloridaJacksonvilleUSA
  2. 2.Department of MathematicsIndian Institute of TechnologyChennaiIndia

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