Generating DNA code words using forbidding and enforcing systems

  • Authors:

  • Daniela Genova;Kalpana Mahalingam

  • Affiliations:

  • Department of Mathematics and Statistics, University of North Florida, Jacksonville, FL;Department of Mathematics, Indian Institute of Technology, Chennai, TN, India

  • Venue:
  • TPNC'12 Proceedings of the First international conference on Theory and Practice of Natural Computing
  • Year:
  • 2012

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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.