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Natural Computing

, Volume 8, Issue 1, pp 157–170 | Cite as

DNA splicing: computing by observing

  • Matteo CavaliereEmail author
  • Nataša Jonoska
  • Peter Leupold
Article

Abstract

Motivated by several techniques for observing molecular processes in real-time we introduce a computing device that stresses the role of the observer in biological computations and that is based on the observed behavior of a splicing system. The basic idea is to introduce a marked DNA strand into a test tube with other DNA strands and restriction enzymes. Under the action of these enzymes the DNA starts to splice. An external observer monitors and registers the evolution of the marked DNA strand. The input marked DNA strand is then accepted if its observed evolution follows a certain expected pattern. We prove that using simple observers (finite automata), applied on finite splicing systems (finite set of rules and finite set of axioms), the class of recursively enumerable languages can be recognized.

Keywords

DNA computing Splicing Formal languages Observer 

Notes

Acknowledgments

The authors want to thank Peter R. Cook for providing extremely useful references. P. Leupold has been supported by the FPU grant of the Spanish Ministry of Science and Education. N. Jonoska has been supported in part by NSF Grants CCF #0432009 and CCF #0523928. The paper is based on the work presented at the 11th International Meeting on DNA Based Computers held in London, Canada, June 2005.

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Matteo Cavaliere
    • 1
    Email author
  • Nataša Jonoska
    • 2
  • Peter Leupold
    • 3
  1. 1.Centre for Computational and Systems Biology, Microsoft Research – University of TrentoTrentoItaly
  2. 2.Department of MathematicsUniversity of South FloridaTampaUSA
  3. 3.Research Group on Mathematical LinguisticsRovira i Virgili UniversityTarragonaSpain

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