DNA Complementarity and Paradigms of Computing

  • Arto Salomaa
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2387)


Watson-Crick complementarity is one of the central components of DNA computing, the other central component being the massive parallelism of DNA strands. While the parallelism drastically reduces (provided the laboratory techniques will become adequate) the computational complexity, the complementarity is the actual computational tool “freely” available. It is also the cause behind the Turing universality of models of DNA computing. This paper makes this cause explicit, reducing the matter to some previously known issues in computability theory. We also discuss some specific models.


Matching System Massive Parallelism Partial Recursive Function Enumerable Language Alphabet Versus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    L.M. Adleman, P.W.K. Rothemund, S. Roweiss and E. Winfree, On applying molecular computations to the Data Encryption Standard. In: E. Baum, D. Boneh, P. Kaplan, R. Lipton, J. Reif and N. Seeman (eds.), DNA Based Computers. Proc. of the Second Annual Meeting, Princeton (1996) 28–48.Google Scholar
  2. 2.
    L. M. Adleman, Molecular computation of solutions to combinatorial problems. Science 266 (1994) 1021–1024.CrossRefGoogle Scholar
  3. 3.
    M. Amos, G. Paun, G. Rozenberg and A. Salomaa, DNA-based computing: a survey. To appear in Theoretical Computer Science.Google Scholar
  4. 4.
    J. Csima, E. Csuhaj Varjú and A. Salomaa, Power and size of extended Watson-Crick L systems, TUCS report 424, Turku Centre for Computer Science, Turku, 2001, to appear in Theoretical Computer Science.Google Scholar
  5. 5.
    J. Engelfriet and G. Rozenberg, Fixed-point languages, equality languages, and representations of recursively enumerable languages. J.Assoc.Comput.Mach. 27 (1980) 499–518.zbMATHMathSciNetGoogle Scholar
  6. 6.
    R. Freund, G. Paun, G. Rozenberg and A. Salomaa, Watson-Crick finite automata. Proceedings of the 3rd DIMACS Conf. on DNA Based Computers, 1997, 305–317.Google Scholar
  7. 7.
    D. Gifford, On the path to computation with DNA. Science 266 (1994) 993–994.CrossRefGoogle Scholar
  8. 8.
    J. Honkala and A. Salomaa, Watson-Crick D0L systems with regular triggers. Theoretical Computer Science 259 (2001) 689–698.zbMATHCrossRefMathSciNetGoogle Scholar
  9. 9.
    V. Mihalache and A. Salomaa, Language-theoretic aspects of DNA complementarity. Theoretical Computer Science 250 (2001) 163–178.zbMATHCrossRefMathSciNetGoogle Scholar
  10. 10.
    G. Păun, G. Rozenberg and A. Salomaa, DNA Computing. New Computing Paradigms. Springer-Verlag, Berlin, Heidelberg, New York (1998).Google Scholar
  11. 11.
    G. Rozenberg and A. Salomaa (eds.), Handbook of Formal Languages, Vol. 1-3. Springer-Verlag, Berlin, Heidelberg, New York, 1997.zbMATHGoogle Scholar
  12. 12.
    G. Rozenberg and A. Salomaa, Watson-Crick complementarity, universal computations and genetic engineering. Leiden University, Computer Science Technical Report 28 (1996).Google Scholar
  13. 13.
    G. Rozenberg and A. Salomaa, DNA computing: new ideas and paradigms. Springer LNCS 1644 (1999) 106–118.Google Scholar
  14. 14.
    A. Salomaa, Formal Languages. Academic Press, New York, 1773.Google Scholar
  15. 15.
    A. Salomaa, Jewels of Formal Language Theory. Computer Science Press, Rockville, Md. (1981).Google Scholar
  16. 16.
    A. Salomaa, Turing, Watson-Crick and Lindenmayer. Aspects of DNA complementarity. In: C.S. Calude, J. Casti and M.J. Dinneen (eds.), Unconventional Models of Computation. Springer-Verlag, Singapore (1998) 94–107.Google Scholar
  17. 17.
    A. Salomaa, Computability paradigms based on DNA complementarity. In V. Keränen (ed.), Innovation in Mathematics, Proc. 2nd Intern. Mathematica Symposium, Computational Mechanics Publications, Southampton, Boston (1997) 15–28.Google Scholar
  18. 18.
    A. Salomaa, Watson-Crick walks and roads in D0L graphs. Acta Cybernetica 14 (1999) 179–192.zbMATHMathSciNetGoogle Scholar
  19. 19.
    A. Salomaa, Uni-transitional Watson-Crick D0L systems. TUCS report 389, Turku Centre for Computer Science, Turku, 2001, to appear in Theoretical Computer Science.Google Scholar
  20. 20.
    A. Salomaa, Iterated morphisms with complementarity on the DNA alphabet. In M. Ito, G. Paun and S. Yu (eds.) Words, Semigroups, Transductions, World Scientific Publ. Co. (2001) 405–420.Google Scholar
  21. 21.
    A. Salomaa and P. Sosík, Watson-Crick D0L systems: the power of one transition. TUCS report 439, Turku Centre for Computer Science, Turku, 2002. Submitted for publication.Google Scholar
  22. 22.
    P. Sosík, D0L Systems + Watson-Crick Complement = Universal Computation. Springer LNCS 2055 (2001) 308–320.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Arto Salomaa
    • 1
  1. 1.Turku Centre for Computer ScienceTurkuFinland

Personalised recommendations