Skip to main content
SpringerLink
Log in

Generating DNA Code Words Using Forbidding and Enforcing Systems

  • Conference paper
Theory and Practice of Natural Computing (TPNC 2012)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7505))

Included in the following conference series:

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 54.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 72.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adleman, L.: Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994)

    Article  Google Scholar 

  2. Cavaliere, M., Jonoska, N.: Forbidding and enforcing in membrane computing. Natural Computing 2, 215–228 (2003)

    Article  MathSciNet  MATH  Google Scholar 

  3. Deaton, R., Murphy, R., Rose, J., Garzon, M., Franceschetti, D., Stevens Jr., S.: A DNA based implementation of an evolutionary search for good encodings for DNA computation. In: Proc. IEEE Conference on Evolutionary Computation ICEC 1997, pp. 267–271. Institute of Electrical and Electronics Engineers (1997)

    Google Scholar 

  4. Ehrenfeucht, A., Hoogeboom, H.J., Rozenberg, G., van Vugt, N.: Forbidding and enforcing. In: DNA Based Computers V, vol. 54, pp. 195–206. AMS DIMACS, Providence (2000)

    Google Scholar 

  5. Ehrenfeucht, A., Rozenberg, G.: Forbidding-enforcing systems. Theoretical Computer Science 292, 611–638 (2003)

    Article  MathSciNet  MATH  Google Scholar 

  6. Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular computation: RNA solutions to chess problems. Proceedings of the National Academy of Sciences, USA 97(4), 1385–1389 (2000)

    Article  Google Scholar 

  7. Franco, G., Jonoska, N.: Forbidding and enforcing conditions in DNA self-assembly of graphs. In: Nanotechnology: Science and Computation. Natural Computing Series Part I, pp. 105–118 (2006)

    Google Scholar 

  8. Garzon, M.: On codeword design in metric spaces. Natural Computing 8(3), 571–588 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  9. Genova, D.: Defining Languages by Forbidding-Enforcing Systems. In: Löwe, B., Normann, D., Soskov, I., Soskova, A. (eds.) CiE 2011. LNCS, vol. 6735, pp. 92–101. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  10. Genova, D.: Forbidding Sets and Normal Forms for Language Forbidding-Enforcing Systems. In: Dediu, A.-H., Martín-Vide, C. (eds.) LATA 2012. LNCS, vol. 7183, pp. 289–300. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  11. Genova, D., Jonoska, N.: Topological properties of forbidding-enforcing systems. Journal of Automata, Languages and Combinatorics 11(4), 375–397 (2006)

    MathSciNet  MATH  Google Scholar 

  12. Genova, D., Jonoska, N.: Forbidding and enforcing on graphs. Theoretical Computer Science 429, 108–117 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  13. Hussini, S., Kari, L., Konstantinidis, S.: Coding properties of DNA languages. Theoretical Computer Science 290, 1557–1579 (2003)

    Article  MathSciNet  MATH  Google Scholar 

  14. Jonoska, N., Mahalingam, K., Chen, J.: Involution codes: with application to DNA coded languages. Natural Computing 4, 141–162 (2005)

    Article  MathSciNet  Google Scholar 

  15. Kari, L., Konstantinidis, S., Losseva, E., Wozniak, G.: Sticky-free and overhang-free DNA languages. Acta Informatica 40, 119–157 (2003)

    Article  MathSciNet  MATH  Google Scholar 

  16. Kari, L., Mahalingam, K.: DNA Codes and Their Properties. In: Mao, C., Yokomori, T. (eds.) DNA12. LNCS, vol. 4287, pp. 127–142. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  17. Liu, Q., Wang, L., Frutos, A.G., Condon, A., Corn, R.M., Smith, L.M.: DNA computing on surfaces. Nature 403, 175–179 (2000)

    Article  Google Scholar 

  18. Marathe, A., Condon, A.E., Corn, R.M.: On combinatorial word design. Preliminary Preproceedings of the 5th International Meeting on DNA Based Computers, Boston, pp. 75–88 (1999)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Mathematics and Statistics, University of North Florida, Jacksonville, FL, 32224, USA

    Daniela Genova

  2. Department of Mathematics, Indian Institute of Technology, Chennai, TN, 600036, India

    Kalpana Mahalingam

Authors
  1. Daniela Genova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kalpana Mahalingam
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Research Group on Mathematical Linguistics, Universitat Rovira i Virgili, Avinguda Catalunya, 35, 43002, Tarragona, Spain

    Adrian-Horia Dediu  & Carlos Martín-Vide  & 

  2. Fakultät für Informatik, Otto-von-Guericke-Universität Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany

    Bianca Truthe

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Genova, D., Mahalingam, K. (2012). Generating DNA Code Words Using Forbidding and Enforcing Systems. In: Dediu, AH., Martín-Vide, C., Truthe, B. (eds) Theory and Practice of Natural Computing. TPNC 2012. Lecture Notes in Computer Science, vol 7505. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33860-1_13

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-33860-1_13

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33859-5

  • Online ISBN: 978-3-642-33860-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation