Skip to main content
SpringerLink
Log in

Counting Time in Computing with Cells

  • Conference paper
DNA Computing (DNA 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3892))

Included in the following conference series:

Abstract

We consider models of P systems using time either as the output of a computation or as a means of synchronizing the hugely complex processes that take place in a cell. In the first part of the paper, we introduce and study the properties of “timed symport/antiport systems”. In the second part we introduce several new features for P systems: the association/deassociation of molecules (modeling for example the protein-protein interactions), ion channel rules and gene activation rules. We show that such timed systems are universal. We also prove several properties concerning these systems.

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 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
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.M.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1024 (1994)

    Article  Google Scholar 

  2. Alberts, B.: Essential Cell Biology. An Introduction to the Molecular Biology of the Cell. Garland Publ. Inc., New York (1998)

    Google Scholar 

  3. Bernardini, F., Gheorghe, M.: On the Power of Minimal Symport/Antiport. In: Alhazov, A., et al. (eds.) WMC 2003. Workshop on Membrane Computing, July 17-22 (2003); Technical Report N. 28/03, Research Group on Mathematical Linguistics, Universitat Rovira i Virgili, Tarragona, pp. 72–83 (2003)

    Google Scholar 

  4. Bernardini, F., Păun, A.: Universality of Minimal Symport/Antiport: Five Membranes Suffice. In: Martín-Vide, C., Mauri, G., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2003. LNCS, vol. 2933, pp. 43–54. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  5. Cavaliere, M.: Towards Asynchronous P Systems. In: Mauri, G., Păun, G., Jesús Pérez-Jímenez, M., Rozenberg, G., Salomaa, A. (eds.) WMC 2004. LNCS, vol. 3365, pp. 161–173. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  6. Cavaliere, M., Freund, R., Păun, Gh.: Event–Related Outputs of Computations in P Systems, personal communication (manuscript)

    Google Scholar 

  7. Freund, R., Păun, A.: Membrane Systems with Symport/Antiport: Universality Results. In: Păun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) WMC 2002. LNCS, vol. 2597, pp. 270–287. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  8. Frisco, P., Hogeboom, J.H.: Simulating Counter Automata by P Systems with Symport/Antiport. In: Păun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) WMC 2002. LNCS, vol. 2597, pp. 288–301. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  9. Friso, P.: About P Systems with Symport/Antiport, Second Brainstorming Week in Membrane Computing, Sevilla, Technical Report 01/2004 of the Research Group in Natural Computing, University of Sevilla, Spain, pp. 224–236 (February 2004)

    Google Scholar 

  10. Hopcroft, J., Ulmann, J.: Introduction to Automata Theory, Languages, and Computation. Addison-Wesley, Reading (1979)

    Google Scholar 

  11. Kari, L., Martin-Vide, C., Păun, A.: On the Universality of P Systems with Minimal Symport/Antiport Rules. In: Jonoska, N., Păun, G., Rozenberg, G. (eds.) Aspects of Molecular Computing. LNCS, vol. 2950, pp. 254–265. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  12. Maas, W.: Computing with Spikes. Spec. Iss. on Found. of Inf. Processing of TELEMATIK 8(1), 32–36 (2002)

    Google Scholar 

  13. Minsky, M.L.: Recursive Unsolvability of Post’s Problem of “Tag” and Other Topics in Theory of Turing Machines. Annals of Mathematics 74, 437–455 (1961)

    Article  MathSciNet  MATH  Google Scholar 

  14. Sburlan, D.: Clock-free P Systems. In: Pre-proceedings of the Fifth Workshop on Membrane Computing (WMC5), Milano, Italy, June 14-16, pp. 372–383 (2004)

    Google Scholar 

  15. Păun, A., Păun, G.: The Power of Communication: P Systems with Symport/Antiport. New Generation Computing 20(3), 295–306 (2002)

    Article  MATH  Google Scholar 

  16. Păun, G.: Membrane Computing – An Introduction. Springer, Berlin (2002)

    Book  MATH  Google Scholar 

  17. Păun, G., Perez-Jimenez, M., Sancho-Caparrini, F.: On the Reachability Problem for P Systems with Symport/Antiport. In: Proc. Automata and Formal Languages Conf., Debrecen, Hungary (2002)

    Google Scholar 

  18. Păun, Gh.: Further Twenty-six Open Problems in Membrane Computing. In: Third Brainstorming Meeting on Membrane Computing, Sevilla, Spain (February 2005)

    Google Scholar 

  19. Rozenberg, G., Salomaa, A. (eds.): Handbook of Formal Languages, 3 volumes. Springer, Berlin (1997)

    MATH  Google Scholar 

  20. Vazil, G.: On the Size of P Systems with Minimal Symport/Antiport. In: Mauri, G., Păun, G., Jesús Pérez-Jímenez, M., Rozenberg, G., Salomaa, A. (eds.) WMC 2004. LNCS, vol. 3365, pp. 422–431. Springer, Heidelberg (2005)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science, University of California – Santa Barbara, Santa Barbara, CA, 93106, USA

    Oscar H. Ibarra

  2. Department of Computer Science/IfM, Louisiana Tech University, P.O. Box 10348, Ruston, LA, 71272, USA

    Andrei Păun

Authors
  1. Oscar H. Ibarra
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrei Păun
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Computer Science, Université Pierre et Marie Curie, INSERM U511,, 91 Boulevard de L’Hôpital, 75013, Paris, France

    Alessandra Carbone

  2. California Institute of Technology, Applied and Computational Mathematics, Bioengineering,, MC 114-96, 91125, Pasadena, CA, USA

    Niles A. Pierce

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Ibarra, O.H., Păun, A. (2006). Counting Time in Computing with Cells. In: Carbone, A., Pierce, N.A. (eds) DNA Computing. DNA 2005. Lecture Notes in Computer Science, vol 3892. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11753681_9

Download citation

  • DOI: https://doi.org/10.1007/11753681_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-34161-1

  • Online ISBN: 978-3-540-34165-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation