Skip to main content
SpringerLink
Log in

Kinetic investigation of small systems using different algorithms

  • Article
  • Published:
Journal of the Iranian Chemical Society Aims and scope Submit manuscript

Abstract

We have investigated different algorithms for the simulation of kinetics of small systems. We have simulated the first order reversible reaction with the Gillespie, Gibson and Bruck time simulation as a function of Poisson distribution and compared the results of three algorithms. We have also simulated intracellular viral kinetics for a genome with Gillespie and Poisson distribution algorithms.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. D.A. McQuarrie, J. Chem. Phys. 38 (1963) 433.

    CAS  Google Scholar 

  2. T.E. Turner, S. Schnell, K. Burrage, Com. Biol. & Chem. 28 (2004)165.

    CAS  Google Scholar 

  3. R. Srivastava, L. You, J. Summers, J. Yin, J. Theor. Biol. 218 (2002) 309.

    CAS  Google Scholar 

  4. J. Rose, Q. Zheng, J. Chem. Phys. 94 (1991) 3644.

    Google Scholar 

  5. H. Qian, E.L. Elson, Biophys. Chem. 101 (2002) 565.

    Google Scholar 

  6. D.A. McQuarrie, C.J. Jachimowski, M.E. Russell, J. Chem. Phys. 40 (1964) 2914.

    CAS  Google Scholar 

  7. D.A. McQuarri, Stochastic Approach to Chemical Kinetics, Methuen, London, 1967.

    Google Scholar 

  8. D.T. Gillespie, J. Phys. Chem. 81 (1977) 2340.

    CAS  Google Scholar 

  9. M.A. Gibson, J. Bruck, J. Phys. Chem. A 104 (2000) 1876.

    CAS  Google Scholar 

  10. P. Erdi, J. Toth, Mathematical Models of Chemical Reaction. Theory and Applications of Deterministic and Stochastic Models, Princeton University Press, Princeton, NJ, 1988.

  11. D.T. Gillespie, J. Comput. Phys. 22 (1976) 403.

    CAS  Google Scholar 

  12. D.T. Gillespie, J. Stat. Phys. 16 (1977) 311.

    Google Scholar 

  13. N.G. Van Kampen, Stochastic Processes in Physics and Chemistry, Elsevier, Amsterdam, 1992.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry and Nanotechnology Research Center, Sharif University of Technology, Tehran, Iran

    F. Taherkhani & G. A. Parsafar

  2. Department of Physics, Sharif University of Technology, Tehran, Iran

    M. R. Rahimitabar

Authors
  1. F. Taherkhani
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. G. A. Parsafar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. R. Rahimitabar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to G. A. Parsafar.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Taherkhani, F., Parsafar, G.A. & Rahimitabar, M.R. Kinetic investigation of small systems using different algorithms. JICS 3, 327–333 (2006). https://doi.org/10.1007/BF03245955

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF03245955

Keyword

Search

Navigation