Skip to main content
Journal of Biological Physics logoLink to Journal of Biological Physics
. 2008 Jun 6;33(4):305–312. doi: 10.1007/s10867-008-9075-2

Superdiffusion in a Model for Diffusion in a Molecularly Crowded Environment

Dietrich Stauffer 1, Christian Schulze 1, Dieter W Heermann 2,
PMCID: PMC2646401  PMID: 19669520

Abstract

We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in a percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times but anomalous diffusion at intermediate times. The effective exponents for square distance vs time usually are below one at these intermediate times, but they can also be larger than one for high barrier concentrations. Thus, we observe sub- and superdiffusion in a crowded environment.

Keywords: Anomalous diffusion, Effective exponents, Random walk

Contributor Information

Dietrich Stauffer, Email: stauffer@thp.uni-koeln.de.

Dieter W. Heermann, Email: heermann@tphys.uni-heidelberg.de

References

  • 1.Pederson, T.: Diffusional protein transport within the nucleus: a message in the medium. Nat. Cell Biol. 2, E73–E74 (2000) [DOI] [PubMed]
  • 2.Guthold, M., Zhu, X., Rivetti, C., Yang, G., Thomson, N., Kasas, S., Hansma, H., Smith, B., Hansma, P., Bustamante, C.: Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. Biophys. J. 77, 2284–2294 (1999) [DOI] [PMC free article] [PubMed]
  • 3.Berry, H.: Monte Carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation. Biophys. J. 83, 1891–1901 (2002) [DOI] [PMC free article] [PubMed]
  • 4.Valdez-Taubas, J., Pelham, H.: Slow diffusion of proteins in the yeast plasma membrane allows polarity to be maintained by endocytic cycling. Curr. Biol. 13, 1636–1640 (2003) [DOI] [PubMed]
  • 5.Weiss, M., Elsner, M., Kartberg, F., Nilsson, T.: Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells. Biophys. J. 87, 3518 (2004) [DOI] [PMC free article] [PubMed]
  • 6.Binder, K., Heermann, D.W.: Monte Carlo Simulation in Statistical Physics: An Introduction, 4th edn. Springer, Heidelberg (2002)
  • 7.Bouchaud, J.P., Georges, A.: Anomalous diffusion in disordered media: statistical mechanisms, models and physical applications. Phys. Rep. 195, 127 (1990) [DOI]
  • 8.Frey, E., Kroy, K.: Brownian motion: a paradigm of soft matter and biological physics. Ann. Phys. (Leipzig) 14, 20 (2005) [DOI]
  • 9.Lindenberg, K., Oshanin, G., Tachiya, M.: Chemical kinetics beyond the textbook: fluctuations, many- particle effects and anomalous dynamics. J. Phys. Condens. Mat. 19, 060301 (2007)
  • 10.Saxton, M.J.: A biological interpretation of transient anomalous subdiffusion. Biophys. J. 92, 1178–1191 (2007) [DOI] [PMC free article] [PubMed]
  • 11.Ratynskaia, S., Rypdal, K., Knapek, C., Khrapak, S., Milovanov, A.V., Ivlev, A., Rasmussen, J.J., Morfill, G.E.: Superdiffusion and Viscoelastic Vortex Flows in a Two-Dimensional Complex Plasma. Phys. Rev. Lett. 96, 105010 (2006) [DOI] [PubMed]
  • 12.Liu, B., Goree, J.: Superdiffusion in two-dimensional Yukawa liquids. Phys. Rev. E 75, 016405 (2007) [DOI] [PubMed]
  • 13.Stauffer, D., Aharony, A.: Introduction to Percolation Theory. Taylor & Francis, London (1992)
  • 14.Ruiz-Lorenzo, J.J., Yuste, S.B., Lindenberg, K.: Simulations for trapping reactions with subdiffusive traps and subdiffusive particles. J. Phys. Condens. Mat. 19, 065120 (2007) [DOI]

Articles from Journal of Biological Physics are provided here courtesy of Springer Science+Business Media B.V.

RESOURCES