Facilitated diffusion in a crowded environment: From kinetics to stochastics

Journal of Physics A: Mathematical and Theoretical

Volumn 42, Issue 43, 2009, Pages

  Meroz, Yasmine ^a   Eliazar, Iddo ^b   Klafter, Joseph ^a,c  

^a TEL AVIV UNIVERSITY   (Israel)

^b HOLON INSTITUTE OF TECHNOLOGY   (Israel)

^c UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 72149101003     PISSN: 17518113     EISSN: 17518121     Source Type: Journal    
DOI: 10.1088/1751-8113/42/43/434012     Document Type: Article

References (19)

1. Richter P and Eigen M 1974 Diffusion controlled reaction rates in spheroidal geometry: application to repressor operator association and membrane bound enzymes Biophys. Chem. 2 255-63
2. Riggs A D, Bourgeois S and Cohn M 1970 The lac repressor-operator interaction: 3. Kinetic studies J. Mol. Biol. 53 401-17
3. Berg O G, Winter R B and von Hippel P H 1981 Diffusion-driven mechanisms of protein translocation on nucleic acids: 1. Models and theory Biochemistry 20 6929-48
4. Montroll E W 1969 Random walks on lattices: III. Calculation of first-passage times with application to exciton trapping on photosynthetic units J. Math. Phys. 10 753
5. Lomholt M A, Koren T, Metzler R and Klafter J 2008 Lévy strategies in intermittent search processes are advantageous Proc. Natl Acad. Sci. 105 11055-9
6. Coppey M, Benichou O, Voituriez R and Moreau M 2004 Kinetics of target site localization of a protein on DNA: a stochastic approach Biophys. J. 87 1640-9
7. Li G, Berg O G and Elf J 2009 Effects of macromolecular crowding and DNA looping on gene regulation kinetics Nat. Phys. 5 294-7
8. Eliazar I, Koren T and Klafter J 2007 Searching circular DNA strands J. Phys.: Condens. Matter 19 065140
9. Eliazar I, Koren T and Klafter J 2008 Parallel search of long circular strands: modeling, analysis, and optimization J. Phys. Chem. B 112 5905-9
10. McGhee J D and von Hippel P H 1974 Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice J. Mol. Biol. 86 469-89
11. Flyvbjerg H, Keatch S A and Dryden D T F 2006 Strong physical constraints on sequence-specific target location by proteins on DNA Nucleic Acids Res. 34 2550-7
12. Kärger J 1992 Straightforward derivation of the long-time limit of the mean-square displacement in one-dimensional diffusion. Phys. Rev. A 45 4173-4
13. Taloni A and Marchesoni F 2006 Single-file diffusion on a periodic substrate Phys. Rev. Lett. 96 020601
14. Mandelbrot B B and van Ness J W 1968 Fractional Brownian motions, fractional noises and applications SIAM Rev. 10 422-37
15. Embrechts P and Maejima M 2002 Self-similar Processes (Princeton, NJ: Princeton University Press)
16. Taloni A and Lomholt M A 2008 Langevin formulation for single-file diffusion Phys. Rev. E 78 051116
17. Golding I and Cox E C 2006 Physical nature of bacterial cytoplasm Phys. Rev. Lett. 96 098102
18. Eliazar I and Klafter J 2009 Universal generation of statistical self-similarity: a randomized central limit theorem Phys. Rev. Lett. 103 040602
19. Metzler R and Klafter J 2000 The random walk's guide to anomalous diffusion: a fractional dynamics approach Phys. Rep. 339 1-77