Walking, Hopping and Jumping: A Model of Transcription Factor Dynamics on DNA

ECAL 2011: The 11th European Conference on Artificial Life

Volumn , Issue , 2011, Pages

  Barnes, David J ^a   Chu, Dominique ^a  

^a UNIVERSITY OF KENT   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; DNA; TRANSCRIPTION;

BINDING TIME; BINDING-SITES; KEYS PARAMETERS; SINGLE-STEP; SPECIFIC BINDING; SPECIFIC TIME; STEP MOVEMENT;

TRANSCRIPTION FACTORS;

EID: 84873525003     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.7551/978-0-262-29714-1-ch014     Document Type: Conference Paper

References (9)

1. Barnes, D. and Chu, D. (2010). An efficient model for investigating specific site binding of transcription factors. In Proceedings of the 4th International Conference on Bioinformatics and Biomedical Engineering, June 18-20, Chengdu, China, 2010, page 4. IEE Xplore.
2. Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry, 81(25):2340-2361.
3. Knuth, D. E. (1997). Art of Computer Programming, Volume 1: Fundamental Algorithms (3rd Edition). Addison-Wesley Professional.
4. Meyers, S. (2001). Effective STL: 50 Specific Ways to Improve the Use of the Standard Template Library. Addison-Wesley Professional Computing Series. Addison Wesley.
5. Murugan, R. (2009). Packaging effects on site-specific dna-protein interactions. Physical Review E, 79(6 Pt 1):061920.
6. Slutsky, M., Kardar, M., and Mirny, L. (2004). Diffusion in correlated random potentials, with applications to DNA. Physical Review E, 69(6):061903.
7. The University of Wisconsin, M. (2009). E. coli genome project.
8. Winter, R., Berg, O., and von Hippel, P. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. the escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry, 20(24):6961-6977.
9. Wunderlich, Z. and Mirny, L. (2008). Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Research, 36(11):3570-3578.