Out-of-equilibrium dynamics of gene expression and the Jarzynski equality

Physical Review Letters

Volumn 100, Issue 18, 2008, Pages

  Berg, Johannes ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMIC MODELS; MOLECULAR STRUCTURE; STATISTICAL MECHANICS; THEOREM PROVING;

GENE TRANSCRIPTION; JARZYNSKI EQUALITY;

TRANSCRIPTION;

EID: 43249087233     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.100.188101     Document Type: Article

References (30)

1. E. Davidson, Genomic Regulatory Systems: Development and Evolution (Academic, San Diego, CA, 2001).
2. H.H. McAdams and A. Arkin, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 94, 814 (1997). 10.1073/pnas.94.3.814
3. M. Sasai and P.G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 100, 2374 (2003). 10.1073/pnas.2627987100
4. J. Paulsson, Nature (London) NATUAS 0028-0836 427, 415 (2004). 10.1038/nature02257
5. J. Monod, A. Pappenheimer, Jr, and G. Cohen-Bazire, Biochim. Biophys. Acta 9, 648 (1952). BBACAQ 0006-3002 10.1016/0006-3002(52)90227-8
6. E. Ozbudak, Nat. Genet. 31, 69 (2002). NGENEC 1061-4036 10.1038/ng869
7. W. Chen, J. England, and E. Shakhnovich, http://arxiv.org/abs/q-bio.MN/ 0402021 2004.
8. N. van Kampen, Stochastic Processes in Physics and Chemistry (Elsevier Science, Amsterdam, 1992).
9. P.T. Spellman, Mol. Biol. Cell 9, 3273 (1998). MBCEEV 1059-1524
10. E. Carlon and T. Heim, Physica (Amsterdam) 362A, 433 (2006). PHYADX 0378-4371 10.1016/j.physa.2005.09.067
11. J. Berg, Europhys. Lett. 82, 28010 (2008). EULEEJ 0295-5075 10.1209/0295-5075/82/28010
12. Yeastgenome database: http://db.yeastgenome.org/cgi-bin/locus.pl?locus= SWI4.
13. G. Chen, N. Hata, and M. Zhang, Nucleic Acids Res. 32, 2362 (2004). NARHAD 0305-1048 10.1093/nar/gkh557
14. R. Khanin, V. Vinciotti, and E. Wit, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 18592 (2006). 10.1073/pnas.0603390103
15. U. Gerland, D. Moroz, and T. Hwa, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 99, 12015 (2002). 10.1073/pnas.192693599
16. L. Michaelis and M. Menten, Biochem. Z. BIZEA2 0366-0753 49, 333 (1913).
17. U. Alon, An Introduction to System Biology: Design Principles of Biological Circuits (Chapman & Hall, Boca Raton, FL, 2007).
18. C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997). PRLTAO 0031-9007 10.1103/PhysRevLett.78.2690
19. T. Schmiedl and U. Seifert, J. Chem. Phys. 126, 044101 (2007). JCPSA6 0021-9606 10.1063/1.2428297
20. G. Gallavotti and E.G.D. Cohen, Phys. Rev. Lett. 74, 2694 (1995). PRLTAO 0031-9007 10.1103/PhysRevLett.74.2694
21. G.E. Crooks, Phys. Rev. E 60, 2721 (1999). PLEEE8 1063-651X 10.1103/PhysRevE.60.2721
22. M. Baiesi, T. Jacobs, C. Maes, and N.S. Skantzos, Phys. Rev. E 74, 021111 (2006). PLEEE8 1063-651X 10.1103/PhysRevE.74.021111
23. H. Bussemacher, H. Li, and E. Siggia, Nat. Genet. 27, 167 (2001); NGENEC 1061-4036 10.1038/84792
24. K. Basso, Nat. Genet. 37, 382 (2005); NGENEC 1061-4036 10.1038/ng1532
25. N. Friedman, Science 303, 799 (2004); SCIEAS 0036-8075 10.1126/science.1094068
26. Z. Bar-Joseph, Bioinformatics 20, 2493 (2004). BOINFP 1367-4803 10.1093/bioinformatics/bth283
27. YEASTRACT: http://www.yeastract.com/ (2007).
28. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 98, 3658 (2001); 10.1073/pnas.071034098
29. J. Liphardt, Science SCIEAS 0036-8075 296, 1832 (2002). 10.1126/science.1071152
30. V. Blickle, Phys. Rev. Lett. 96, 070603 (2006). PRLTAO 0031-9007 10.1103/PhysRevLett.96.070603