Fluctuations for good and bad: The role of noise in living systems

Physics of Life Reviews

Volumn 3, Issue 3, 2006, Pages 133-161

  Blomberg, C ^a  

^a ALBANOVA UNIVERSITY CENTER   (Sweden)

Author keywords

Brownian motion; Fluctuation dissipation; Noise; Noise in non linear systems; Transition over barriers

Indexed keywords

EID: 33749644563     PISSN: 15710645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plrev.2006.06.001     Document Type: Review

References (68)

1. Århem P. Molecular background to neural fluctuations. An introduction to ion channel kinetics. In: Århem P., et al. (Ed). Disorder versus order in brain function (2000), World Scientific, Singapore [chapter 3]
2. In: Århem P., Blomberg C., and Liljenström H. (Eds). Disorder versus order in brain function. Essays in theoretical neurobiology (2000), World Scientific, Singapore
3. Århem P., and Johansson S. Spontaneous signaling in small central neurons: mechanisms and roles of spike amplitude and space interval fluctuations. Int J Neur Syst 7 (1996) 369-376
4. Astumian R.D. Thermodynamics and kinetics of a Brownian ratchet. Science 276 (1997) 912-922
5. Austin R.H., Beeson D.W., Eisenstein L., Frauenfelder H., and Gunsalus I.C. Biochemistry 14 (1975) 5335
6. Bak P. How nature works (1996), Springer-Verlag Telos
7. Berg H.C. Random walks in biology (1993), Princeton University Press, New Jersey
8. Berg O.G. A model for statistical fluctuations of protein numbers in a microbial population. J Theor Biol 73 (1978) 307
9. Bialek W., and Goldstein R.F. Biophys J 48 (1985) 1027
10. Blomberg C. The Brownian motion theory of chemical transition rates. Physica A 86 (1977) 49-66
11. Blomberg C. Free energy and time economy for the mutual selection of monomers in biosynthesis, primarily protein synthesis. J Theor Biol 128 (1987) 87-107
12. Blomberg C. Beyond the fluctuating enzyme: The Brownian motion picture of internal molecule motion. J Mol Liquids 42 (1989) 1-17
13. Blomberg C. On the appearance of function and organisation in the origin of life. J Theor Biol 187 (1997) 541-554
14. Blomberg C., Elinder F., and Århem P. Na channel kinetics developing models from non-stationary current fluctuations by analytic methods. Biosystems 62 (2001) 29-41
15. Carter N.J., and Cross R.A. Mechanism of the kinesin step. Nature 435 (2005) 308-312
16. Demeriel Y., and Sandler S.I. Thermodynamics and bioenergetics. Bioph Chem 97 (2002) 87-111
17. Dykman M.I., Luchinsky D.G., Manella R., McClintock P.V.E., Stein N.D., and Stocks N.G. Stochastic resonance in perspective. Il Nuovo Cimento D 17 (1995) 661-685
18. Dykman M.I., and McClintock P.V.E. What can stochastic resonance do?. Nature 391 (1998) 344
19. Edholm O., and Blomberg C. Brownian motion description of activation energies from NMR relaxation times for rotating molecular groups. Chem Phys 56 (1981) 9-14
20. Edholm O., and Blomberg C. Stretched exponentials and barrier distribution. Chem Phys 252 (2000) 221-225
21. Ehrenberg M., and Blomberg C. Thermodynamic constraints on kinetic proofreading in biosynthetic pathways. Biophys J 31 (1980) 333-358
22. Eigen M., and Schuster P. The hypercycle: A principle of natural self-organisation (1979), Springer, Berlin
23. Essig A. Energetics of active transport processes. Biophys J 15 (1975) 651-661
24. Feynman R.P., Leighton R.B., and Sands M. The Feynman lecture on physics, vol. 1 (1963), Addison-Wesley, Reading, MA [chapter 46]
25. FitzHugh R.A. Impulses and physiological states in models of nerve membranes. Biophys J 1 (1961) 445-466
26. Fox R.F. Rectified Brownian movement in molecular and cell biology. Phys Rev E 57 (1998) 2177-2203
27. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 812 (1977) 2340
28. Go N. Protein folding as a stochastic process. J Stat Phys 30 (1983) 413-423
29. Goldbeter A. Biochemical oscillations and cellular rhythms: The molecular basis of periodic and chaotic behaviour (1996), Cambridge University Press, Cambridge
30. Goldstein R.F., and Bialek W. Protein dynamics and reaction rates: Are simple models useful. Comm Mol Cell Biophys 3 (1986) 407-438
31. Haken H. Principles of brain functioning (1996), Springer, Berlin
32. Hanggi. Physics of ligand migration in biomolecules. J Stat Phys 30 (1983) 413-423
33. Hille B. Ion channels of excitable membranes (1992), Sinauer, Sunderland, MA
34. Holden A.V. Models of the stochastic activity of neurons (1976), Springer, Berlin
35. Kauffman S. Investigations (2000), Oxford University Press, New York
36. King R.B. Modeling membrane transport. Adv Food Nutr Res 40 (1996) 243-262
37. In: Kirkwood T.B.L., Rosenberger R.F., and Galas D.J. (Eds). Accuracy in molecular processes. Its control and relevance to living systems (1986), Chapman and Hall, London
38. Kramers H.A. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7 (1940) 284-304
39. Lecarpentier Y., Blanc F.-X., Quillard J., Hébert J.-L., Krokidis X., and Couirault C. Statistical mechanics of myosin molecular motors in skeletal muscles. J Theor Biol 235 (2005) 381-392
40. Leibler S., and Huse D.A. Porters versus rowers: a unified stochastic model of motor proteins. J Cell Biol 121 (1993) 1357-1368
41. Liebovitch L.S., and Toth T.I. A model of ion channel kinetics using deterministic chaos rather than stochastic processes. J Theor Biol 148 (1991) 243
42. Liljenström H. Global effects of fluctuations in neural information processing. Int J Neur Syst 7 (1996) 497-505
43. Liljenström H., and Wu X. Noise-enhanced performance ion a cortical associative memory model. Int J Neur Syst 6 (1995) 19-29
44. McNamara B., Wiesenfeld K., and Roy R. Observation of stochastic resonance in a ring laser. Phys Rev Lett 60 (1988) 2626-2629
45. Manella R. Computer experiments in non-linear stochastic physics. Moss and McClintock, vol. 3 (1989) [chapter 7]
46. Moss F., and Braun H.A. Do neurons recognize patterns or rates? One example. In: Århem P., et al. (Ed). Disorder versus order in brain function (2000), World Scientific, Singapore [chapter 6]
47. In: Moss F., and McClintock P.V.E. (Eds). Noise in nonlinear dynamic systems, 3 vols (1989), Cambridge University Press, Cambridge
48. Moss F., and Wiesenfeld K. The benefits of background noise. Scientific American (1995) 50-53
49. Nagle J.F. Long tail kinetics in biophysics. Biophys J 63 (1992) 366-379
50. Nicolis C. Long-term climatic transitions and stochastic resonance. J Stat Phys 70 (1993) 3-14
51. Nicolis G., and Prigogine I. Self-organisation in nonequilibrium systems (1977), John Wiley and Sons, New York
52. Noguti T., and Go N. Structural basis of hierarchical multiple substrates of a protein. I; Introduction. Proteins 5 (1989) 97-103
53. +-channels. Physiol Rev 71 (1991) 1047-1080
54. Paulsson J. Models of Stochastic gene expression. Phys Life Rev 2 (2005) 15-175
55. Paulsson J., and Ehrenberg M. Noise in minimal regulatory network. Plasmid copy number control. Quart Rev Bioph 34 (2001) 1
56. Pollack G.H. Muscles and molecules: Uncovering the principles of biological motion (1990), Ebners & Sons, Seattle
57. Risken H. The Fokker-Planck equation. Springer series in synergetics vol. 18 (1984), Springer, Berlin
58. In: Schilwa M. (Ed). Molecular motors (2003), Wiley-VCH
59. Smetters D.K., and Zador A.M. Noisy synapses and noisy neurons. Curr Biol 6 (1996) 1217
60. Stein WB, Honig B. Models for the active transport of cations ... the steady state analysis; 1977
61. Tsong T.Y., and Chang C.-H. Ion pump as Brownian motor: theory of electro-conformational coupling and proof of ratchet mechanism for Na, K-ATPase action. Physica A 321 (2003) 124-138
62. Van Kampen N.G. Itô versus Stratonovich. J Stat Phys 24 (1981) 175-187
63. Van Kampen N.G. Stochastic processes in physics and chemistry. New ed (1992), North-Holland, Amsterdam
64. Visscher K., Schnitzer M.J., and Block S.M. Single kinesin molecules studied with a molecular force clamp. Nature 400 (1999) 184-189
65. Volgodskii A. Energy transformation in biological molecular motors. Phys Life Rev 3 (2006) 119-132
66. Wiesenfeld K. Period doubling bifurcations: what good are they?, in Moss and to crayfish and SQIDs. Nature 373 (1989) 33-36
67. Wiesenfeld K., and Moss F. Stochastic resonance and the benefits of noise: from ice ages using the folding funnel: The fly-casting mechanism. Natl Acad Sci USA 97 (1995) 8868
68. Zwanzig R. Nonequilibrium statistical mechanics (2001), Oxford University Press, New York