Switching dynamics in reaction networks induced by molecular discreteness

Journal of Physics Condensed Matter

Volumn 19, Issue 6, 2007, Pages

  Togashi, Yuichi ^a   Kaneko, Kunihiko ^b,c  

^a FRITZ HABER INSTITUT DER MAX PLANCK GESELLSCHAFT   (Germany)

^b UNIVERSITY OF TOKYO   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CHEMICAL REACTIONS; DIFFERENTIAL EQUATIONS; DISCRETE EVENT SIMULATION; RANDOM PROCESSES; SURFACE RECONSTRUCTION;

BIOCHEMICAL REACTIONS; MOLECULAR DISCRETENESS; STOCHASTIC DIFFERENTIAL EQUATIONS; SWITCHING DYNAMICS;

MOLECULAR DYNAMICS;

EID: 33947575324     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/19/6/065150     Document Type: Article

References (28)

1. Nicolis G and Prigogine I 1977 Self-Organization in Nonequilibrium Systems (New York: Wiley)
2. van Kampen N G 1992 Stochastic Processes in Physics and Chemistry (New York: North-Holland) rev. edn
3. Horsthemke W and Lefever R 1984 Noise-Induced Transitions ed H Haken (Berlin: Springer)
4. Matsumoto K and Tsuda I 1983 Noise-induced order J. Stat. Phys. 31 87
5. Wiesenfeld K and Moss F 1995 Stochastic resonance and the benefits of noise: from ice ages to crayfish and SQUIDs Nature 373 33
6. Olsson N, Piek E, ten Dijke P and Nilsson G 2000 Human mast cell migration in response to members of the transforming growth factor-β family J. Leukocyte Biol. 67 350
7. Wang X, Feuerstein G Z, Gu J, Lysko P G and Yue T 1995 Interleukin-1β induces expression of adhesion molecules in human vascular smooth muscle cells and enhances adhesion of leukocytes to smooth muscle cells Atherosclerosis 115 89
8. McAdams H H and Arkin A 1999 It's a noisy business! Genetic regulation at the nanomolar scale Trends Genet. 15 65
9. Rao C V, Wolf D M and Arkin A P 2002 Control, exploitation and tolerance of intracellular noise Nature 420 231
10. Elowitz M B, Levine A J, Siggia E D and Swain P S 2002 Stochastic gene expression in a single cell Science 297 1183
11. Togashi Y and Kaneko K 2001 Transitions induced by the discreteness of molecules in a small autocatalytic system Phys. Rev. Lett. 86 2459
12. Togashi Y and Kaneko K 2003 Alteration of chemical concentrations through discreteness-induced transitions in small autocatalytic systems J. Phys. Soc. Japan 72 62
13. Bettelheim E, Agam O and Shnerb N M 2001 Quantum phase transitions in classical nonequilibrium processes Physica E 9 600
14. Marion G, Mao X, Renshaw E and Liu J 2002 Spatial heterogeneity and the stability of reaction states in autocatalysis Phys. Rev. E 66 051915
15. Zhdanov V P 2002 Cellular oscillator with a small number of particles Eur. Phys. J. B 29 485
16. Gibson M A and Bruck J 2000 Efficient exact stochastic simulation of chemical systems with many species and many channels J. Phys. Chem. A 104 1876
17. van Zon J S and ten Wolde P R 2005 Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space J. Chem. Phys. 123 234910
18. 3 receptor channel clusters and concentration profiles Biophys. J. 86 2660
19. Hess B and Mikhailov A 1994 Self-organization in living cells Science 264 223
20. Mikhailov A S and Hess B 2002 Self-organization in living cells: networks of protein machines and nonequilibrium soft matter J. Biol. Phys. 28 655
21. Kuramoto Y 1973 Fluctuations around steady states in chemical kinetics Prog. Theor. Phys. 49 1782
22. Togashi Y and Kaneko K 2004 Molecular discreteness in reaction-diffusion systems yields steady states not seen in the continuum limit Phys. Rev. E 70 020901
23. Togashi Y and Kaneko K 2005 Discreteness-induced stochastic steady state in reaction diffusion systems: self-consistent analysis and stochastic simulations Physica D 205 87
24. Shnerb N M, Louzoun Y, Bettelheim E and Solomon S 2000 The importance of being discrete: life always wins on the surface Proc. Natl Acad. Sci. 97 10322
25. Shnerb N M, Bettelheim E, Louzoun Y, Agam O and Solomon S 2001 Adaptation of autocatalytic fluctuations to diffusive noise Phys. Rev. E 63 021103
26. Tokita K and Yasutomi A 1999 Mass extinction in a dynamical system of evolution with variable dimension Phys. Rev. E 60 842
27. Tokita K and Yasutomi A 2003 Emergence of a complex and stable network in a model ecosystem with extinction and mutation Theor. Popul. Biol. 63 131
28. Ebeling W, Feistel R, Hartmann-Sonntag I, Schimansky-Geier L and Scharnhorst A 2006 New species in evolving networks-stochastic theory of sensitive networks and applications on the metaphorical level BioSystems 85 65