-
1
-
-
36549100203
-
Objections to a proposal on the rate of entropy production in systems far from equilibrium
-
doi:10.1063/1.447402
-
Andresen, B., Zimmermann, E. C. & Ross, J. 1984 Objections to a proposal on the rate of entropy production in systems far from equilibrium. J. Chem. Phys. 81, 4676-4677. (doi:10.1063/1.447402)
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 4676-4677
-
-
Andresen, B.1
Zimmermann, E.C.2
Ross, J.3
-
2
-
-
34247215029
-
Fluctuation theorem for currents and Schnakenberg network theory
-
doi:10.1007/s10955-006-9233-5
-
Andrieux, D. & Gaspard, P. 2007 Fluctuation theorem for currents and Schnakenberg network theory. J. Stat. Phys. 127, 107-131. (doi:10.1007/s10955- 006-9233-5)
-
(2007)
J. Stat. Phys.
, vol.127
, pp. 107-131
-
-
Andrieux, D.1
Gaspard, P.2
-
3
-
-
33947301301
-
Resonance of relaxation time in the temperature modulated Schlögl model
-
doi:10.1063/1.2698467
-
Antoine, C. & Lemarchand, A. 2007 Resonance of relaxation time in the temperature modulated Schlögl model. J. Chem. Phys. 126, 104103. (doi:10.1063/1.2698467)
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 104103
-
-
Antoine, C.1
Lemarchand, A.2
-
4
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
-
Arkin, A., Ross, J. & McAdams, H. H. 1998 Stochastic kinetic analysis of developmental pathway bifurcation in phage-λ infected E. coli cells. Genetics 149, 1633-1648. (Pubitemid 28375939)
-
(1998)
Genetics
, vol.149
, Issue.4
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
5
-
-
0000846054
-
Particle simulations of chemical systems
-
Baras, F. & Mansour, M. M. 1997 Particle simulations of chemical systems. Adv. Chem. Phys. 100, 393-474.
-
(1997)
Adv. Chem. Phys.
, vol.100
, pp. 393-474
-
-
Baras, F.1
Mansour, M.M.2
-
6
-
-
0001220722
-
Microscopic simulation of chemical bistability in homogeneous systems
-
doi:10.1063/1.472679
-
Baras, F., Mansour, M. M. & Pearson, J. E. 1996 Microscopic simulation of chemical bistability in homogeneous systems. J. Chem. Phys. 105, 8257-8261. (doi:10.1063/1.472679)
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 8257-8261
-
-
Baras, F.1
Mansour, M.M.2
Pearson, J.E.3
-
7
-
-
46649103793
-
Relationship between thermodynamic driving force and one-way fluxes in reversible processes
-
doi:10.1371/journal.pone.0000144
-
Beard, D. A. & Qian, H. 2007 Relationship between thermodynamic driving force and one-way fluxes in reversible processes. PLoS One 2, e144. (doi:10.1371/journal.pone.0000144)
-
(2007)
PLoS One
, vol.2
-
-
Beard, D.A.1
Qian, H.2
-
9
-
-
36149020420
-
Principle of minimum entropy production
-
doi:10.1103/PhysRev.105.360
-
Callen, H. B. 1957 Principle of minimum entropy production. Phys. Rev. 105, 360-365. (doi:10.1103/PhysRev.105.360)
-
(1957)
Phys. Rev.
, vol.105
, pp. 360-365
-
-
Callen, H.B.1
-
11
-
-
0000296912
-
Statistical fluctuations in autocatalytic reactions
-
doi:10.1063/1.1750549
-
Delbrück, M. 1940 Statistical fluctuations in autocatalytic reactions. J. Chem. Phys. 8, 120-124. (doi:10.1063/1.1750549)
-
(1940)
J. Chem. Phys.
, vol.8
, pp. 120-124
-
-
Delbrück, M.1
-
12
-
-
18744364770
-
Maximum entropy production and the fluctuation theorem
-
doi:10.1088/0305-4470/38/21/L01
-
Dewar, R. C. 2005 Maximum entropy production and the fluctuation theorem. J. Phys. A Math. Gen. 38, L371-L381. (doi:10.1088/0305-4470/38/21/L01)
-
(2005)
J. Phys. A Math. Gen.
, vol.38
-
-
Dewar, R.C.1
-
13
-
-
20844455677
-
Spontaneous separation of bistable biochemical systems into spatial domains of opposite phases
-
doi:10.1049/sb:20045021
-
Elf, J. & Ehrenberg, M. 2004 Spontaneous separation of bistable biochemical systems into spatial domains of opposite phases. Syst. Biol. 1, 230-236. (doi:10.1049/sb:20045021)
-
(2004)
Syst. Biol.
, vol.1
, pp. 230-236
-
-
Elf, J.1
Ehrenberg, M.2
-
15
-
-
0003392158
-
-
New York, NY: Springer
-
Gardiner, C. W. 1985 Handbook of stochastic methods for physics, chemistry, and the natural sciences, 2nd edn. New York, NY: Springer.
-
(1985)
Handbook of Stochastic Methods for Physics, Chemistry, and the Natural Sciences, 2nd Edn.
-
-
Gardiner, C.W.1
-
16
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
doi:10.1146/annurev.physchem.58.032806.104637
-
Gillespie, D. T. 2007 Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58, 35-55. (doi:10.1146/annurev.physchem.58.032806.104637)
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, pp. 35-55
-
-
Gillespie, D.T.1
-
17
-
-
0001494074
-
The thermodynamic stability theory of non-equilibrium states
-
doi:10.1073/pnas.71.1.197
-
Glansdorff, P., Nicolis, G. & Prigogine, I. 1974 The thermodynamic stability theory of non-equilibrium states. Proc. Natl Acad. Sci. USA 71, 197-199. (doi:10.1073/pnas.71.1.197)
-
(1974)
Proc. Natl Acad. Sci. USA
, vol.71
, pp. 197-199
-
-
Glansdorff, P.1
Nicolis, G.2
Prigogine, I.3
-
18
-
-
34250320968
-
Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives
-
DOI 10.1529/biophysj.106.094821
-
Han, B. & Wang, J. 2007 Quantifying robustness and dissipation cost of yeast cell cycle network: the funneled energy landscape perspectives. Biophys. J. 92, 3755-3763. (doi:10.1529/biophysj.106.094821) (Pubitemid 46910564)
-
(2007)
Biophysical Journal
, vol.92
, Issue.11
, pp. 3755-3763
-
-
Han, B.1
Wang, J.2
-
19
-
-
41549149539
-
Least dissipation cost as a design principle for robustness and function of cellular networks
-
doi:10.1103/PhysRevE.77.031922
-
Han, B. & Wang, J. 2008 Least dissipation cost as a design principle for robustness and function of cellular networks. Phys. Rev. E 77, 031922. (doi:10.1103/PhysRevE.77.031922)
-
(2008)
Phys. Rev. E
, vol.77
, pp. 031922
-
-
Han, B.1
Wang, J.2
-
20
-
-
33746047649
-
Grand canonical Markov model: A stochastic theory for open nonequilibrium biochemical networks
-
doi:10.1063/1.2165193
-
Heuett, W. J. & Qian, H. 2006 Grand canonical Markov model: a stochastic theory for open nonequilibrium biochemical networks. J. Chem. Phys. 124, 044110. (doi:10.1063/1.2165193)
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 044110
-
-
Heuett, W.J.1
Qian, H.2
-
23
-
-
28344442016
-
Exponentially slow transitions on a Markov chain: The frequency of calcium sparks
-
doi:10.1017/S0956792505006194
-
Hinch, R. & Chapman, S. J. 2005 Exponentially slow transitions on a Markov chain: the frequency of calcium sparks. Eur. J. Appl. Math. 16, 427-446. (doi:10.1017/S0956792505006194)
-
(2005)
Eur. J. Appl. Math.
, vol.16
, pp. 427-446
-
-
Hinch, R.1
Chapman, S.J.2
-
24
-
-
0038590101
-
Mean-field theory of critical behavior and first order transition: A comparison between the master equation and the nonlinear Fokker-Planck equation
-
doi:10.1007/BF01325452
-
Horsthemke, W., Malek Mansour, M. & Brenig, L. 1977 Mean-field theory of critical behavior and first order transition: a comparison between the master equation and the nonlinear Fokker-Planck equation. Z. Physik B 28, 135-139. (doi:10.1007/BF01325452)
-
(1977)
Z. Physik B
, vol.28
, pp. 135-139
-
-
Horsthemke, W.1
Malek Mansour, M.2
Brenig, L.3
-
25
-
-
0001260529
-
Bistable systems: Master equation versus Fokker-Planck modeling
-
doi:10.1103/PhysRevA.29.371
-
Hänggi, P., Grabert, H., Talkner, P. & Thomas, H. 1984 Bistable systems: master equation versus Fokker-Planck modeling. Phys. Rev. A 29, 371-378. (doi:10.1103/PhysRevA.29.371)
-
(1984)
Phys. Rev. A
, vol.29
, pp. 371-378
-
-
Hänggi, P.1
Grabert, H.2
Talkner, P.3
Thomas, H.4
-
26
-
-
0001735664
-
The minimum entropy production principle
-
doi:10.1146/annurev.pc.37.100186.001105
-
Jaynes, E. T. 1986 The minimum entropy production principle. Annu. Rev. Phys. Chem. 37, 157-187. (doi:10.1146/annurev.pc.37.100186.001105)
-
(1986)
Annu. Rev. Phys. Chem.
, vol.37
, pp. 157-187
-
-
Jaynes, E.T.1
-
27
-
-
26944490533
-
-
New York, NY: Springer
-
Jiang, D.-Q., Qian, M. & Qian, M.-P. 2004 Mathematical theory of nonequilibrium steady states LNM, vol.1833. New York, NY: Springer.
-
(2004)
Mathematical Theory of Nonequilibrium Steady States LNM
, vol.1833
-
-
Jiang, D.-Q.1
Qian, M.2
Qian, M.-P.3
-
28
-
-
0011091925
-
Nonequilibrium thermodynamics and the stability of states far from equilibrium
-
doi:10.1021/ar50139a004
-
Keizer, J. 1979 Nonequilibrium thermodynamics and the stability of states far from equilibrium. Acc. Chem. Res. 12, 243-249. (doi:10.1021/ar50139a004)
-
(1979)
Acc. Chem. Res.
, vol.12
, pp. 243-249
-
-
Keizer, J.1
-
29
-
-
0008626383
-
Qualms regarding the range of validity of the Glansdorff-Prigogine criterion for stability of non-equilibrium states
-
doi:10.1073/pnas.71.1.192
-
Keizer, J. & Fox, R. F. 1974 Qualms regarding the range of validity of the Glansdorff-Prigogine criterion for stability of non-equilibrium states. Proc. Natl Acad. Sci. USA 71, 192-196. (doi:10.1073/pnas.71.1.192)
-
(1974)
Proc. Natl Acad. Sci. USA
, vol.71
, pp. 192-196
-
-
Keizer, J.1
Fox, R.F.2
-
31
-
-
0003010776
-
Limit theorems and diffusion approximations for density dependent Markov chains
-
Kurtz, T. G. 1976 Limit theorems and diffusion approximations for density dependent Markov chains. Math. Prog. Stud. 5, 67.
-
(1976)
Math. Prog. Stud.
, vol.5
, pp. 67
-
-
Kurtz, T.G.1
-
32
-
-
0000660738
-
Strong approximation theorems for density dependent Markov chains
-
doi:10.1016/0304-4149(78)90020-0
-
Kurtz, T. G. 1978 Strong approximation theorems for density dependent Markov chains. Stoch. Proc. Appl. 6, 223. (doi:10.1016/0304-4149(78)90020-0)
-
(1978)
Stoch. Proc. Appl.
, vol.6
, pp. 223
-
-
Kurtz, T.G.1
-
33
-
-
0001147594
-
Inadequacy of entropy and entropy derivatives in characterizing the steady state
-
doi:10.1103/PhysRevA.12.636
-
Landauer, R. 1975 Inadequacy of entropy and entropy derivatives in characterizing the steady state. Phys. Rev. A 12, 636-638. (doi:10.1103/ PhysRevA.12.636)
-
(1975)
Phys. Rev. A
, vol.12
, pp. 636-638
-
-
Landauer, R.1
-
34
-
-
0001743153
-
A new principle of equilibrium
-
doi:10.1073/pnas.11.3.179
-
Lewis, G. N. 1925 A new principle of equilibrium. Proc. Natl Acad. Sci. USA 11, 179-183. (doi:10.1073/pnas.11.3.179)
-
(1925)
Proc. Natl Acad. Sci. USA
, vol.11
, pp. 179-183
-
-
Lewis, G.N.1
-
35
-
-
0036376002
-
Effect of critical fluctuations to stochastic thermodynamic behavior of chemical reaction systems at steady state far from equilibrium
-
doi:10.1039/b201564c
-
Luo, J.-L., Zhao, N. & Hu, B. 2002 Effect of critical fluctuations to stochastic thermodynamic behavior of chemical reaction systems at steady state far from equilibrium. Phys. Chem. Chem. Phys. 4, 4149-4154. (doi:10.1039/ b201564c)
-
(2002)
Phys. Chem. Chem. Phys.
, vol.4
, pp. 4149-4154
-
-
Luo, J.-L.1
Zhao, N.2
Hu, B.3
-
36
-
-
0013197954
-
Asymptotic properties of Markovian master equations
-
doi:10.1016/0003-4916(81)90033-6
-
Mansour, M. M., Van den Broek, C., Nicolis, G. & Turner, J. W. 1981 Asymptotic properties of Markovian master equations. Ann. Phys. (USA) 131, 283-313. (doi:10.1016/0003-4916(81)90033-6)
-
(1981)
Ann. Phys. (USA)
, vol.131
, pp. 283-313
-
-
Mansour, M.M.1
Van Den Broek, C.2
Nicolis, G.3
Turner, J.W.4
-
37
-
-
32344439328
-
Maximum entropy production principle in physics, chemistry and biology
-
doi:10.1016/j.physrep.2005.12.001
-
Martyusheva, L. M. & Seleznev, V. D. 2006 Maximum entropy production principle in physics, chemistry and biology. Phys. Rep. 426, 1-45. (doi:10.1016/j.physrep.2005.12.001)
-
(2006)
Phys. Rep.
, vol.426
, pp. 1-45
-
-
Martyusheva, L.M.1
Seleznev, V.D.2
-
38
-
-
0008329365
-
Stochastic models of first-order nonequilibrium phase transitions in chemical reactions
-
doi:10.1007/BF01024182
-
Matheson, I., Walls, D. F. & Gardiner, C. W. 1974 Stochastic models of first-order nonequilibrium phase transitions in chemical reactions. J. Stat. Phys. 12, 21-34. (doi:10.1007/BF01024182)
-
(1974)
J. Stat. Phys.
, vol.12
, pp. 21-34
-
-
Matheson, I.1
Walls, D.F.2
Gardiner, C.W.3
-
40
-
-
34548743446
-
Noise-induced alternations in an attractor network model of perceptual bistability
-
DOI 10.1152/jn.00116.2007
-
Moreno-Bote, R., Rinzel, J. & Rubin, N. 2007 Noise-induced alternations in an attractor network model of perceptual bistability. J. Neurophys. 98, 1125-1139. (doi:10.1152/jn.00116.2007) (Pubitemid 47435869)
-
(2007)
Journal of Neurophysiology
, vol.98
, Issue.3
, pp. 1125-1139
-
-
Moreno-Bote, R.1
Rinzel, J.2
Rubin, N.3
-
43
-
-
5544250707
-
Stochastic analysis of a nonequilibrium phase transition: Some exact results
-
doi:10.1016/0378-4371(77)90107-8
-
Nicolis, G. & Turner, J. W. 1977 Stochastic analysis of a nonequilibrium phase transition: some exact results. Physica A 89, 326-338. (doi:10.1016/0378-4371(77)90107-8)
-
(1977)
Physica A
, vol.89
, pp. 326-338
-
-
Nicolis, G.1
Turner, J.W.2
-
44
-
-
20344389483
-
Models of stochastic gene expression
-
doi:10.1016/j.plrev.2005.03.003
-
Paulsson, J. 2005 Models of stochastic gene expression. Phys. Life Rev. 2, 157-175. (doi:10.1016/j.plrev.2005.03.003)
-
(2005)
Phys. Life Rev.
, vol.2
, pp. 157-175
-
-
Paulsson, J.1
-
45
-
-
41349105441
-
Entropy production and excess entropy in nonequilibrium steady-state of single macromolecules
-
doi:10.1103/PhysRevE.65.021111
-
Qian, H. 2002 Entropy production and excess entropy in nonequilibrium steady-state of single macromolecules. Phys. Rev. E 65, 021111. (doi:10.1103/PhysRevE.65.021111)
-
(2002)
Phys. Rev. E
, vol.65
, pp. 021111
-
-
Qian, H.1
-
46
-
-
33748096830
-
Open-system nonequilibrium steady-state: Statistical thermodynamics, fluctuations and chemical oscillations
-
doi:10.1021/jp061858z
-
Qian, H. 2006 Open-system nonequilibrium steady-state: statistical thermodynamics, fluctuations and chemical oscillations. J. Phys. Chem. B 110, 15063-15074. (doi:10.1021/jp061858z)
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 15063-15074
-
-
Qian, H.1
-
47
-
-
33748107406
-
Phosphorylation energy hypothesis: Open chemical systems and their biological functions
-
doi:10.1146/annurev.physchem.58.032806.104550
-
Qian, H. 2007 Phosphorylation energy hypothesis: open chemical systems and their biological functions. Annu. Rev. Phys. Chem. 58, 113-142. (doi:10.1146/annurev.physchem.58.032806.104550)
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, pp. 113-142
-
-
Qian, H.1
-
48
-
-
0037058951
-
Single-molecule enzymology: Stochastic Michaelis-Menten kinetics
-
doi:10.1016/S0301-4622(02)00145-X
-
Qian, H. & Elson, E. L. 2002 Single-molecule enzymology: stochastic Michaelis-Menten kinetics. Biophys. Chem. 101, 565-576. (doi:10.1016/S0301- 4622(02)00145-X)
-
(2002)
Biophys. Chem.
, vol.101
, pp. 565-576
-
-
Qian, H.1
Elson, E.L.2
-
50
-
-
0002066151
-
Nonlinear kinetics and new approaches to complex reaction mechanisms
-
doi:10.1146/annurev.physchem.50.1.51
-
Ross, J. & Vlad, M. O. 1999 Nonlinear kinetics and new approaches to complex reaction mechanisms. Ann. Rev. Phys. Chem. 50, 51-78. (doi:10.1146/annurev.physchem.50.1.51)
-
(1999)
Ann. Rev. Phys. Chem.
, vol.50
, pp. 51-78
-
-
Ross, J.1
Vlad, M.O.2
-
51
-
-
34250450481
-
Chemical reaction models for nonequilibrium phase transition
-
doi:10.1007/BF01379769
-
Schlögl, F. 1972 Chemical reaction models for nonequilibrium phase transition. Z. Physik. 253, 147-161. (doi:10.1007/BF01379769)
-
(1972)
Z. Physik.
, vol.253
, pp. 147-161
-
-
Schlögl, F.1
-
52
-
-
0000013996
-
Network theory of microscopic and macroscopic behaviour of master equation systems
-
doi:10.1103/RevModPhys.48.571
-
Schnakenberg, J. 1976 Network theory of microscopic and macroscopic behaviour of master equation systems. Rev. Mod. Phys. 48, 571-585. (doi:10.1103/RevModPhys.48.571)
-
(1976)
Rev. Mod. Phys.
, vol.48
, pp. 571-585
-
-
Schnakenberg, J.1
-
53
-
-
42449114277
-
Fluctuation theorems
-
doi:10.1146/annurev.physchem.58.032806.104555
-
Sevick, E. M., Prabhakar, R., Williams, S. R. & Searles, D. J. 2008 Fluctuation theorems. Annu. Rev. Phys. Chem. 59, 603-633. (doi:10.1146/annurev. physchem.58.032806.104555)
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 603-633
-
-
Sevick, E.M.1
Prabhakar, R.2
Williams, S.R.3
Searles, D.J.4
-
55
-
-
34250698472
-
A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox
-
doi:10.1007/s11538-006-9188-3
-
Vellela, M. & Qian, H. 2007 A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox. Bull. Math. Biol. 69, 1727-1746. (doi:10.1007/s11538-006-9188-3)
-
(2007)
Bull. Math. Biol.
, vol.69
, pp. 1727-1746
-
-
Vellela, M.1
Qian, H.2
-
56
-
-
0001508049
-
Comparison of deterministic and stochastic kinetics for nonlinear systems
-
doi:10.1063/1.459735
-
Zheng, Q. & Ross, J. 1991 Comparison of deterministic and stochastic kinetics for nonlinear systems. J. Chem. Phys. 94, 3644-3648. (doi:10.1063/1.459735)
-
(1991)
J. Chem. Phys.
, vol.94
, pp. 3644-3648
-
-
Zheng, Q.1
Ross, J.2
-
57
-
-
7644234438
-
Calculating biological behaviors of epigenetic states in the phage λ life cycle
-
Zhu, X.-M., Yin, L., Hood, L. & Ao, P. 2004 Calculating biological behaviors of epigenetic states in the phage λ life cycle. Funct. Integ. Genomics 4, 188-195.
-
(2004)
Funct. Integ. Genomics
, vol.4
, pp. 188-195
-
-
Zhu, X.-M.1
Yin, L.2
Hood, L.3
Ao, P.4
|