References
1 Wegscheider, R. Über simultane Gleichgewichte und die beziehungen zwischen Thermodynamik und Reaktionskinetik. Z Phys Chem 1902, 39:257–303.
2 Lewis, GN. A new principle of equilibrium. Proc Natl Acad Sci U S A 1925, 11:179–183.
3 Tolman, RC. Duration of molecules in upper quantum states. Phys Rev 1924, 23:693–709.
4 Tolman, RC. The Principle of microscopic reversibility. Proc Natl Acad Sci U S A 1925, 11:436–439.
5 Tolman, RC.
Statistical Mechanics. Oxford:
Oxford University Press; 1938.
6 Onsager, L. Reciprocal relations in irreversible processes I. Phys Rev 1931, 37:405–426.
7 Onsager, L. Reciprocal relations in irreversible processes II. Phys Rev 1931, 38:2265–2279.
8 Hearon, JZ. The kinetics of linear systems with special reference to periodic reactions. Bull Math Biophys 1953, 15:121–141.
9 Arkin, A, Ross, J. Statistical construction of chemical reaction mechanisms from measured time‐series. J Phys Chem 1995, 99:970–979.
10 Chevalier, T, Schreiber, I, Ross, J. Toward a systematic determination of complex reaction mechanism. J Phys Chem 1993, 97:6776–6787.
11 Vlad, MO, Segal, E. The general form of Wegscheider cyclicity conditions. Rev Roum Chim 1979, 24:807–808.
12 Popa, VT, Segal, E, Vlad, MO. A new general form of Wegscheider cyclicity conditions. Rev Roum Chim 1984, 29:625–629.
13 Schuster, S, Schuster, R. A generalization of Wegscheider`s condition. Implicsations for properties of steady states and for quasi‐steady state approximation. J Math Chem 1989, 3:25–42.
14 Schuster, S, Schuster, R. Detecting strictly detailed balanced subnetworks in open chemical reaction networks. J Math Chem 1991, 6:17–40.
15 Feinberg, M. Complex balancing in general kinetic systems. Arch Ration Mech Anal 1972, 49(
3): 187–194.
16 Horn, F. Necessary and sufficient conditions for complex balancing in chemical kinetics. Arch Ration Mech Anal 1972, 49(
3): 172–186.
17 Horn, F, Jackson, R. General mass action kinetics. Arch Ration Mech Anal 1972, 47(
2): 81–116.
18 Colquhoun, D, Dowsland, KA, Beato, M, Plested, AJR. How to impose microscopic reversibility in complex reaction mechanisms. Biophys J 2004, 86(
6): 3510–3518.
19 Ederer, M, Gilles, ED. Thermodynamically feasible kinetic models of reaction networks. Biophys J 2007, 92(
6): 1846–1857.
20 Ederer, M, Gilles, E. Thermodynamic constraints in kinetic modeling: thermodynamic‐kinetic modeling in comparison to other approaches. Eng Life Sci 2008, 8(
5): 467–476.
21 Liebermeister, W, Klipp, E. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model 2006, 3:41.
22 Yang, J, Bruno, WJ, Hlavacek, WS, Pearson, JE. On imposing detailed balance in complex reaction mechanisms. Biophys J 2006, 91(
3): 1136–1141.
23 Beard, DA, Liang, S, Qian, H. Energy balance for analysis of complex metabolic networks. Biophys J 2002, 83(
1): 79–86.
24 Beard, DA, Liang, S, Qian, H. Energy balance for analysis of complex metabolic networks. Biophys J 2002, 83(
1): 79–86.
25 Beard, DA, Babson, E, Curtis, E, Qian, H. Thermodynamic constraints for biochemical networks. J Theor Biol 2004, 228(
3): 327–333.
26 Qian, H, Beard, DA, Liang, S. Stoichiometric network theory for nonequilibrium biochemical systems. Eur J Biochem 2003, 270(
3): 415–421.
27 Yang, F, Qian, H, Beard, DA. Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry. Metab Eng, 2005, 7(
4): 251–259.
28 Henry, CS, Jankowski, MD, Broadbelt, LJ, Hatzimanikatis, V. Genome‐scale thermodynamic analysis of Escherichia coli metabolism. Biophys J 2006, 90(
4): 1453–1461.
29 Henry, CS, Broadbelt, LJ, Hatzimanikatis, V. Thermodynamics‐based metabolic flux analysis. Biophys J 2007, 92(
5): 1792–1805.
30 Hoppe, A, Hoffmann, S, Holzhütter, H. Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC Syst Biol 2007, 1:23.
31 Kümmel, A, Panke, S, Heinemann, M. Putative regulatory sites unraveled by network‐embedded thermodynamic analysis of metabolome data. Mol Syst Biol 2006, 2:0034.
32 Kümmel, A, Panke, S, Heinemann, M. Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics 2006, 7:512.
33 Vlad, MO, Ross, J. Statistical ensemble approach and fluctuation‐dissipation relations for multivariable chemical systems far from equilibrium. J Phys Chem A 2000, 104:3159–3176.
34 Boudart, M. Consistency between kinetics and thermodynamics. J PhysChem 1976, 80:2869–2870.
35 Vlad, MO, Moran, F, Popa_, VT, Szedlacsek, SE, Ross, J. Functional, fractal nonlinear response with application to rate processes with memory, allometry, and population genetics. Proc Natl Acad Sci U S A 2007.
36 Vlad, MO, Corlan, AD, Moran, F, Spang, R, Oefner, P,
et al. Kinetic laws, phase–phase expansions, renormalization group, and INR calibration.Accepted for publication in PNAS on 02/4/2009.
37 Palsson, BO.
Systems Biology: Properties of Reconstructed Networks. Cambridge:
Cambridge University Press; 2006.
38 Ross, J, Schreiber, I, Vlad, MO.
Determination of Complex Reaction Mechanisms: Analysis of Chemical, Biological, and Genetic Networks. Oxford:
Oxford University Press; 2006.
