Thermodynamically based constraints for rate coefficients of large biochemical networks

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 1, Issue 3, 2009, Pages 348-358

  Vlad, Marcel O ^a,b,c   Ross, John ^a  

^a STANFORD UNIVERSITY   (United States)

^b ACADEMY OF ROMANIAN SCIENTISTS   (Romania)

^c UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOCHEMISTRY; BIOLOGICAL MODEL; KINETICS; SYSTEMS BIOLOGY; THERMODYNAMICS;

ALGORITHMS; BIOCHEMICAL PROCESSES; KINETICS; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY; THERMODYNAMICS;

EID: 78649420465     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.50     Document Type: Article

References (38)

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.JMath 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. LiebermeisterW, 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, HeinemannM. 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.