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Volumn 292, Issue , 2012, Pages 71-77

A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks

Author keywords

Constraint based modeling; Convex optimization; Entropy function; Flux balance analysis; Thermodynamics

Indexed keywords

BIOCHEMISTRY; ENERGY CONSERVATION; ENTROPY; GENOME; OPTIMIZATION; REACTION KINETICS; STEADY-STATE EQUILIBRIUM; THERMODYNAMICS;

EID: 80054052364     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.09.029     Document Type: Article
Times cited : (30)

References (52)
  • 1
    • 82755167152 scopus 로고    scopus 로고
    • Existence of Positive Equilibria for Mass Conserving and Mass-Action Chemical Reaction Networks with a Single-Terminal-Linkage Class
    • Akle, S., Dalal, O., Fleming, R.M.T., Saunders, M.A., Taheri, N.A., Ye, Y., 2011. Existence of Positive Equilibria for Mass Conserving and Mass-Action Chemical Reaction Networks with a Single-Terminal-Linkage Class.
    • (2011)
    • Akle, S.1    Dalal, O.2    Fleming, R.M.T.3    Saunders, M.A.4    Taheri, N.A.5    Ye, Y.6
  • 4
    • 0032119468 scopus 로고    scopus 로고
    • A computational study of the homogeneous algorithm for large-scale convex optimization
    • Andersen E.D., Ye Y. A computational study of the homogeneous algorithm for large-scale convex optimization. Comput. Optim. Appl. 1998, 10(3):243-269.
    • (1998) Comput. Optim. Appl. , vol.10 , Issue.3 , pp. 243-269
    • Andersen, E.D.1    Ye, Y.2
  • 5
    • 0036286631 scopus 로고    scopus 로고
    • Energy balance for analysis of complex metabolic networks
    • Beard D.A., Liang S., Qian H. Energy balance for analysis of complex metabolic networks. Biophys. J. 2002, 83(1):79-86.
    • (2002) Biophys. J. , vol.83 , Issue.1 , pp. 79-86
    • Beard, D.A.1    Liang, S.2    Qian, H.3
  • 6
  • 11
    • 34247560347 scopus 로고    scopus 로고
    • Enzymes in context: kinetic characterization of enzymes for systems biology
    • Cornish-Bowden A., Hofmeyr J.H.S. Enzymes in context: kinetic characterization of enzymes for systems biology. Biochemist 2005, 27(1):11-13.
    • (2005) Biochemist , vol.27 , Issue.1 , pp. 11-13
    • Cornish-Bowden, A.1    Hofmeyr, J.H.S.2
  • 12
    • 0035641176 scopus 로고    scopus 로고
    • Primal-dual solution perturbations in convex optimization
    • Dontchev A.L., Rockafellar R.T. Primal-dual solution perturbations in convex optimization. Set-Valued Anal. 2001, 9(1):49-65.
    • (2001) Set-Valued Anal. , vol.9 , Issue.1 , pp. 49-65
    • Dontchev, A.L.1    Rockafellar, R.T.2
  • 13
    • 0000457977 scopus 로고
    • Nonlinear networks IIa
    • Duffin R.J. Nonlinear networks IIa. Bull. Am. Math. Soc. 1947, 53:963-971.
    • (1947) Bull. Am. Math. Soc. , vol.53 , pp. 963-971
    • Duffin, R.J.1
  • 14
    • 33947677189 scopus 로고    scopus 로고
    • Thermodynamically feasible kinetic models of reaction networks
    • Ederer M., Gilles E. Thermodynamically feasible kinetic models of reaction networks. Biophys. J. 2007, 92(6):1846-1857.
    • (2007) Biophys. J. , vol.92 , Issue.6 , pp. 1846-1857
    • Ederer, M.1    Gilles, E.2
  • 16
    • 78650541419 scopus 로고    scopus 로고
    • Von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
    • Fleming R.M.T., Thiele I. von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics 2011, 27(1):142-143.
    • (2011) Bioinformatics , vol.27 , Issue.1 , pp. 142-143
    • Fleming, R.M.T.1    Thiele, I.2
  • 17
    • 70350560332 scopus 로고    scopus 로고
    • Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli
    • Fleming R.M.T., Thiele I., Nasheuer H.P. Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophys. Chem. 2009, 145(2-3):47-56.
    • (2009) Biophys. Chem. , vol.145 , Issue.2-3 , pp. 47-56
    • Fleming, R.M.T.1    Thiele, I.2    Nasheuer, H.P.3
  • 18
    • 77952643400 scopus 로고    scopus 로고
    • Integrated stoichiometric, thermodynamic and kinetic modeling of steady state metabolism
    • Fleming R.M.T., Thiele I., Provan G., Nasheuer H.P. Integrated stoichiometric, thermodynamic and kinetic modeling of steady state metabolism. J. Theor. Biol. 2010, 264:683-692.
    • (2010) J. Theor. Biol. , vol.264 , pp. 683-692
    • Fleming, R.M.T.1    Thiele, I.2    Provan, G.3    Nasheuer, H.P.4
  • 19
    • 77952573312 scopus 로고    scopus 로고
    • Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling
    • Garg S., Yang L., Mahadevan R. Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling. BMC Res. Notes 2010, 3:125.
    • (2010) BMC Res. Notes , vol.3 , pp. 125
    • Garg, S.1    Yang, L.2    Mahadevan, R.3
  • 20
    • 33847797256 scopus 로고    scopus 로고
    • Thermodynamics-based metabolic flux analysis
    • Henry C.S., Broadbelt L.J., Hatzimanikatis V. Thermodynamics-based metabolic flux analysis. Biophys. J. 2007, 92(5):1792-1805.
    • (2007) Biophys. J. , vol.92 , Issue.5 , pp. 1792-1805
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 21
    • 33645752331 scopus 로고    scopus 로고
    • Genome-scale thermodynamic analysis of Escherichia coli metabolism
    • Henry C.S., Jankowski M.D., Broadbelt L.J., Hatzimanikatis V. Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys. J. 2006, 90(4):1453-1461.
    • (2006) Biophys. J. , vol.90 , Issue.4 , pp. 1453-1461
    • Henry, C.S.1    Jankowski, M.D.2    Broadbelt, L.J.3    Hatzimanikatis, V.4
  • 22
    • 3242795003 scopus 로고    scopus 로고
    • The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
    • Holzhütter H. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur. J. Biochem. 2004, 271(14):2905-2922.
    • (2004) Eur. J. Biochem. , vol.271 , Issue.14 , pp. 2905-2922
    • Holzhütter, H.1
  • 23
    • 42949164125 scopus 로고    scopus 로고
    • Formulating genome-scale kinetic models in the post-genome era
    • Jamshidi N., Palsson B.Ø. Formulating genome-scale kinetic models in the post-genome era. Mol. Syst. Biol. 2008, 4:171.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 171
    • Jamshidi, N.1    Palsson, B.Ø.2
  • 24
    • 51049107514 scopus 로고    scopus 로고
    • Group contribution method for thermodynamic analysis of complex metabolic networks
    • Jankowski M.D., Henry C.S., Broadbelt L.J., Hatzimanikatis V. Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys. J. 2008, 95(3):1487-1499.
    • (2008) Biophys. J. , vol.95 , Issue.3 , pp. 1487-1499
    • Jankowski, M.D.1    Henry, C.S.2    Broadbelt, L.J.3    Hatzimanikatis, V.4
  • 26
    • 33745433792 scopus 로고    scopus 로고
    • Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
    • Kummel A., Panke S., Heinemann M. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol. Syst. Biol. 2006, 2:34.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 34
    • Kummel, A.1    Panke, S.2    Heinemann, M.3
  • 27
    • 77954196484 scopus 로고    scopus 로고
    • Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
    • Liebermeister W., Uhlendorf J., Klipp E. Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation. Bioinformatics 2010, 26(12):1528-1534.
    • (2010) Bioinformatics , vol.26 , Issue.12 , pp. 1528-1534
    • Liebermeister, W.1    Uhlendorf, J.2    Klipp, E.3
  • 29
    • 0000109943 scopus 로고
    • Some general theorems for non-linear systems possessing resistance
    • Millar W. Some general theorems for non-linear systems possessing resistance. Philos. Mag. Ser. 7 1951, 42(333):1150-1160.
    • (1951) Philos. Mag. Ser. 7 , vol.42 , Issue.333 , pp. 1150-1160
    • Millar, W.1
  • 30
    • 34249708861 scopus 로고    scopus 로고
    • Integrated energy and flux balance based multiobjective framework for large-scale metabolic networks
    • Nagrath D., Avila-Elchiver M., Berthiaume F., Tilles A.W., Messac A., Yarmush M.L. Integrated energy and flux balance based multiobjective framework for large-scale metabolic networks. Ann. Biomed. Eng. 2007, 35(6):863-885.
    • (2007) Ann. Biomed. Eng. , vol.35 , Issue.6 , pp. 863-885
    • Nagrath, D.1    Avila-Elchiver, M.2    Berthiaume, F.3    Tilles, A.W.4    Messac, A.5    Yarmush, M.L.6
  • 32
    • 0000058879 scopus 로고
    • Network thermodynamics
    • Oster G., Perelson A., Katchalsky A. Network thermodynamics. Nature 1971, 234(5329):393-399.
    • (1971) Nature , vol.234 , Issue.5329 , pp. 393-399
    • Oster, G.1    Perelson, A.2    Katchalsky, A.3
  • 33
    • 0015111533 scopus 로고
    • Tellegen's theorem and thermodynamic inequalities
    • Oster G.F., Desoer C.A. Tellegen's theorem and thermodynamic inequalities. J. Theor. Biol. 1971, 32(2):219-241.
    • (1971) J. Theor. Biol. , vol.32 , Issue.2 , pp. 219-241
    • Oster, G.F.1    Desoer, C.A.2
  • 35
  • 36
    • 33645461762 scopus 로고    scopus 로고
    • Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints
    • Price N.D., Thiele I., Palsson B.Ø. Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophys. J. 2006, 90:3919-3928.
    • (2006) Biophys. J. , vol.90 , pp. 3919-3928
    • Price, N.D.1    Thiele, I.2    Palsson, B.Ø.3
  • 37
    • 33748107406 scopus 로고    scopus 로고
    • Phosphorylation energy hypothesis: open chemical systems and their biological functions
    • Qian H. Phosphorylation energy hypothesis: open chemical systems and their biological functions. Annu. Rev. Phys. Chem. 2007, 58:113-142.
    • (2007) Annu. Rev. Phys. Chem. , vol.58 , pp. 113-142
    • Qian, H.1
  • 38
    • 17244378347 scopus 로고    scopus 로고
    • Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium
    • Qian H., Beard D.A. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophys. Chem. 2005, 114(2-3):213-220.
    • (2005) Biophys. Chem. , vol.114 , Issue.2-3 , pp. 213-220
    • Qian, H.1    Beard, D.A.2
  • 42
    • 0026516223 scopus 로고
    • Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism
    • Savinell J.M., Palsson B.Ø. Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J. Theor. Biol. 1992, 154(4):421-454.
    • (1992) J. Theor. Biol. , vol.154 , Issue.4 , pp. 421-454
    • Savinell, J.M.1    Palsson, B.Ø.2
  • 43
    • 79551676901 scopus 로고    scopus 로고
    • Elimination of thermodynamically infeasible loops in steady-state metabolic models
    • Schellenberger J., Lewis N.E., Palsson B.Ø. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys. J. 2011, 100(3):544-553.
    • (2011) Biophys. J. , vol.100 , Issue.3 , pp. 544-553
    • Schellenberger, J.1    Lewis, N.E.2    Palsson, B.Ø.3
  • 45
    • 77952952952 scopus 로고    scopus 로고
    • Network thermodynamics in the post-genomic era
    • Soh K., Hatzimanikatis V. Network thermodynamics in the post-genomic era. Curr. Opin. Microbiol. 2010, 13(3):350-357.
    • (2010) Curr. Opin. Microbiol. , vol.13 , Issue.3 , pp. 350-357
    • Soh, K.1    Hatzimanikatis, V.2
  • 47
    • 63549148162 scopus 로고    scopus 로고
    • Genome-scale reconstruction of E. coli's transcriptional and translational machinery: a knowledge-base, its mathematical formulation, and its functional characterization
    • Thiele I., Jamshidi N., Fleming R.M.T., Palsson B.Ø. Genome-scale reconstruction of E. coli's transcriptional and translational machinery: a knowledge-base, its mathematical formulation, and its functional characterization. PLoS Comput. Biol. 2009, 5(3):e1000312.
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.3
    • Thiele, I.1    Jamshidi, N.2    Fleming, R.M.T.3    Palsson, B.Ø.4
  • 48
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I., Palsson B.Ø. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc. 2010, 5:93-121.
    • (2010) Nat. Protoc. , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.Ø.2
  • 49
    • 34548567437 scopus 로고    scopus 로고
    • Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism
    • Warren P.B., Jones J.L. Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism. Phys. Rev. Lett. 2007, 99(10):108101.
    • (2007) Phys. Rev. Lett. , vol.99 , Issue.10 , pp. 108101
    • Warren, P.B.1    Jones, J.L.2
  • 50
    • 49549090451 scopus 로고    scopus 로고
    • Optimization of productivity and thermodynamic performance of metabolic pathways
    • Xu M., Smith R., Sadhukhan J. Optimization of productivity and thermodynamic performance of metabolic pathways. Ind. Eng. Chem. Res. 2008, 47(15):5669-5679.
    • (2008) Ind. Eng. Chem. Res. , vol.47 , Issue.15 , pp. 5669-5679
    • Xu, M.1    Smith, R.2    Sadhukhan, J.3
  • 51
    • 24044514673 scopus 로고    scopus 로고
    • Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry
    • Yang F., Qian H., Beard D.A. Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry. Metab. Eng. 2005, 7(4):251-259.
    • (2005) Metab. Eng. , vol.7 , Issue.4 , pp. 251-259
    • Yang, F.1    Qian, H.2    Beard, D.A.3
  • 52
    • 0004212716 scopus 로고    scopus 로고
    • Interscience Series in Discrete Mathematics and Optimization, Wiley, New York
    • Ye Y. Interior Point Algorithms: Theory and Analysis 1997, Interscience Series in Discrete Mathematics and Optimization, Wiley, New York.
    • (1997) Interior Point Algorithms: Theory and Analysis
    • Ye, Y.1


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