Esposito, Massimiliano ; University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Physics and Materials Science (DPHYMS)
External co-authors :
no
Language :
English
Title :
Free-energy transduction in chemical reaction networks: From enzymes to metabolism
X. Yang, M. Heinemann, J. Howard, G. Huber, S. Iyer-Biswas, G. L. Treut, M. Lynch, K. L. Montooth, D. J. Needleman, S. Pigolotti, J. Rodenfels, P. Ronceray, S. Shankar, I. Tavassoly, S. Thutupalli, D. V. Titov, J. Wang, and P. J. Foster, "Physical bioenergetics: Energy fluxes, budgets, and constraints in cells," Proc. Natl. Acad. Sci. U. S. A. 118, e2026786118 (2021). 10.1073/pnas.2026786118
D. Nelson and M. Cox, Lehninger Principles of Biochemistry (W. H. Freeman, 2008).
D. Voet, J. G. Voet, and C. W. Pratt, Fundamentals of Biochemistry (Wiley, 2016).
A. Bejan, Advanced Engineering Thermodynamics (John Wiley & Sons, 2016).
T. L. Hill, Free Energy Transduction in Biology: The Steady-State Kinetic and Thermodynamic Formalism (Academic Press, New York, 1977).
A. Wachtel, R. Rao, and M. Esposito, "Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis-Menten," New J. Phys. 20, 042002 (2018). 10.1088/1367-2630/aab5c9
F. Jülicher, A. Ajdari, and J. Prost, "Modeling molecular motors," Rev. Mod. Phys. 69, 1269 (1997). 10.1103/revmodphys.69.1269
A. Parmeggiani, F. Jülicher, A. Ajdari, and J. Prost, "Energy transduction of isothermal ratchets: Generic aspects and specific examples close to and far from equilibrium," Phys. Rev. E 60, 2127 (1999). 10.1103/physreve.60.2127
J. M. R. Parrondo and B. J. de Cisneros, "Energetics of Brownian motors: A review," Appl. Phys. A 75, 179 (2002). 10.1007/s003390201332
U. Seifert, "Stochastic thermodynamics, fluctuation theorems and molecular machines," Rep. Prog. Phys. 75, 126001 (2012). 10.1088/0034-4885/75/12/126001
A. I. Brown and D. A. Sivak, "Theory of nonequilibrium free energy transduction by molecular machines," Chem. Rev. 120, 434 (2020). 10.1021/acs.chemrev.9b00254
S. Amano, M. Esposito, E. Kreidt, D. A. Leigh, E. Penocchio, and B. M. W. Roberts, "Insights from an information thermodynamics analysis of a synthetic molecular motor," Nat. Chem. 14, 530 (2022). 10.1038/s41557-022-00899-z
J. Schnakenberg, "Network theory of microscopic and macroscopic behavior of master equation systems," Rev. Mod. Phys. 48, 571 (1976). 10.1103/revmodphys.48.571
D. Andrieux and P. Gaspard, "Fluctuation theorem for currents and Schnakenberg network theory," J. Stat. Phys. 127, 107 (2007). 10.1007/s10955-006-9233-5
M. Polettini and M. Esposito, "Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws," J. Chem. Phys. 141, 024117 (2014). 10.1063/1.4886396
R. Rao and M. Esposito, "Nonequilibrium thermodynamics of chemical reaction networks: Wisdom from stochastic thermodynamics," Phys. Rev. X 6, 041064 (2016). 10.1103/physrevx.6.041064
F. Avanzini, G. Falasco, and M. Esposito, "Thermodynamics of non-elementary chemical reaction networks," New J. Phys. 22, 093040 (2020). 10.1088/1367-2630/abafea
F. Avanzini, E. Penocchio, G. Falasco, and M. Esposito, "Nonequilibrium thermodynamics of non-ideal chemical reaction networks," J. Chem. Phys. 154, 094114 (2021). 10.1063/5.0041225
R. A. Alberty, Thermodynamics of Biochemical Reactions (Wiley-Interscience, 2003).
F. Horn and R. Jackson, "General mass action kinetics," Arch. Ration. Mech. Anal. 47, 81 (1972). 10.1007/bf00251225
S. Schuster and R. Schuster, "A generalization of Wegscheider's condition. Implications for properties of steady states and for quasi-steady-state approximation," J. Math. Chem. 3, 25 (1989). 10.1007/bf01171883
F. Avanzini and M. Esposito, "Thermodynamics of concentration vs flux control in chemical reaction networks," J. Chem. Phys. 156, 014116 (2022). 10.1063/5.0076134
G. Falasco, R. Rao, and M. Esposito, "Information thermodynamics of Turing patterns," Phys. Rev. Lett. 121, 108301 (2018). 10.1103/physrevlett.121.108301
E. Penocchio, R. Rao, and M. Esposito, "Thermodynamic efficiency in dissipative chemistry," Nat. Commun. 10, 3865 (2019). 10.1038/s41467-019-11676-x
D. A. Beard, S.-d. Liang, and H. Qian, "Energy balance for analysis of complex metabolic networks," Biophys. J. 83, 79 (2002). 10.1016/s0006-3495(02)75150-3
F. Yang, H. Qian, and D. A. Beard, "Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry," Metab. Eng. 7, 251 (2005). 10.1016/j.ymben.2005.03.002
B. Ø. Palsson, Systems Biology: Constraint-Based Network Reconstruction and Analysis (Cambridge University Press, 2015).
B. Niebel, S. Leupold, and M. Heinemann, "An upper limit on Gibbs energy dissipation governs cellular metabolism," Nat. Metab. 1, 125 (2019). 10.1038/s42255-018-0006-7
J. Saldida, A. P. Muntoni, D. de Martino, G. Hubmann, B. Niebel, A. M. Schmidt, A. Braunstein, A. Milias-Argeitis, and M. Heinemann, "Unbiased metabolic flux inference through combined thermodynamic and 13C flux analysis," bioRxiv:2020.06.29.177063 (2020).
O. Oftadeh, P. Salvy, M. Masid, M. Curvat, L. Miskovic, and V. Hatzimanikatis, "A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics," Nat. Commun. 12, 4790 (2021). 10.1038/s41467-021-25158-6
A. Akbari, J. T. Yurkovich, D. C. Zielinski, and B. O. Palsson, "The quantitative metabolome is shaped by abiotic constraints," Nat. Commun. 12, 3178 (2021). 10.1038/s41467-021-23214-9
A. Bar-Even, A. Flamholz, E. Noor, and R. Milo, "Thermodynamic constraints shape the structure of carbon fixation pathways," Biochim. Biophys. Acta, Bioenerg. 1817, 1646 (2012). 10.1016/j.bbabio.2012.05.002
E. Noor, A. Bar-Even, A. Flamholz, E. Reznik, W. Liebermeister, and R. Milo, "Pathway thermodynamics highlights kinetic obstacles in central metabolism," PLoS Comput. Biol. 10, e1003483 (2014). 10.1371/journal.pcbi.1003483
E. Noor, H. S. Haraldsdóttir, R. Milo, and R. M. Fleming, "Consistent estimation of Gibbs energy using component contributions," PLoS Comput. Biol. 9, e1003098 (2013). 10.1371/journal.pcbi.1003098
