MAREHALLI SRINIVAS, Shesha Gopal ; University of Luxembourg > Faculty of Science, Technology and Medicine > Department of Physics and Materials Science
AVANZINI, Francesco ; University of Luxembourg > Faculty of Science, Technology and Medicine > Department of Physics and Materials Science > Team Massimiliano ESPOSITO
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 :
Characterizing the conditions for indefinite growth in open chemical reaction networks
P. Gaspard, Fluctuation theorem for nonequilibrium reactions, J. Chem. Phys. 120, 8898 (2004) 0021-9606 10.1063/1.1688758.
D. Andrieux and P. Gaspard, Fluctuation theorem and mesoscopic chemical clocks, J. Chem. Phys. 128, 154506 (2008) 0021-9606 10.1063/1.2894475.
P. Gaspard, Stochastic approach to entropy production in chemical chaos, Chaos 30, 113103 (2020) 1054-1500 10.1063/5.0025350.
S. G. Marehalli Srinivas, M. Polettini, M. Esposito, and F. Avanzini, Deficiency, kinetic invertibility, and catalysis in stochastic chemical reaction networks, J. Chem. Phys. 158, 204108 (2023) 0021-9606 10.1063/5.0147283.
G. Falasco, R. Rao, and M. Esposito, Information thermodynamics of turing patterns, Phys. Rev. Lett. 121, 108301 (2018) 0031-9007 10.1103/PhysRevLett.121.108301.
F. Avanzini, G. Falasco, and M. Esposito, Chemical cloaking, Phys. Rev. E 101, 060102 (R) (2020) 2470-0045 10.1103/PhysRevE.101.060102.
T. Aslyamov, F. Avanzini, E. Fodor, and M. Esposito, Nonideal reaction-diffusion systems: Multiple routes to instability, Phys. Rev. Lett. 131, 138301 (2023) 0031-9007 10.1103/PhysRevLett.131.138301.
F. Avanzini, G. Falasco, and M. Esposito, Thermodynamics of chemical waves, J. Chem. Phys. 151, 234103 (2019) 0021-9606 10.1063/1.5126528.
P. Kumar and G. Gangopadhyay, Nonequilibrium thermodynamics of glycolytic traveling wave: Benjamin-Feir instability, Phys. Rev. E 104, 014221 (2021) 2470-0045 10.1103/PhysRevE.104.014221.
H. Qian and D. A. Beard, Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium, Biophys. Chem. 114, 213 (2005) 0301-4622 10.1016/j.bpc.2004.12.001.
T. Schmiedl and U. Seifert, Stochastic thermodynamics of chemical reaction networks, J. Chem. Phys. 126, 044101 (2007) 0021-9606 10.1063/1.2428297.
M. Polettini and M. Esposito, Irreversible thermodynamics of open chemical networks. I. emergent cycles and broken conservation laws, J. Chem. Phys. 141, 024117 (2014) 0021-9606 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) 2160-3308 10.1103/PhysRevX.6.041064.
R. Rao and M. Esposito, Conservation laws and work fluctuation relations in chemical reaction networks, J. Chem. Phys. 149, 245101 (2018) 0021-9606 10.1063/1.5042253.
F. Avanzini, E. Penocchio, G. Falasco, and M. Esposito, Nonequilibrium thermodynamics of non-ideal chemical reaction networks, J. Chem. Phys. 154, 094114 (2021) 0021-9606 10.1063/5.0041225.
F. Avanzini and M. Esposito, Thermodynamics of concentration vs flux control in chemical reaction networks, J. Chem. Phys. 156, 014116 (2022) 0021-9606 10.1063/5.0076134.
X. Yang, M. Heinemann, J. Howard, G. Huber, S. Iyer-Biswas, G. L. Treut, M. Lynch, K. L. Montooth, D. J. Needleman, S. Pigolotti, Physical bioenergetics: Energy fluxes, budgets, and constraints in cells, Proc. Natl. Acad. Sci. USA 118, e2026786118 (2021) 0027-8424 10.1073/pnas.2026786118.
J. J. Heijnen and J. P. Van Dijken, In search of a thermodynamic description of biomass yields for the chemotrophic growth of microorganisms, Biotechnol. Bioeng. 39, 833 (1992) 0006-3592 10.1002/bit.260390806.
D. Deamer and A. L. Weber, Bioenergetics and life's origins, Cold Spring Harbor Persp. Biol. 2, a004929 (2010) 1943-0264 10.1101/cshperspect.a004929.
P. Adamski, M. Eleveld, A. Sood, Á. Kun, A. Szilágyi, T. Czárán, E. Szathmáry, and S. Otto, From self-replication to replicator systems en route to de novo life, Nat. Rev. Chem. 4, 386 (2020) 2397-3358 10.1038/s41570-020-0196-x.
P. L. Luisi, The Emergence of Life: From Chemical Origins to Synthetic Biology (Cambridge University Press, New York, 2006).
E. Smith and H. J. Morowitz, The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere (Cambridge University Press, Cambridge, 2016).
W.-H. Lin, E. Kussell, L.-S. Young, and C. Jacobs-Wagner, Origin of exponential growth in nonlinear reaction networks, Proc. Natl. Acad. Sci. USA 117, 27795 (2020) 0027-8424 10.1073/pnas.2013061117.
E. Szathmáry, Simple growth laws and selection consequences, Trends Ecol. Evol. 6, 366 (1991) 0169-5347 10.1016/0169-5347(91)90228-P.
P. R. Wills, S. A. Kauffman, B. M. Stadler, and P. F. Stadler, Selection dynamics in autocatalytic systems: Templates replicating through binary ligation, Bull. Math. Biol. 60, 1073 (1998) 0092-8240 10.1016/S0092-8240(98)90003-9.
S. Iyer-Biswas, G. E. Crooks, N. F. Scherer, and A. R. Dinner, Universality in stochastic exponential growth, Phys. Rev. Lett. 113, 028101 (2014) 0031-9007 10.1103/PhysRevLett.113.028101.
D. Angeli, P. D. Leenheer, and E. Sontag, Chemical networks with inflows and outflows: A positive linear differential inclusions approach, Biotech. Prog. 25, 632 (2009) 8756-7938 10.1002/btpr.162.
P. Nandori and L.-S. Young, Growth and depletion in linear stochastic reaction networks, Proc. Natl. Acad. Sci. USA 119, e2214282119 (2022) 0027-8424 10.1073/pnas.2214282119.
S. G. M. Srinivas, F. Avanzini, and M. Esposito, companion paper, Thermodynamics of growth in open chemical reaction networks, Phys. Rev. Lett. 132, 268001 (2024) 10.1103/PhysRevLett.132.268001.
G. Svehla, Nomenclature of kinetic methods of analysis (IUPAC recommendations 1993), Pure Appl. Chem. 65, 2291 (1993) 1365-3075 10.1351/pac199365102291.
A. Cornish-Bowden, Fundamentals of Enzyme Kinetics (Wiley-Blackwell, Weinheim, 2004).
R. Aris, Elementary Chemical Reactor Analysis (Butterworth-Heinemann, Boston, 1989), pp. 156-228.
K. Liu, A. Blokhuis, C. van Ewijk, A. Kiani, J. Wu, W. H. Roos, and S. Otto, Light-driven eco-evolutionary dynamics in a synthetic replicator system, Nat. Chem. 16, 79 (2024) 1755-4330 10.1038/s41557-023-01301-2.
Edited by U. van Stockar and L. A. M. van der Wielen, Biothermodynamics: The Role of Thermodynamics in Biochemical Engineering (EPFL Press, New York, 2013).
A. Sorrenti, J. Leira-Iglesias, A. Sato, and T. M. Hermans, Non-equilibrium steady states in supramolecular polymerization, Nat. Commun. 8, 15899 (2017) 2041-1723 10.1038/ncomms15899.
F. Avanzini, G. Falasco, and M. Esposito, Thermodynamics of non-elementary chemical reaction networks, New J. Phys. 22, 093040 (2020) 1367-2630 10.1088/1367-2630/abafea.
F. Avanzini, N. Freitas, and M. Esposito, Circuit theory for chemical reaction networks, Phys. Rev. X 13, 021041 (2023) 2160-3308 10.1103/PhysRevX.13.021041.
A. Blokhuis, D. Lacoste, and P. Gaspard, Reaction kinetics in open reactors and serial transfers between closed reactors, J. Chem. Phys. 148, 144902 (2018) 0021-9606 10.1063/1.5022697.
N. G. Van Kampen, Stochastic Processes in Physics and Chemistry (North Holland, 2007).
T. Tomé and M. J. De Oliveira, Stochastic Dynamics and Irreversibility, Graduate Texts in Physics (Springer International Publishing, Cham, 2015), pp. 159-163.
E. Penocchio, R. Rao, and M. Esposito, Thermodynamic efficiency in dissipative chemistry, Nat. Commun. 10, 3865 (2019) 2041-1723 10.1038/s41467-019-11676-x.
D. F. Anderson, Boundedness of trajectories for weakly reversible, single linkage class reaction systems, J. Math. Chem. 49, 2275 (2011) 0259-9791 10.1007/s10910-011-9886-4.
M. Feinberg, Foundations of Chemical Reaction Network Theory (Springer, Cham, 2019), pp. 79-80.
M. Gopalkrishnan, E. Miller, and A. Shiu, A geometric approach to the global attractor conjecture, SIAM J. Appl. Dyn. 13, 758 (2014) 1536-0040 10.1137/130928170.
B. E. Meserve, Fundamental Concepts of Algebra (Addison-Wesley, Cambridge, MA, 1953), pp. 156-158.
T. L. Hill, Studies in irreversible thermodynamics IV. Diagrammatic representation of steady state fluxes for unimolecular systems, J. Theor. Biol. 10, 442 (1966) 0022-5193 10.1016/0022-5193(66)90137-8.
A. Wachtel, R. Rao, and M. Esposito, Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis-Menten, New J. Phys. 20, 042002 (2018) 1367-2630 10.1088/1367-2630/aab5c9.
K. Eckel-Mahan and P. Sassone-Corsi, Metabolism and the circadian clock converge, Physiol. Rev. 93, 107 (2013) 0031-9333 10.1152/physrev.00016.2012.
M. J. Berridge, P. Lipp, and M. D. Bootman, The versatility and universality of calcium signalling, Nat. Rev. Mol. Cell Biol. 1, 11 (2000) 1471-0072 10.1038/35036035.
E. Bigan, J. Steyaert, and S. Douady, On necessary and sufficient conditions for proto-cell stationary growth, Electron. Notes Theor. Comput. Sci. 316, 3 (2015) 1571-0661 10.1016/j.entcs.2015.06.007, 5th International Workshop on Static Analysis and Systems Biology (SASB 2014).
Y. Kondo and K. Kaneko, Growth states of catalytic reaction networks exhibiting energy metabolism, Phys. Rev. E 84, 011927 (2011) 1539-3755 10.1103/PhysRevE.84.011927.
Y. Sughiyama, A. Kamimura, D. Loutchko, and T. J. Kobayashi, Chemical thermodynamics for growing systems, Phys. Rev. Res. 4, 033191 (2022) 2643-1564 10.1103/PhysRevResearch.4.033191.
A. Kamimura, Y. Sughiyama, and T. J. Kobayashi, Thermodynamic and stoichiometric laws ruling the fates of growing systems, Phys. Rev. Res. 6, 023173 (2024) 2643-1564 10.1103/PhysRevResearch.6.023173.
J. Unterberger and P. Nghe, Stoechiometric and dynamical autocatalysis for diluted chemical reaction networks, J. Math. Biol. 85, 26 (2022) 0303-6812 10.1007/s00285-022-01798-0.
S. Sarkar and J. L. England, Design of conditions for self-replication, Phys. Rev. E 100, 022414 (2019) 2470-0045 10.1103/PhysRevE.100.022414.
R. Rao, D. Lacoste, and M. Esposito, Glucans monomer-exchange dynamics as an open chemical network, J. Chem. Phys. 143, 244903 (2015) 0021-9606 10.1063/1.4938009.
A. Sharko, D. Livitz, S. De Piccoli, K. J. M. Bishop, and T. M. Hermans, Insights into chemically fueled supramolecular polymers, Chem. Rev. 122, 11759 (2022) 0009-2665 10.1021/acs.chemrev.1c00958.
R. Horn and C. Johnson, Matrix Analysis (Cambridge University Press, Cambridge, 2013).
O. Taussky, A recurring theorem on determinants, Am. Math. Month. 56, 672 (1949) 0002-9890 10.1080/00029890.1949.11990209.
D. Andrieux, Spectral signature of nonequilibrium conditions, arXiv:1103.2243 [cond-mat.stat-mech].
M. Polettini, Fisher information of Markovian decay modes, Eur. Phys. J. B 87, 215 (2014) 1434-6028 10.1140/epjb/e2014-50142-1.
L. Perko, Differential Equations and Dynamical Systems (Springer, New York, 2014).
C. D. Meyer, Matrix Analysis and Applied Linear Algebra (Society for Industrial and Applied Mathematics, Philadelphia, 2001), p. 123.