AVANZINI, Francesco ; University of Luxembourg > Faculty of Science, Technology and Medicine > Department of Physics and Materials Science > Team Massimiliano ESPOSITO
ASLYAMOV, Timur ; University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Physics and Materials Science (DPHYMS)
Fodor, Étienne
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 :
Nonequilibrium thermodynamics of non-ideal reaction–diffusion systems: Implications for active self-organization
J. W. Cahn and J. E. Hilliard, “ Free energy of a nonuniform system. I. Interfacial free energy,” J. Chem. Phys. 28, 258- 267 ( 1958). 10.1063/1.1744102
A. J. Bray, “ Theory of phase-ordering kinetics,” Adv. Phys. 43, 357- 459 ( 1994). 10.1080/00018739400101505
M. L. Huggins, “ Solutions of long chain compounds,” J. Chem. Phys. 9, 440 ( 1941). 10.1063/1.1750930
P. J. Flory, “ Thermodynamics of high polymer solutions,” J. Chem. Phys. 10, 51- 61 ( 1942). 10.1063/1.1723621
A. M. Turing, “ The chemical basis of morphogenesis,” Philos. Trans. R. Soc., B 237, 37- 72 ( 1952). 10.1098/rstb.1952.0012
I. Prigogine and G. Nicolis, “ Biological order, structure and instabilities,” Q. Rev. Biophys. 4, 107- 148 ( 1971). 10.1017/s0033583500000615
G. Nicolis and I. Prigogine, Self-organization in Nonequilibrium Systems: From Dissipative Structures to Order through Fluctuations ( Wiley-Blackwell, 1977).
R. Lefever, “ The rehabilitation of irreversible processes and dissipative structures’ 50th anniversary,” Philos. Trans. R. Soc., A 376, 20170365 ( 2018). 10.1098/rsta.2017.0365
V. Castets, E. Dulos, J. Boissonade, and P. De Kepper, “ Experimental evidence of a sustained standing turing-type nonequilibrium chemical pattern,” Phys. Rev. Lett. 64, 2953 ( 1990). 10.1103/physrevlett.64.2953
G. Falasco, R. Rao, and M. Esposito, “ Information thermodynamics of turing patterns,” Phys. Rev. Lett. 121, 108301 ( 2018). 10.1103/physrevlett.121.108301
F. Avanzini, G. Falasco, and M. Esposito, “ Thermodynamics of chemical waves,” J. Chem. Phys. 151, 234103 ( 2019). 10.1063/1.5126528
F. Avanzini, G. Falasco, and M. Esposito, “ Chemical cloaking,” Phys. Rev. E 101, 060102 ( 2020). 10.1103/physreve.101.060102
L. A. Segel and J. L. Jackson, “ Dissipative structure: An explanation and an ecological example,” J. Theor. Biol. 37, 545- 559 ( 1972). 10.1016/0022-5193(72)90090-2
X. Wang and F. Lutscher, “ Turing patterns in a predator-prey model with seasonality,” J. Math. Biol. 78, 711- 737 ( 2019). 10.1007/s00285-018-1289-8
M. Rietkerk and J. van de Koppel, “ Regular pattern formation in real ecosystems,” Trends Ecol. Evol. 23, 169- 175 ( 2008). 10.1016/j.tree.2007.10.013
D. Ruiz-Reynés, D. Gomila, T. Sintes, E. Hernández-García, N. Marbà, and C. M. Duarte, “ Fairy circle landscapes under the sea,” Sci. Adv. 3, e1603262 ( 2017). 10.1126/sciadv.1603262
M. Cross and H. Greenside, Pattern Formation and Dynamics in Nonequilibrium Systems ( Cambridge University Press, 2009).
S. F. Banani, H. O. Lee, A. A. Hyman, and M. K. Rosen, “ Biomolecular condensates: Organizers of cellular biochemistry,” Nat. Rev. Mol. Cell Biol. 18, 285- 298 ( 2017). 10.1038/nrm.2017.7
A. S. Lyon, W. B. Peeples, and M. K. Rosen, “ A framework for understanding the functions of biomolecular condensates across scales,” Nat. Rev. Mol. Cell Biol. 22, 215- 235 ( 2021). 10.1038/s41580-020-00303-z
A. Klosin, F. Oltsch, T. Harmon, A. Honigmann, F. Julicher, A. A. Hyman, and C. Zechner, “ Phase separation provides a mechanism to reduce noise in cells,” Science 367, 464- 468 ( 2020). 10.1126/science.aav6691
M. Castellana, M. Z. Wilson, Y. Xu, P. Joshi, I. M. Cristea, J. D. Rabinowitz, Z. Gitai, and N. S. Wingreen, “ Enzyme clustering accelerates processing of intermediates through metabolic channeling,” Nat. Biotechnol. 32, 1011- 1018 ( 2014). 10.1038/nbt.3018
W. Peeples and M. K. Rosen, “ Phase separation can increase enzyme activity by concentration and molecular organization,” bioRxiv:10.1101/2020.09.15.299115 ( 2020).
F. Frottin, F. Schueder, S. Tiwary, R. Gupta, R. Körner, T. Schlichthaerle, J. Cox, R. Jungmann, F. U. Hartl, and M. S. Hipp, “ The nucleolus functions as a phase-separated protein quality control compartment,” Science 365, 342- 347 ( 2019). 10.1126/science.aaw9157
L. Demarchi, A. Goychuk, I. Maryshev, and E. Frey, “ Enzyme-enriched condensates show self-propulsion, positioning, and coexistence,” Phys. Rev. Lett. 130, 128401 ( 2023). 10.1103/physrevlett.130.128401
S. C. Glotzer, E. A. Di Marzio, and M. Muthukumar, “ Reaction-controlled morphology of phase-separating mixtures,” Phys. Rev. Lett. 74, 2034 ( 1995). 10.1103/physrevlett.74.2034
F. Brauns, J. Halatek, and E. Frey, “ Phase-space geometry of mass-conserving reaction-diffusion dynamics,” Phys. Rev. X 10, 041036 ( 2020). 10.1103/physrevx.10.041036
P. A. Haas and R. E. Goldstein, “ Turing’s diffusive threshold in random reaction-diffusion systems,” Phys. Rev. Lett. 126, 238101 ( 2021). 10.1103/physrevlett.126.238101
J. Berry, C. P. Brangwynne, and M. Haataja, “ Physical principles of intracellular organization via active and passive phase transitions,” Rep. Prog. Phys. 81, 046601 ( 2018). 10.1088/1361-6633/aaa61e
C. A. Weber, D. Zwicker, F. Julicher, and C. F. Lee, “ Physics of active emulsions,” Rep. Prog. Phys. 82, 064601 ( 2019). 10.1088/1361-6633/ab052b
D. Zwicker, “ The intertwined physics of active chemical reactions and phase separation,” Curr. Opin. Colloid Interface Sci. 61, 101606 ( 2022). 10.1016/j.cocis.2022.101606
J. Kirschbaum and D. Zwicker, “ Controlling biomolecular condensates via chemical reactions,” J. R. Soc. Interface 18, 20210255 ( 2021). 10.1098/rsif.2021.0255
J. Bauermann, C. A. Weber, and F. Julicher, “ Energy and matter supply for active droplets,” Ann. Phys. 534, 2200132 ( 2022). 10.1002/andp.202200132
T. Aslyamov, F. Avanzini, E. Fodor, and M. Esposito, “ Nonideal reaction-diffusion systems: Multiple routes to instability,” Phys. Rev. Lett. 131, 138301 ( 2023). 10.1103/physrevlett.131.138301
H. Othmer, “ Nonuniqueness of equilibria in closed reacting systems,” Chem. Eng. Sci. 31, 993- 1003 ( 1976). 10.1016/0009-2509(76)87020-0
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
S. Klamt, U.-U. Haus, and F. Theis, “ Hypergraphs and cellular networks,” PLoS Comput. Biol. 5, e1000385- e1000386 ( 2009). 10.1371/journal.pcbi.1000385
M. Feinberg, “ Chemical reaction network structure and the stability of complex isothermal reactors—I. The deficiency zero and deficiency one theorems,” Chem. Eng. Sci. 42, 2229- 2268 ( 1987). 10.1016/0009-2509(87)80099-4
G. Craciun, Y. Tang, and M. Feinberg, “ Understanding bistability in complex enzyme-driven reaction networks,” Proc. Natl. Acad. Sci. U. S. A. 103, 8697- 8702 ( 2006). 10.1073/pnas.0602767103
D. K. Lubensky, “ Equilibriumlike behavior in chemical reaction networks far from equilibrium,” Phys. Rev. E 81, 060102 ( 2010). 10.1103/physreve.81.060102
D. F. Anderson, G. Craciun, M. Gopalkrishnan, and C. Wiuf, “ Lyapunov functions, stationary distributions, and non-equilibrium potential for reaction networks,” Bull. Math. Biol. 77, 1744- 1767 ( 2015). 10.1007/s11538-015-0102-8
M. Polettini, A. Wachtel, and M. Esposito, “ Dissipation in noisy chemical networks: The role of deficiency,” J. Chem. Phys. 143, 184103 ( 2015). 10.1063/1.4935064
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). 10.1063/5.0147283
G. Falasco and M. Esposito, “ Macroscopic stochastic thermodynamics,” arXiv:2307.12406 [cond-mat.stat-mech] ( 2024).
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, M. Bilancioni, V. Cavina, S. Dal Cengio, M. Esposito, G. Falasco, D. Forastiere, N. Freitas, A. Garilli, P. E. Harunari, V. Lecomte, A. Lazarescu, S. G. Marehalli Srinivas, C. Moslonka, I. Neri, E. Penocchio, W. D. Piñeros, M. Polettini, A. Raghu, P. Raux, K. Sekimoto, and A. Soret, “ Methods and conversations in (post)modern thermodynamics,” SciPost Phys. Lect. Notes 80 ( 2024). 10.21468/scipostphyslectnotes.80
L. Peliti and S. Pigolotti, Stochastic Thermodynamics: An Introduction ( Princeton University Press, 2021).
R. Rao and M. Esposito, “ Conservation laws and work fluctuation relations in chemical reaction networks,” J. Chem. Phys. 149, 245101 ( 2018). 10.1063/1.5042253
S. R. de Groot and P. Mazur, Non-Equilibrium Thermodynamics ( Dover, 1984).
J. Ross, K. L. C. Hunt, and P. M. Hunt, “ Thermodynamic and stochastic theory for nonequilibrium systems with multiple reactive intermediates: The concept and role of excess work,” J. Chem. Phys. 96, 618- 629 ( 1992). 10.1063/1.462445
J. Ross and X. Chu, “ Thermodynamic and stochastic theory for nonideal systems far from equilibrium,” J. Chem. Phys. 98, 9765- 9770 ( 1993). 10.1063/1.464355
K. J. Laidler, Chemical Kinetics ( Harper Collins Publishers, 1987).
M. Pekař, “ Thermodynamics and foundations of mass-action kinetics,” Prog. React. Kinet. Mech. 30, 3- 113 ( 2005). 10.3184/007967405777874868
D. F. Anderson, G. Craciun, and T. G. Kurtz, “ Product-form stationary distributions for deficiency zero chemical reaction networks,” Bull. Math. Biol. 72, 1947- 1970 ( 2010). 10.1007/s11538-010-9517-4
D. Cappelletti and C. Wiuf, “ Product-form Poisson-like distributions and complex balanced reaction systems,” SIAM J. Appl. Math. 76, 411- 432 ( 2016). 10.1137/15m1029916
D. F. Anderson, “ A short note on the Lyapunov function for complex-balanced chemical reaction networks,” https://people.math.wisc.edu/~dfanderson/CRNT_Lyapunov.pdf ( 2014).
A. M. Miangolarra and M. Castellana, “ On non-ideal chemical-reaction networks and phase separation,” J. Stat. Phys. 190, 23 ( 2023). 10.1007/s10955-022-03037-8
D. Zwicker, “ py-pde: A python package for solving partial differential equations,” J. Open Source Softw. 5, 2158 ( 2020). 10.21105/joss.02158
S. Saha, J. Agudo-Canalejo, and R. Golestanian, “ Scalar active mixtures: The nonreciprocal Cahn-Hilliard model,” Phys. Rev. X 10, 041009 ( 2020). 10.1103/physrevx.10.041009
E. Ilker and J.-F. m. c. Joanny, “ Phase separation and nucleation in mixtures of particles with different temperatures,” Phys. Rev. Res. 2, 023200 ( 2020). 10.1103/physrevresearch.2.023200
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, N. Freitas, and M. Esposito, “ Circuit theory for chemical reaction networks,” Phys. Rev. X 13, 021041 ( 2023). 10.1103/physrevx.13.021041
R. Tiani and U. C. Täuber, “ Stochastic analysis of chemical reactions in multi-component interacting systems at criticality,” Europhys. Lett. 144, 11005 ( 2023). 10.1209/0295-5075/acff15
L. Menou, C. Luo, and D. Zwicker, “ Physical interactions in non-ideal fluids promote turing patterns,” J. R. Soc. Interface 20, 20230244 ( 2023). 10.1098/rsif.2023.0244
C. Luo and D. Zwicker, “ Influence of physical interactions on spatiotemporal patterns,” Phys. Rev. E 108, 034206 ( 2023). 10.1103/physreve.108.034206
P. Gaspard and R. Kapral, “ Thermodynamics and statistical mechanics of chemically powered synthetic nanomotors,” Adv. Phys.: X 4, 1602480 ( 2019). 10.1080/23746149.2019.1602480
T. Markovich, E. Fodor, E. Tjhung, and M. E. Cates, “ Thermodynamics of active field theories: Energetic cost of coupling to reservoirs,” Phys. Rev. X 11, 021057 ( 2021). 10.1103/physrevx.11.021057
É. Fodor, R. L. Jack, and M. E. Cates, “ Irreversibility and biased ensembles in active matter: Insights from stochastic thermodynamics,” Annu. Rev. Condens. Matter Phys. 13, 215- 238 ( 2022). 10.1146/annurev-conmatphys-031720-032419
R. Bebon, J. F. Robinson, and T. Speck, “ Thermodynamics of active matter: Tracking dissipation across scales,” arXiv:2401.02252 [cond-mat.soft] ( 2024).
M. Chatzittofi, J. Agudo-Canalejo, and R. Golestanian, “ Entropy production and thermodynamic inference for stochastic microswimmers,” Phys. Rev. Res. 6, L022044 ( 2024). 10.1103/physrevresearch.6.l022044
