BILANCIONI, Massimo ; 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 :
yes
Language :
English
Title :
Gears in chemical reaction networks for optimizing energy transduction efficiency
Hill, T. L. Free Energy Transduction in Biology (Academic Press, 1977).
A. Wachtel R. Rao M. Esposito Free-energy transduction in chemical reaction networks: From enzymes to metabolism J. Chem. Phys. 157 024109 2022JChPh.157b4109W 1:CAS:528:DC%2BB38XhvVWktbzL 10.1063/5.0091035 35840395
F. Jülicher A. Ajdari J. Prost Modeling molecular motors Rev. Mod. Phys. 69 1269 1997RvMP..69.1269J 10.1103/RevModPhys.69.1269
A.I. Brown D.A. Sivak Theory of nonequilibrium free energy transduction by molecular machines Chem. Rev. 120 434 1:CAS:528:DC%2BC1MXhsFKgs7%2FO 10.1021/acs.chemrev.9b00254 31411455
S. Kassem et al. Artificial molecular motors Chem. Soc. Rev. 46 9 2592 10.1039/C7CS00245A
S. Erbas-Cakmak et al. Rotary and linear molecular motors driven by pulses of a chemical fuel Science 358 340 2017Sci..358.340E 1:CAS:528:DC%2BC2sXhs1Kns7%2FI 10.1126/science.aao1377 29051374
M.R. Wilson et al. An autonomous chemically fuelled small-molecule motor Nature 534 235 2016Natur.534.235W 1:CAS:528:DC%2BC28XpsFClsL0%3D 10.1038/nature18013 27279219
S. Amano et al. Insights from an information thermodynamics analysis of a synthetic molecular motor Nat. Chem. 14 530 1:CAS:528:DC%2BB38Xntlyisrg%3D 10.1038/s41557-022-00899-z 35301472
L. Zhang et al. An electric molecular motor Nature 613 280 2023Natur.613.280Z 1:CAS:528:DC%2BB3sXpt12lsg%3D%3D 10.1038/s41586-022-05421-6 36631649 9834048
Credi, A. Silvi, S. & Venturi, M. Photochemically Driven Molecular Devices and Machines (Wiley Online Library, 2012).
S. Amano S. Borsley D.A. Leigh Z. Sun Chemical engines: driving systems away from equilibrium through catalyst reaction cycles Nat. Nanotechnol. 16 1057 2021NatNa.16.1057A 1:CAS:528:DC%2BB3MXit1Wkt7jI 10.1038/s41565-021-00975-4 34625723
S. Corra et al. Kinetic and energetic insights into the dissipative non-equilibrium operation of an autonomous light-powered supramolecular pump Nat. Nanotechnol. 17 746 2022NatNa.17.746C 1:CAS:528:DC%2BB38XhslWis7bJ 10.1038/s41565-022-01151-y 35760895
Cox, M. & Nelson, D. Lehninger Principles of Biochemistry (W. H. Freeman, 2000).
Voet, D., Voet, J. G. & Pratt, C. Fundamentals of Biochemistry: Life at the Molecular Level (Wiley, 2016).
X. Yang et al. Physical bioenergetics: energy fluxes, budgets, and constraints in cells Proc. Natl Acad. Sci. USA 118 e2026786118 1:CAS:528:DC%2BB3MXhsVOis7jP 10.1073/pnas.2026786118 34140336 8255778
J. Zanghellini D.E. Ruckerbauer M. Hanscho C. Jungreuthmayer Elementary flux modes in a nutshell: properties, calculation and applications Biotechnol. J. 8 1009 1:CAS:528:DC%2BC3sXpvVCjsrs%3D 10.1002/biot.201200269 23788432
M. Yasemi M. Jolicoeur Modelling cell metabolism: a review on constraint-based steady-state and kinetic approaches Processes 9 322 1:CAS:528:DC%2BB3MXhvF2nsbzO 10.3390/pr9020322
C.T. Trinh A. Wlaschin F. Srienc Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism Appl. Microbiol. Biotechnol. 81 813 1:CAS:528:DC%2BD1cXhsFart7%2FI 10.1007/s00253-008-1770-1 19015845
J.M.R. Parrondo B.J. de Cisneros Energetics of brownian motors: a review Appl. Phys. A 75 2002ApPhA.75.179P 1:CAS:528:DC%2BD38XktlSnsr0%3D 10.1007/s003390201332 179
Y. Zhang H.V. Westerhoff Gear shifting in biological energy transduction Entropy 25 993 2023Entrp.25.993Z 1:CAS:528:DC%2BB3sXhs1WntLrF 10.3390/e25070993 37509940 10378313
F. Rojo Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment FEMS Microbiol. Rev. 34 658 1:CAS:528:DC%2BC3cXhtFSlu7jJ 10.1111/j.1574-6976.2010.00218.x 20412307
R.H. De Deken The crabtree effect: a regulatory system in yeast Microbiology 44 149
O. Frick C. Wittmann Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13c flux analysis Microb. Cell Fact. 4 10.1186/1475-2859-4-30 16269086 1291395 30
A.I. Mahmoud Metabolic switches during development and regeneration Development 150 202008 10.1242/dev.202008
H. Link et al. Real-time metabolome profiling of the metabolic switch between starvation and growth Nat. Methods 12 1091 1097 1:CAS:528:DC%2BC2MXhsV2ltr3N 10.1038/nmeth.3584 26366986
T. Koyama M.J. Texada K.A. Halberg K. Rewitz Metabolism and growth adaptation to environmental conditions in drosophila Cell. Mol. Life Sci. 77 4523 1:CAS:528:DC%2BB3cXpvFCqtr8%3D 10.1007/s00018-020-03547-2 32448994 7599194
R. Karimi A. Cleven F. Elbarbry H. Hoang The impact of fasting on major metabolic pathways of macronutrients and pharmacokinetics steps of drugs Eur. J. Drug Metab. Pharmacokinet. 46 25 1:CAS:528:DC%2BB3cXit1GqtbvN 10.1007/s13318-020-00656-y 33151502
R. Rao M. Esposito Conservation laws and work fluctuation relations in chemical reaction networks J. Chem. Phys. 149 245101 2018JChPh.149x5101R 10.1063/1.5042253 30599709
M. Terzer J. Stelling Large-scale computation of elementary flux modes with bit pattern trees Bioinformatics 24 2229 1:CAS:528:DC%2BD1cXhtFOgs7%2FI 10.1093/bioinformatics/btn401 18676417
F. Avanzini N. Freitas M. Esposito Circuit theory for chemical reaction networks Phys. Rev. X 13 021041 1:CAS:528:DC%2BB3sXhsFKht77F
A. Wachtel R. Rao M. Esposito Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten N. J. Phys. 20 042002 10.1088/1367-2630/aab5c9
R. Rao M. Esposito Nonequilibrium thermodynamics of chemical reaction networks: wisdom from stochastic thermodynamics Phys. Rev. X 6 041064
