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Thermodynamics of Open Chemical Reaction Networks

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Thermodynamics of Open Chemical Reaction Networks Thermodynamics of Open Chemical Reaction Networks Massimiliano Esposito Riccardo Rao (PhD), Gianmaria Falasco (postdoc), Ma!eo Pole!ini (researcher) Harvard, November 13, 2019 Motivation Cell Metabolism Thermodynamics of Classical thermodynamics Stochastic thermodynamics Chemical Reaction Networks !"Thermodynamics# is the only physical theory of %niversal content which I am convinced will never be overthrown, within the framewor of a$$licability of its basic conce$ts'( A' Einstein " O%tline ● ,eterministic Dynamics of Open CNRs ● Thermodynamics of Open CRNs . First and Second Law . Role of To$ology ● Reaction.,i2%sion ● Concl%din1 Remarks $ Dynamics of Closed CRNs +toichiometric matrix Environment Chemical Network k'( A + E E* k)( k'& k)" k)& k'" k)$ E** E + B k'$ Rate e4%ations Reactions Ideal Dil%te Sol%tion + Elementary Reactions = Mass action inetics & Dynamics of Open CRNs Environment Chemical Network k'( A + E E* k)( Ae k'& k)" k)& k'" k)$ E** E + B Stoichiometric matrix k'$ Be Internal Chemosta7ed Rate e4%ations )%tonomous CRNs Reactions *3change * Thermodynamics of CRNs Enthal$y of formation Entro$y of formation &deal Dil%te Sol%tions 0ocal e4%ilibrium Standard-state chemical potential 0ocal Detailed 8alance Elementary Reactions “0th law of Thermodynamics”9 Closed CRN rela3 to e4%ilibrium detailed-balance + First and Second Law total CRN Enthal$y9 CRN Entropy9 concentration Chemical ?or 1st law Enthalpy Balance Heat /low 2nd law Entropy Balance *ntropy chan1e in (thermal & chemical; reservoirs Entropy prod%ction9 (total entropy change; , "Rao & *s$osito, Phys. Rev. X 6, 0=10>= (2016;# 0ork principle: E3%ili4rium of Closed CRN Non-Eq' Gibbs free energy *4%ilibrium of closed CRN !Relative entropy( In a closed CRN, , is minimized by the dynamics until the CRN reaches e4%ilibrium / "Rao & *s$osito, Phys. Rev. X 6, 0=10>= (2016;# Conservation Laws & Cycles in Closed CRNs Conservation 0aws9 Cycles9 Environment Chemical Network k'( A + E E* k)( k'& k)" k)& k'" k)$ E** E + B k'$ 5 Conser#ation Laws & Cycles in Open CRNs Environment Chemical Network k'( A + E E* k)( Ae k'& k)" k)& k'" k)$ E** E + B k'$ Be -$ening may brea some conservation laws %nbroken: broken: -$ening may create emergent cycles emergent9 1 = 1 + 0 2 = 1 + 1 2 = 2 + 0 (7 "Pole7ini < Es$osito, J. Chem. Phys. 141, 02411C (201=;# 2ntropy Production shaped by Topology /%ndamental Forces Emer1ent Cycle )2inities Nonconservative ?ork Driving Work NonE4 semigrand @ibbs free energy (( "Falasco, Dao & *s$osito, Phys. Rev. Lett. 121, 108301 (2018;# +ome special class of CRNs Detailed Balanced CRNs9 ,8 & a%tonomous9 Rela3ation to E4'9 minimized by dynamics Non.*4' Steady State9 /orce./l%x pairs :a%tonomous; ?ork principle *4%ilibrium of open CRN Minimal work to generate a Non-E4 distrib%tion (" "Falasco, Dao & *s$osito, Phys. Rev. Lett. 121, 108301 (2018;# 2:ample μA Wd Environment Chemical Network A + E E* Ae E** E + B Wnc Be None4' semigrand ,riving ?or Nonconservative Work @ibbs free energy ($ ;dding Diffusion Reaction—Diff%sion E4%ations Mass.action inetics ,i2%sion: /ic Gs 0aw Diff%sion Reactions *3change Diff%sion coe2icients g n vi ri . d eq on n +$acial struct%ring ta es work9 iving eq. dr (& "Falasco, Dao & *s$osito, Phys. Rev. Lett. 121, 108301 (2018;# Final remarks The big iss%e of coarse grainin9 Non.*4' thermodynamics needs to describe all the degrees of freedom that are out-of-e4%ilibrium m%st be described' We need coarse graining strate1ies which $reserves thermodynamic consistency' *39 Coarse.grainin1 Biocatalysts "?achtel, Dao & Es$osito, New J. Phys. 20 0=2002 (201E;# Usef%l> - Performance of energy storage and energy con#ersion (from molecular motors to meta4olic networks) 2:1 Dri#en synthesis "Benocchio, Dao & Es$osito, Nature Communications, 10 3E>H (2019;# - Cost of Chemical Information Brocessing 2:1 T%ring pa!erns "/alasco, Dao & Es$osito, Phys. Rev. Lett. 121, 10E301 (201E)] Chemical waves ")vanzini, Falasco & Es$osito, arXiv9190='0EEC=# Stochasticity? +tochastic Thermodynamics of CRNs (nonlinear; "Dao & Es$osito, J. Chem. Phys. 149, 2=H101 (201E;# Thermo at stochastic vs deterministic level9 yes at steady state for com$lex balanced CRNs "Bole7ini, Wachtel & Es$osito, J. Chem. Phys. 143, 1E=103 (201H;# Bhase transitions "0aAaresc%, Cosse7o, Falasco & Es$osito, J. Chem. Phys. 151, 0>=11C (2019;# (*.
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