Conservation laws and work fluctuation relations in chemical reaction networks

Rao, Riccardo; Esposito, Massimiliano

doi:10.1063/1.5042253

Cited by 56 publications

(73 citation statements)

References 81 publications

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“…Here A is the (dimensionless) chemical affinity of the chemical network [12] A := ln p 0 being the reference value of the product concentration around which we will consider periodic modulation. The steady-state entropy production of this system can be written in terms of the steady-state current and affinity, asσ…”

Section: B Steady-stated Analysismentioning

confidence: 99%

“…Before dealing with this general approach, we will obtain the mean values of the dynamical observables in the time-dependent case via a direct method. We point out that in the general case of driving with an arbitrary protocol, the symmetry (11) does not hold anymore and should be substituted by the generalization in [12], that includes periodic driving, as well as boundary contributions. The periodic driving we will consider is the time variation of the chemostatted concentration p according to the protocol (with 0 < γ < 1)…”

Section: Periodic Drivingmentioning

confidence: 99%

“…The thermodynamics of this model can be formulated in terms of the entropy production [12] in the periodic steady-state, that averaged on a period readṡ…”

Section: Periodic Drivingmentioning

confidence: 99%

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Strong current response to slow modulation: A metabolic case-study

Forastiere

Falasco

Esposito

2020

The Journal of Chemical Physics

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We study the current response to periodic driving of a crucial biochemical reaction network, namely, substrate inhibition. We focus on the conversion rate of substrate into product under timevarying metabolic conditions, modeled by a periodic modulation of the product concentration. We find that the system exhibits a strong nonlinear response to small driving frequencies both for the mean time-averaged current and for the fluctuations. For the first, we obtain an analytic formula by coarse-graining the original model to a solvable one. The result is nonperturbative in the modulation amplitude and frequency. We then refine the picture by studying the stochastic dynamics of the full system using a large deviations approach, that allows to show the resonant effect at the level of the time-averaged variance and signal-to-noise ratio. Finally, we discuss how this nonequilibrium effect may play a role in metabolic and synthetic networks.

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Section: B Steady-stated Analysismentioning

confidence: 99%

Section: Periodic Drivingmentioning

confidence: 99%

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Strong current response to slow modulation: A metabolic case-study

Forastiere

Falasco

Esposito

2020

The Journal of Chemical Physics

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“…In the macroscopic limit, the mean field dynamics is exact and nonlinear [48][49][50] and can give rise to all sorts of complex behaviors [51]. The thermodynamics of chemical reaction networks has started to raise some attention in recent years [52][53][54][55][56].…”

Section: Introductionmentioning

confidence: 99%

Stochastic thermodynamics of all-to-all interacting many-body systems

et al. 2020

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We provide a stochastic thermodynamic description across scales for N identical units with allto-all interactions that are driven away from equilibrium by different reservoirs and external forces. We start at the microscopic level with Poisson rates describing transitions between many-body states. We then identify an exact coarse graining leading to a mesoscopic description in terms of Poisson transitions between systems occupations. We also study macroscopic fluctuations using the Martin-Siggia-Rose formalism and large deviation theory. In the macroscopic limit (N → ∞), we derive an exact nonlinear (mean-field) rate equation describing the deterministic dynamics of the most likely occupations. Thermodynamic consistency, in particular the detailed fluctuation theorem, is demonstrated across microscopic, mesoscopic and macroscopic scales. The emergent notion of entropy at different scales is also outlined. Macroscopic fluctuations are calculated semianalytically in an out-of-equilibrium Ising model. Our work provides a powerful framework to study thermodynamics of nonequilibrium phase transitions.

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“…This theory has been successful in various contexts, e.g. Brownian particles [8,9], electronic systems [10], chemical reaction networks [11,12], active matter [13,14] and information processing [15]. In a nutshell, stochastic thermodynamics consistently builds a thermodynamic structure on top of a stochastic process described by master equations [16] or Fokker-Planck equations [17], implicitly assuming that the traced out degrees of freedom always stay at equilibrium.…”

Section: Introductionmentioning

confidence: 99%

Effective thermodynamics of two interacting underdamped Brownian particles

2020

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Starting from the stochastic thermodynamics description of two coupled underdamped Brownian particles, we showcase and compare three different coarse-graining schemes leading to an effective thermodynamic description for the first of the two particles: Marginalization over one particle, bipartite structure with information flows and the Hamiltonian of mean force formalism. In the limit of time-scale separation where the second particle locally equilibrates, the effective thermodynamics resulting from the first and third approach is shown to capture the full thermodynamics and to coincide with each other. In the bipartite approach, the slow part does not, in general, allow for an exact thermodynamic description as the entropic exchange between the particles is ignored. Physically, the second particle effectively becomes part of the heat reservoir. In the limit where the second particle becomes heavy and thus deterministic, the effective thermodynamics of the first two coarse-graining methods coincides with the full one. The Hamiltonian of mean force formalism however is shown to be incompatible with that limit. Physically, the second particle becomes a work source. These theoretical results are illustrated using an exactly solvable harmonic model.

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Conservation laws and work fluctuation relations in chemical reaction networks

Cited by 56 publications

References 81 publications

Strong current response to slow modulation: A metabolic case-study

Strong current response to slow modulation: A metabolic case-study

Stochastic thermodynamics of all-to-all interacting many-body systems

Effective thermodynamics of two interacting underdamped Brownian particles

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