Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws

In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated to nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation $a + b = s^Y$ between the number of fundamental affinities $a$, that of broken conservation laws $b$ and the number of chemostats $s^Y$. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction and of thermodynamic constraints for network reconstruction.Comment: 18 page

Entropic fluctuations in thermally driven harmonic networks

We consider a general network of harmonic oscillators driven out of thermal equilibrium by coupling to several heat reservoirs at different temperatures. The action of the reservoirs is implemented by Langevin forces. Assuming the existence and uniqueness of the steady state of the resulting process, we construct a canonical entropy production functional which satisfies the Gallavotti--Cohen fluctuation theorem, i.e., a global large deviation principle with a rate function I(s) obeying the Gallavotti--Cohen fluctuation relation I(-s)-I(s)=s for all s. We also consider perturbations of our functional by quadratic boundary terms and prove that they satisfy extended fluctuation relations, i.e., a global large deviation principle with a rate function that typically differs from I(s) outside a finite interval. This applies to various physically relevant functionals and, in particular, to the heat dissipation rate of the network. Our approach relies on the properties of the maximal solution of a one-parameter family of algebraic matrix Riccati equations. It turns out that the limiting cumulant generating functions of our functional and its perturbations can be computed in terms of spectral data of a Hamiltonian matrix depending on the harmonic potential of the network and the parameters of the Langevin reservoirs. This approach is well adapted to both analytical and numerical investigations

Nonequilibrium phase transition in a non integrable zero-range process

The present work is an endeavour to determine analytically features of the stationary measure of a non-integrable zero-range process, and to investigate the possible existence of phase transitions for such a nonequilibrium model. The rates defining the model do not satisfy the constraints necessary for the stationary measure to be a product measure. Even in the absence of a drive, detailed balance with respect to this measure is violated. Analytical and numerical investigations on the complete graph demonstrate the existence of a first-order phase transition between a fluid phase and a condensed phase, where a single site has macroscopic occupation. The transition is sudden from an imbalanced fluid where both species have densities larger than the critical density, to a critical neutral fluid and an imbalanced condensate

Level 2.5 large deviations for continuous time Markov chains with time periodic rates

We consider an irreducible continuous time Markov chain on a finite state space and with time periodic jump rates and prove the joint large deviation principle for the empirical measure and flow and the joint large deviation principle for the empirical measure and current. By contraction we get the large deviation principle of three types of entropy production flow. We derive some Gallavotti-Cohen duality relations and discuss some applications.Comment: 37 pages. corrected versio