We show that the extension of Casimir-like forces to fluctuating fluids driven out of equilibrium can exhibit two interrelated phenomena forbidden at equilibrium: self-forces can be induced on single asymmetric objects and the action--reaction principle between two objects can be violated. These effects originate in asymmetric restrictions imposed by the objects' boundaries on the fluid's fluctuations. They are not ruled out by the second law of thermodynamics since the fluid is in a nonequilibrium state. Considering a simple reaction--diffusion model for the fluid, we explicitly calculate the self-force induced on a deformed circle. We also show that the action--reaction principle does not apply for the internal Casimir forces exerting between a circle and a plate. Their sum, instead of vanishing, provides the self-force on the circle-plate assembly.
Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in nonequilibrium thermodynamics provide new insight on how CRNs process energy and perform sophisticated tasks, and describe open challenges in the field.
The Zubarev nonequilibrium statistical operator (NSO) method in Renyi statistics is discussed. The solution of $q$-parametrized Liouville equation within the NSO method is obtained. A statistical approach for a consistent description of reaction-diffusion processes in "gas-adsorbate-metal" system is proposed using the NSO method in Renyi statistics.
We investigate nonequilibrium chemical reaction systems from the view point of steady state thermodynamics proposed by Oono and Paniconi [Prog. Theor. Phys. Suppl. 130, 29 (1998)]. The concentrations of some compounds are operated by an external system, so that a transition from a steady state to other steady state takes place. We show that an analogue of Clausius inequality holds macroscopically for the operation processes. This implies that the second law of thermodynamics can be generalized, including nonequilibrium steady states.
We study dynamics of pattern formation in systems belonging to class of reaction-Cattaneo models including persistent diffusion (memory effects of the diffusion flux). It was shown that due to the memory effects pattern seletion process are realized. We have found that oscillatory behavior of the radius of the adsorbate islands is governed by finite propagation speed. It is shown that stabilization of nano-patterns in such models is possible only by nonequilibrium chemical reactions. Oscillatory dynamics of pattern formation is studied in details by numerical simulations.
Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviours. Here, we extend the theory to include incoherent light as a source of free energy. We do so by relying on a local equilibrium assumption to derive the chemical potential of photons relative to the system they interact with. This allows us to identify the thermodynamic potential and the thermodynamic forces driving light-reacting chemical systems out of equilibrium. We use this framework to treat two paradigmatic photochem…
In a nonequilibrium steady state, the violation of the fluctuation-dissipation theorem (FDT) is connected to breaking detailed balance. For the velocity correlations of a driven colloidal particle we calculate an explicit expression of the FDT violation. The equilibrium form of the FDT can be restored by measuring the velocity with respect to the local mean velocity.
The computation of free energy differences through an exponential weighting of out of equilibrium paths (known as the Jarzynski equality) is often used for transitions between states described by an external parameter $λ$ in the Hamiltonian. We present here an extension to transitions between states defined by different values of some reaction coordinate, using a projected Brownian dynamics. In contrast with other approaches, we use a projection rather than a constraining potential to let the constraints associated with the reaction coordinate evolve. We show how to use the Lagrange multiplier…
We investigate a class of nonequilibrium media described by Langevin dynamics that satisfies the local detailed balance. For the effective dynamics of a probe immersed in the medium, we derive an inequality that bounds the violation of the second fluctuation-dissipation relation (FDR). We also discuss the validity of the effective dynamics. In particular, we show that the effective dynamics obtained from nonequilibrium linear response theory is consistent with that obtained from a singular perturbation method. As an example of these results, we propose a simple model for a nonequilibrium mediu…
We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of chemical reaction systems based on a master equation defined on the space of microscopic chemical states, and on appropriate definitions of entropy and entropy production, The system is in contact with a heat reservoir, and is placed out of equilibrium by the contact with particle reservoirs. In our approach, the fluxes of various types, such as the heat and …
We study the nonequilibrium steady state of an infinite chain of free fermions, resulting from an initial state where the two sides of the system are prepared at different temperatures. The mutual information is calculated between two adjacent segments of the chain and is found to scale logarithmically in the subsystem size. This provides the first example of the violation of the area law in a quantum many-body system outside a zero temperature regime. The prefactor of the logarithm is obtained analytically and, furthermore, the same prefactor is shown to govern the logarithmic increase of mut…
We identify different schemes to enhance the violation of Leggett-Garg inequalities in open many-body systems. Considering a nonequilibrium archetypical setup of quantum transport, we show that particle interactions control the direction and amplitude of maximal violation and that in the strongly-interacting and strongly-driven regime bulk dephasing enhances the violation. Through an analytical study of a minimal model, we unravel the basic ingredients to explain this decoherence-enhanced quantumness, illustrating that such an effect emerges in a wide variety of systems.
We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of elementary reactions. Their dynamics is described by deterministic rate equations satisfying mass action law. Our most general framework considers open networks driven by time-dependent chemostats. The energy and entropy balances are established and a nonequilibrium Gibbs free energy is introduced. The difference between this latter and its equilibrium form represents the minimal work done by the chemostats to bring the network in its nonequilibrium state. It is minimized in nondriven detailed-b…
We analyze several aspects of the phenomenon of stochastic resonance in reaction-diffusion systems, exploiting the nonequilibrium potential's framework. The generalization of this formalism (sketched in the appendix) to extended systems is first carried out in the context of a simplified scalar model, for which stationary patterns can be found analytically. We first show how system-size stochastic resonance arises naturally in this framework, and then how the phenomenon of array-enhanced stochastic resonance can be further enhanced by letting the diffusion coefficient depend on the field. A ye…
We study a nonequilibrium Langevin many-body system containing two 'test' particles and many 'background' particles. The test particles are spatially confined by a harmonic potential, and the background particles are driven by an external driving force. Employing numerical simulations of the model, we formulate an effective description of the two test particles in a nonequilibrium steady state. In particular, we investigate several different definitions of the effective force acting between the test particles. We find that the law of action and reaction does not hold for the total mechanical f…
Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative similarities between liquid--liquid phase separation in these systems, the extent to which the phase-separation kinetics differ remains unclear. Here we show that inhomogeneous chemical reactions can alter the nucleation kinetics of liquid--liquid phase separation in a manner that is consistent with classical nucleation theory, but can only be rationalized by introduci…
The energy dissipation rate in a nonequilibirum reaction system can be determined by the reaction rates in the underlying reaction network. By developing a coarse-graining process in state space and a corresponding renormalization procedure for reaction rates, we find that energy dissipation rate has an inverse power-law dependence on the number of microscopic states in a coarse-grained state. The dissipation scaling law requires self-similarity of the underlying network, and the scaling exponent depends on the network structure and the flux correlation. Implications of this inverse dissipatio…
All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a mean-field approach using activity coefficients. Thermodynamic consistency requires that rate equations do not obey to standard mass-action kinetics, but account for the interactions with concentration dependent kinetic constants. Many features of the ideal formulations are recovered. Crucially, the thermodynamic potential and the forces driving non-ideal chem…
This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with $N$ species, $M$ reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical thermodynamics under G. N. Lewis' kinetic law of entire equilibrium (detailed balance in nonlinear chemistry kinetics). In doing so, the equilibrium thermodynamics is then naturally generalized to nonequilibrium settings without detailed balance. The kinetic models are represented by a Markovian jumping process. A generalized macroscopic chemical free energy functi…
We present a study of the spatial correlation functions of a one-dimensional reaction-diffusion system in both equilibrium and out of equilibrium. For the numerical simulations we have employed the Gillespie algorithm dividing the system in cells to treat diffusion as a chemical process between adjacent cells. We find that the spatial correlations are spatially short ranged in equilibrium but become long ranged in nonequilibrium. These results are in good agreement with theoretical predictions from fluctuating hydrodynamics for a one-dimensional system and periodic boundary conditions.
Microscopic machines utilize free energy to create and maintain out-of-equilibrium organization in virtually all living things. Often this takes the form of converting the free energy stored in nonequilibrium chemical potential differences into useful work, via a series of reactions involving the binding, chemical catalysis, and unbinding of small molecules. Such chemical reactions occur on timescales much faster than the protein conformational rearrangements they induce. Here, we derive the energetic cost for driving a system out of equilibrium via a series of such effectively instantaneous (…
In a recent letter [PRL 80 (1998) 3539] Fisher, Le Doussal and Monthus report new predictions for the persistence properties of Sinai's model, which they obtain by using an approximate real space renormalization group scheme. In this comment we show that these predictions can be derived in a rigorous and more transparent way by reducing the quantities of interest to particular statistical properties of a simple random walk in a homogeneous environment. We also point out that they are valid in a much more general context: our results are neither restricted to the random force model but are vali…
We study the adsorption-desorption of fluid molecules on a solid substrate by introducing a schematic model in which the adsorption/desorption transition probabilities are given by irreversible kinetic constraints with a tunable violation of local detailed balance condition. Numerical simulations show that in one spatial dimension the model undergoes a continuous nonequilibrium phase transition whose location depends on the irreversibility strength. We show that the hierarchy of equations obeyed by multi-point correlation functions can be closed to the second order by means of a simple decoupl…
Thermodynamic Features of a Heat Engine Coupled with Exponentially Decreasing Temperature Across the Reaction Coordinate, as well as Perspectives on Nonequilibrium Thermodynamics
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal assumption of the whole system meets great challenge, which is indeed the case inside many kinds of living organisms. Here we generalize the nonequilibrium steady-state theory of isothermal biochemical cycle kinetics, in the master-equation models, to the situation in which the temperatures of subsystems can be far from uniform. We first obtain a new thermo…
A direct connection between the magnitude of the violation of the fluctuation-response relation (FRR) and the rate of energy dissipation is presented in terms of field variables of nonequilibrium systems. Here, we consider the density field of a colloidal suspension either in a relaxation process or in a nonequilibrium steady state driven by an external field. Using a path-integral representation of the temporal evolution of the density field, we find an equality that relates the magnitude of the violation of the FRR for scalar and vector potentials of the velocity field to the rate of energy …
The nonequilibrium critical dynamics of the 2D XY model is investigated numerically through Monte Carlo simulations and analytically in the spin-wave approximation. We focus in particular on the behaviour of the two-time response and correlation functions and show that the ageing dynamics depends on the initial conditions. The presence of critical fluctuations leads to non-trivial violations of the fluctuation-dissipation theorem apparently reminiscent of the three dimensional Edwards-Anderson spin glass model. We compute for this reason the finite-size overlap probability distribution functio…
Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport, diffusion, thermochemical, thermomechanical and mechanochemical fluxes. In the present review, we introduce a mesoscopic stochastic formulation of NET by analyzing entropy production in several simple examples. The fundamental role of nonequilibrium steady-state cycle kinetics is emphasized. The statistical mechanics of Onsager's reciprocal relations in this c…
We present the first example of a phase transition in a nonequilibrium steady-state that can be argued analytically to be first order. The system of interest is a two-species reaction-diffusion problem whose control parameter is the total density ρ. Mean-field theory predicts a second-order transition between two stationary states at a critical density ρ=ρ_c. We develop a phenomenological picture that, instead, below the upper critical dimension d_c=4, predicts a first-order transition. This picture is confirmed by hysteresis found in numerical simulations, and by the study of a renormalizatio…
In an equilibrium chemical reaction mixture, the number of molecules present obeys a Poisson distribution. We ask when the same is true of the steady state of a nonequilibrium reaction network and obtain an essentially complete answer. In particular, we show that networks with certain topological features must have a Poisson distribution, whatever the reaction rates. Such driven systems also obey an analog of the fluctuation-dissipation theorem. Our results may be relevant to biological systems and to the larger question of how equilibrium concepts might apply to nonequilibrium systems.
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity, but population wise with statistical rate laws in their syntheses, degradations, spatial diffusion, individual state transitions, and interactions. Such a formal kinetic system in a small volume $V$, like a single cell, can be rigorously treated in terms of a Markov process describing its nonlinear kinetics as well as nonequilibrium thermodynamics at a mesosco…
We present a nonequlibrium approach for the study of a flexible bilayer whose two components induce distinct curvatures. In turn, the two components are interconverted by an externally promoted reaction. Phase separation of the two species in the surface results in the growth of domains characterized by different local composition and curvature modulations. This domain growth is limited by the effective mixing due to the interconversion reaction, leading to a finite characteristic domain size. In addition to these effects, first introduced in our earlier work [Phys. Rev. E {\bf 71}, 051906 (20…
A novel equality relating the rate of energy dissipation to a degree of violation of the fluctuation-response relation (FRR) in nonequilibrium Langevin systems is described. The FRR is a relation between the correlation function of the fluctuations and the response function of macroscopic variables. Although it has been established that the FRR holds in equilibrium, physical significance of violation of the FRR in nonequilibrium systems has been under debate. Recently, the authors have found that an extent of the FRR violation is related in a simple equality to the rate of energy dissipation i…
We introduce a simple nonequilibrium model for a driven diffusive system with nonconservative reaction kinetics which exhibits ergodicity breaking and hysteresis in one dimension. These phenomena can be understood through a description of the dominant stochastic many-body dynamics in terms of an equilibrium single-particle problem, viz. the random motion of a shock in an effective potential. This picture also leads to the exact phase diagram of the system and suggests a new generic mechanism for "freezing by heating".
We present a theoretical framework to analyze the violation of fluctuation-response relation (FRR) for any observable from a finite Markov system with two well-separated time scales. We find that, generally for both slow and fast observables, a broad plateau exists in the intermediate frequency region, which contributes to a finite hidden entropy production. Assuming that non-equilibrium behavior arises only from coupling of slow and fast processes, we find that, at large observation time scae, the effective temperature for a slow observable deviates only slightly from the bath temperature, ac…
We propose a method to study the thermodynamic behaviour of small systems beyond the weak coupling and Markovian approximation, which is different in spirit from conventional approaches. The idea is to redefine the system and environment such that the effective, redefined system is again coupled weakly to Markovian residual baths and thus, allows to derive a consistent thermodynamic framework for this new system-environment partition. To achieve this goal we make use of the reaction coordinate mapping, which is a general method in the sense that it can be applied to an arbitrary (quantum or cl…
Nonequilibrium reaction networks (NRNs) underlie most biological functions. Despite their diverse dynamic properties, NRNs share the signature characteristics of persistent probability fluxes and continuous energy dissipation even in the steady state. Dynamics of NRNs can be described at different coarse-grained levels. Our previous work showed that the apparent energy dissipation rate at a coarse-grained level follows an inverse power law dependence on the scale of coarse-graining. The scaling exponent is determined by the network structure and correlation of stationary probability fluxes. Ho…
We set up a rigorous thermodynamic description of reaction-diffusion systems driven out of equilibrium by time-dependent space-distributed chemostats. Building on the assumption of local equilibrium, nonequilibrium thermodynamic potentials are constructed exploiting the symmetries of the chemical network topology. It is shown that the canonical (resp. semigrand canonical) nonequilibrium free energy works as a Lyapunov function in the relaxation to equilibrium of a closed (resp. open) system and its variation provides the minimum amount of work needed to manipulate the species concentrations. T…
We study the induced interaction between multiple probes locally interacting with driven colloids and trapped in a toroidal geometry. The effective binary forces between the probes break the action-reaction principle and their range decreases with the driving. We demonstrate how in the stationary nonlinear nonequilibrium regime these interactions induce stability of a crystal-like pattern, where the probes are equidistant, when the probe-colloid interaction is either completely attractive or completely repulsive.
A simple kinetic model of a two-component deformable and reactive bilayer is presented. The two differently shaped components are interconverted by a nonequilibrium reaction, and a phenomenological coupling between local composition and curvature is proposed. When the two components are not miscible, linear stability analysis predicts, and numerical simulations show, the formation of stationary nonequilibrium composition/curvature patterns whose typical size is determined by the reactive process. For miscible components, a linearization of the dynamic equations is performed in order to evaluat…
Chemical reaction systems operating in nonequilibrium open-system states arise in a great number of contexts, including the study of living organisms, in which chemical reactions, in general, are far from equilibrium. Here we introduce a theorem that relates forward and re-verse fluxes and free energy for any chemical process operating in a steady state. This rela-tionship, which is a generalization of equilibrium conditions to the case of a chemical process occurring in a nonequilibrium steady state, provides a novel equivalent definition for chemical reaction free energy. In addition, it is …
We analyze the validity of the fluctuation-dissipation theorem for slow relaxation systems in the context of mesoscopic nonequilibrium thermodynamics. We demonstrate that the violation arises as a natural consequence of the elimination of fast variables in the description of a glassy system, and it is intrinsically related to the underlying activated nature of slow relaxation. In addition, we show that the concept of effective temperature, introduced to characterize the magnitude of the violation, is not robust since it is observable-dependent, can diverge, or even be negative.
We present a computational study of the dynamic behavior of a Ziff-Gulari-Barshad model of CO oxidation with CO desorption on a catalytic surface. Our results provide further evidence that below a critical desorption rate the model exhibits a non-equilibrium, first-order phase transition between low and high CO coverage phases. Our kinetic Monte Carlo simulations indicate that the transition process between these phases follows a decay mechanism very similar to the one described by the classic Kolmogorov-Johnson-Mehl-Avrami theory of phase transformation by nucleation and growth. We measure th…
