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Time-dependent response and correlation functions are studied in random quantum systems composed of infinitely many parts without mutual interaction and defined with statistically independent random matrices. The latter are taken within the three Wigner-Dyson universality classes. In these systems, the response functions are shown to be exactly given by statistical averages over the random-matrix ensemble. Analytical results are obtained for the time dependence of the mean response and correlation functions at zero and positive temperatures. At long times, the mean correlation functions are shown to have a power-law decay for GOE at positive temperatures, but for GUE and GSE at zero temperature. Otherwise, the decay is much faster in time. In relation to these power-law decays, the associated spectral densities have a dip around zero frequency. The diagrammatic method is developed to obtain higher-order response functions and the third-order response function is explicitly calculated. The response to impulsive perturbations is also considered. In addition, the quantum fluctuations of the correlation function in individual members of the ensemble are characterised in terms of their probability distribution, which is shown to change with the temperature.

The hydrodynamics of crystals with vacancies is developed on the basis of local-equilibrium thermodynamics, where the chemical potential of vacancies plays a key role together with a constraint relating the concentration of vacancies to the density of mass and the strain tensor. The microscopic foundations are established, leading to Green-Kubo and Einstein-Helfand formulas for the transport coefficients, including the vacancy conductivities and the coefficients of vacancy thermodiffusion. As a consequence of having introduced the chemical potential of vacancies, a relationship is obtained between the conductivities and the Fickian diffusion coefficients for the vacancies. The macroscopic equations are linearized around equilibrium to deduce the dispersion relations of the eight hydrodynamic modes. The theoretical predictions are confirmed by numerical simulations of the hard-sphere crystal with vacancies. The study explicitly shows that the eighth hydrodynamic mode of nonperfect monatomic crystals is indeed a mode of vacancy diffusion., Comment: 24 pages, 6 figures, 8 tables

The elastic and transport coefficients of a perfect face-centered cubic crystal of hard spheres are computed from the poles of the dynamic structure factor and of the spectral functions of transverse momentum density fluctuations. For such crystals, the relevant coefficients are the three isothermal elastic constants $(C_{11}^T,C_{12}^T,C_{44}^T)$, the heat conductivity $\kappa$, and the three viscosities $(\eta_{11},\eta_{12},\eta_{44})$ (in Voigt's notations), which are directly computed using molecular dynamics simulations. The elastic and transport coefficients are then compared to the values of the same coefficients obtained with the method of Helfand moments, showing good agreement and providing strong support for the microscopic hydrodynamic theory of perfect crystals based on the local-equilibrium approach., Comment: 21 pages, 11 figures, 11 tables

We investigate the collective dynamics of the perfect cubic crystal by deriving from the hydrodynamic equations the time-dependent correlation and the spectral functions characterizing the fluctuations of mass and momentum densities. We show that the seven hydrodynamic modes of the perfect crystal can be identified from the resonances of these spectral functions. The comparison with those of a fluid is discussed. Using the numerical values of the thermodynamic, elastic, and transport coefficients computed in our previous paper [J. Mabillard and P. Gaspard, arXiv:2311.00757 (2023)] for a system of hard spheres, the theoretical expressions for the correlation and spectral functions are compared to the same functions directly computed using molecular dynamics simulations. The excellent agreement between theory and simulation provides strong support for the microscopic hydrodynamic theory of perfect crystals based on the local-equilibrium approach. This work sheds light on the fundamental mechanisms governing the collective behavior of matter in the solid state., Comment: 29 pages, 12 figures, 4 tables

Within the framework of the local-equilibrium approach, the equilibrium and nonequilibrium properties relevant to the hydrodynamics of the perfect hard-sphere crystal are obtained with molecular dynamics simulations using the Helfand moments associated with momentum and energy transports. Since this crystal is face-centered cubic, the hydrodynamic properties we consider are the hydrostatic pressure, the isothermal bulk modulus, the specific heat capacities and their ratio, the three isothermal elastic constants $(C_{11}^T,C_{12}^T,C_{44}^T)$, the heat conductivity, and the three viscosities $(\eta_{11},\eta_{12},\eta_{44})$ (in Voigt's notations). These properties are computed as a function of the particle density. The pressure and the transport coefficients diverge near the close-packing density, as the collision frequency per particle does.

The local-equilibrium approach to transport processes is related to the approach based on time-dependent correlation functions and their associated spectral functions characterizing the equilibrium fluctuations of particle, momentum and other densities. On the one hand, the transport coefficients are calculated with the Einstein-Helfand formulas derived in the local-equilibrium approach. On the other hand, the poles of the spectral functions at complex frequencies give the damping rates of the hydrodynamic modes. Since these rates also depend on the transport coefficients, their values can be compared to the predictions of the local-equilibrium approach. This comparison is systematically carried out for the hard-sphere fluid by computing numerically the transport coefficients, the spectral functions, and their poles as a function of the wave number in the hydrodynamic limit. The study shows the consistency between the two approaches for the determination of the transport properties.

The claims by Baras, Garcia, and Malek Mansour [Phys. Rev. E 107, 014106 (2023)] on the validity of path thermodynamics are ill founded and contradict well known results. Following up on a previous comment, I show that, for both models of chemical reaction networks considered in the aforementioned paper, path thermodynamics yields values of the entropy production rates fully consistent with those expected from standard chemical thermodynamics in the large-system limit.

The macroscopic hydrodynamic equations are derived for many-body systems in the local-equilibrium approach, using the Schr\"odinger picture of quantum mechanics. In this approach, statistical operators are defined in terms of microscopic densities associated with the fundamentally conserved quantities and other slow modes possibly emerging from continuous symmetry breaking, as well as macrofields conjugated to these densities. Functional identities can be deduced, allowing us to identify the reversible and dissipative parts of the mean current densities, to obtain general equations for the time evolution of the conjugate macrofields, and to establish the relationship to projection-operator methods. The entropy production is shown to be nonnegative by applying the Peierls-Bogoliubov inequality to a quantum integral fluctuation theorem. Using the expansion in the gradients of the conjugate macrofields, the transport coefficients are given by Green-Kubo formulas and the entropy production rate can be expressed in terms of quantum Einstein-Helfand formulas, implying its nonnegativity in agreement with the second law of thermodynamics. The results apply to multicomponent fluids and can be extended to condensed matter phases with broken continuous symmetries.

Homochirality, i.e. the dominance across all living matter of one enantiomer over the other among chiral molecules, is thought to be a key step in the emergence of life. Building on ideas put forward by Frank and many others, we proposed recently one such mechanism in G. Laurent et al., PNAS (2021) based on the properties of large out of equilibrium chemical networks. We showed that in such networks, a phase transition towards an homochiral state is likely to occur as the number of chiral species in the system becomes large or as the amount of free energy injected into the system increases. This paper aims at clarifying some important points in that scenario, not covered by our previous work. We first analyze the various conventions used to measure chirality, introduce the notion of chiral symmetry of a network, and study its implications regarding the relative chiral signs adopted by different groups of molecules. We then propose a generalization of Frank's model for large chemical networks, which we characterize completely using methods of random matrices. This analysis can be extended to sparse networks, which shows that the emergence of homochirality is a robust transition.

The local equilibrium approach previously developed by the Authors [J. Mabillard and P. Gaspard, J. Stat. Mech. (2020) 103203] for matter with broken symmetries is applied to crystalline solids. The macroscopic hydrodynamics of crystals and their local thermodynamic and transport properties are deduced from the microscopic Hamiltonian dynamics. In particular, the Green-Kubo formulas are obtained for all the transport coefficients. The eight hydrodynamic modes and their dispersion relation are studied for general and cubic crystals. In the same twenty crystallographic classes as those compatible with piezoelectricity, cross effects coupling transport between linear momentum and heat or crystalline order are shown to split the degeneracy of damping rates for modes propagating in opposite generic directions.

The selection of a single molecular handedness, or homochirality across all living matter, is a mystery in the origin of life. Frank's seminal model showed in the fifties how chiral symmetry breaking can occur in non-equilibrium chemical networks. However, an important shortcoming in this classic model is that it considers a small number of species, while there is no reason for the prebiotic system, in which homochirality first appeared, to have had such a simple composition. Furthermore, this model does not provide information on what could have been the size of the molecules involved in this homochiral prebiotic system. Here, we show that large molecular systems are likely to undergo a phase transition towards a homochiral state, as a consequence of the fact that they contain a large number of chiral species. Using chemoinformatics tools, we quantify how abundant are chiral species in the chemical universe of all possible molecules of a given length. Then, we propose that Frank's model should be extended to include a large number of species, in order to possess the transition towards homochirality as confirmed by numerical simulations. Finally, using random matrix theory, we prove that large non-equilibrium reaction networks possess a generic and robust phase transition towards a homochiral state.

Methods are presented to evaluate the entropy production rate in stochastic reactive systems. These methods are shown to be consistent with known results from nonequilibrium chemical thermodynamics. Moreover, it is proved that the time average of the entropy production rate can be decomposed into the contributions of the cycles obtained from the stoichiometric matrix in both stochastic processes and deterministic systems. These methods are applied to a complex reaction network constructed on the basis of Roessler's reinjection principle and featuring chemical chaos.

Active colloidal particles that are propelled by a self-diffusiophoretic mechanism are often described by Langevin equations that are either postulated on physical grounds or derived using the methods of fluctuating hydrodynamics. While these descriptions are appropriate for colloids of micrometric and larger size, they will break down for very small active particles. A fully microscopic derivation of Langevin equations for self-diffusiophoretic particles powered by chemical reactions catalyzed asymmetrically by the colloid is given in this paper. The derivation provides microscopic expressions for the translational and rotational friction tensors, as well as reaction rate coefficients appearing in the Langevin equations. The diffusiophoretic force and torque are expressed in terms of nonequilibrium averages of fluid fields that satisfy generalized transport equations. The results provide a description of active motion on small scales where descriptions in terms of coarse grained continuum fluid equations combined with boundary conditions that account for the presence of the colloid may not be appropriate., Comment: 15 pages, 2 figures

The paper by Malek Mansour and Garcia [Phys. Rev. E 101, 052135 (2020)] is shown to be based on misconceptions in the stochastic formulation of chemical thermodynamics in reactive systems. Their erroneous claims, asserting that entropy production cannot be correctly evaluated using path probabilities whenever the reactive system involves more than one elementary reaction leading to the same composition changes, are refuted.

A unified set of hydrodynamic equations describing condensed phases of matter with broken continuous symmetries is derived using a generalization of the statistical-mechanical approach based on the local equilibrium distribution. The dissipativeless and dissipative parts of the current densities and the entropy production are systematically deduced in this approach by expanding in powers of the gradients of the macrofields. Green-Kubo formulas are obtained for all the transport coefficients. The results apply to both crystalline solids and liquid crystals. The consequences of microreversibility and spatial symmetries are investigated, leading to the prediction of cross effects resulting from Onsager-Casimir reciprocal relations.

Multivariate fluctuation relations are established in three stochastic models of transistors, which are electronic devices with three ports and thus two coupled currents. In the first model, the transistor has no internal state variable and particle exchanges between the ports is described as a Markov jump process with constant rates. In the second model, the rates linearly depend on an internal random variable, representing the occupancy of the transistor by charge carriers. The third model has rates nonlinearly depending on the internal occupancy. For the first and second models, finite-time multivariate fluctuation relations are also established giving insight into the convergence towards the asymptotic form of multivariate fluctuation relations in the long-time limit. For all the three models, the transport properties are shown to satisfy Onsager's reciprocal relations in the linear regime close to equilibrium as well as their generalizations holding in the nonlinear regimes farther away from equilibrium, as a consequence of microreversibility.

Active matter, comprising many active agents interacting and moving in fluids or more complex environments, is a commonly occurring state of matter in biological and physical systems. By its very nature active matter systems exist in nonequilibrium states. In this paper the active agents are small Janus colloidal particles that use chemical energy provided by chemical reactions occurring on their surfaces for propulsion through a diffusiophoretic mechanism. As a result of interactions among these colloids, either directly or through fluid velocity and concentration fields, they may act collectively to form structures such as dynamic clusters. A general nonequilibrium thermodynamics framework for the description of such systems is presented that accounts for both self-diffusiophoresis and diffusiophoresis due to external concentration gradients, and is consistent with microreversibility. It predicts the existence of a reciprocal effect of diffusiophoresis back onto the reaction rate for the entire collection of colloids in the system, as well as the existence of a clustering instability that leads to nonequilibrium inhomogeneous system states.

The theory of multistate template-directed reversible copolymerization is developed by extending the method based on iterated function systems to matrices, taking into account the possibility of multiple activation states instead of a single one for the growth process. In this extended theory, the mean growth velocity is obtained with an iterated matrix function system and the probabilities of copolymer sequences are given by matrix products defined along the template. The theory allows us to understand the effects of template heterogeneity, which include a fractal distribution of local growth velocities far enough from equilibrium, and a regime of sublinear growth in time close to equilibrium.

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of active matter in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines.

Microreversibility constrains the fluctuations of the nonequilibrium currents that cross an open system. This can be seen from the so-called fluctuation relations, which are a direct consequence of microreversibility. Indeed, the latter are known to impose time-reversal symmetry relations on the statistical cumulants of the currents and their responses at arbitrary orders in the deviations from equilibrium. Remarkably, such relations have been recently analyzed by means of Euler's polynomials. Here we show that fluctuation relations can actually be explicitly written in terms of the constant terms of these particular polynomials. We hence demonstrate that Euler's polynomials are indeed fundamentally rooted in fluctuation relations, both in the absence and the presence of an external magnetic field., Comment: 10 pages

A nonequilibrium fluctuation theorem is established for a colloidal particle driven by an external force within the hydrodynamic theory of Brownian motion, describing hydrodynamic memory effects such as the t^(-3/2) power-law decay of the velocity autocorrelation function. The generalized Langevin equation is obtained for the general case of slip boundary conditions between the particle and the fluid. The Gaussian probability distributions for the particle to evolve in position-velocity space are deduced. It is proved that the joint probability distributions of forward and time-reversed paths have a ratio depending only on the work performed by the external force and the fluid temperature, in spite of the nonMarkovian character of the generalized Langevin process., Comment: Dedicated to the memory of Christian Van den Broeck

Langevin equations for the self-thermophoretic dynamics of Janus motors partially coated with an absorbing layer that is heated by a radiation field are presented. The derivation of these equations is based on fluctuating hydrodynamics and radiative heat transfer theory involving stochastic equations for bulk phases and surface processes that are consistent with microscopic reversibility. Expressions for the self-thermophoretic force and torque for arbitrary slip boundary conditions are obtained. The overdamped Langevin equations for the colloid displacement and radiative heat transfer provide expressions for the self-thermophoretic velocity and its reciprocal contribution where an external force can influence the radiative heat transfer. A nonequilibrium fluctuation formula is also derived and shows how the probability density of the Janus particle displacement and radiation energy transfer during the time interval [0,t] are related to the mechanical and thermal affinities that characterize the nonequilibrium system state.

The reversible kinetics of copolymerization is solved analytically for the multistate mechanism proposed by B. D. Coleman and T. G. Fox [J. Chem. Phys. 38, 1065 (1963)] under low conversion conditions where the concentrations of monomeric species are chemostatted and stay constant in time. Although the rates of this mechanism only depends on the currently attached or detached monomer, the growing macromolecular chain forms a nonMarkovian sequence that is characterized by matrices associated with every monomeric unit composing the sequence. These matrices are obtained by solving the kinetic equations and they determine the growth velocity of the copolymers, the statistical properties of its possible sequences, as well as the thermodynamics of the copolymerization process.

We present a stochastic approach for charge transport in transistors. In this approach, the electron and hole densities are governed by diffusion-reaction stochastic differential equations satisfying local detailed balance and the electric field is determined with the Poisson equation. The approach is consistent with the laws of electricity, thermodynamics, and microreversibility. In this way, the signal amplifying effect of transistors is verified under their working conditions. We also perform the full counting statistics of the two electric currents coupled together in transistors and we show that the fluctuation theorem holds for their joint probability distribution. Similar results are obtained including the displacement currents. In addition, the Onsager reciprocal relations and their generalizations to nonlinear transport properties deduced from the fluctuation theorem are numerically shown to be satisfied.

The single-particle and collective dynamics of systems comprising Janus motors, solvent and reactive solute species maintained in nonequilibrium states are investigated. Reversible catalytic reactions with the solute species take place on the catalytic faces of the motors, and the nonequilibrium states are established by imposing either constant-concentration reservoirs that feed and remove reactive species, or through out-of-equilibrium fluid phase reactions. We consider general intermolecular interactions between the Janus motor hemispheres and the reactive species. For single motors, we show that the reaction rate depends nonlinearly on an applied external force when the system is displaced far from equilibrium. We also show that a finite-time fluctuation formula derived for fixed catalytic particles describes the nonequilibrium reactive fluctuations of moving Janus motors. Simulation of the collective dynamics of small ensembles of Janus motors with reversible kinetics under nonequilibrium conditions are carried out and the spatial and orientational correlations of dynamic cluster states are discussed. The conditions leading to the instability of the homogeneous motor distribution and the onset of nonequilibrium dynamical clustering are described.

Colloidal motors without moving parts can be propelled by self-diffusiophoresis, coupling molecular concentration gradients generated by surface chemical reactions to the velocity slip between solid Janus particles and the surrounding fluid solution. The interfacial properties involved in this propulsion mechanism can be described by nonequilibrium thermodynamics and statistical mechanics, disclosing the fundamental role of microreversibility in the coupling between motion and reaction. Among other phenomena, the approach predicts that propulsion by fuel consumption has the reciprocal effect of fuel synthesis by mechanical action.

For open systems subjected to external magnetic fields, relations between the statistical cumulants of their fluctuating currents and their response coefficients are established at arbitrary orders in the deviations from equilibrium, as a consequence of microreversibility. These relations are systematically deduced from the extension of the fluctuation relation for this class of systems, and analyzed by using methods developed in [M. Barbier and P. Gaspard, J. Phys. A: Math. Theor. 51 (2018) 355001]. We unambiguously identify, among the statistical cumulants and their nonequilibrium responses, which of these quantities are independent and thus left unspecified by the fluctuation relation, i.e. by microreversibility. We also find the explicit expression of the dependent quantities in terms of the independent ones by means of coefficients of Euler polynomials., Comment: 30 pages

A finite-time fluctuation theorem for the diffusion-influenced surface reaction A <=> B is investigated for spherical and Janus catalytic particles. The finite-time rates and thermodynamic force are analytically calculated by solving diffusion equations with the special boundary conditions of the finite-time fluctuation theorem. Theory is compared with numerical simulations carried out with two different methods: a random walk algorithm and multiparticle collision dynamics.

A finite-time fluctuation theorem is proved for the diffusion-influenced surface reaction A<->B in a domain with any geometry where the species A and B undergo diffusive transport between the reservoir and the catalytic surface. A corresponding finite-time thermodynamic force or affinity is associated with the symmetry of the fluctuation theorem. The time dependence of the affinity and the reaction rates characterizing the stochastic process can be expressed analytically in terms of the solution of deterministic diffusion equations with specific boundary conditions.

Microreversibility rules the fluctuations of the currents flowing across open systems in nonequilibrium (or equilibrium) steady states. As a consequence, the statistical cumulants of the currents and their response coefficients at arbitrary orders in the deviations from equilibrium obey time-reversal symmetry relations. It is shown that these relations allow us to systematically reduce the amount of independent quantities that need to be measured experimentally or computed theoretically in order to fully characterize the linear and nonlinear transport properties of general open systems. This reduction is shown to approach one half for quantities of arbitrarily high orders., Comment: 31 pages

A stochastic approach for charge transport in diodes is developed in consistency with the laws of electricity, thermodynamics, and microreversibility. In this approach, the electron and hole densities are ruled by diffusion-reaction stochastic partial differential equations and the electric field generated by the charges is determined with the Poisson equation. These equations are discretized in space for the numerical simulations of the mean density profiles, the mean electric potential, and the current-voltage characteristics. Moreover, the full counting statistics of the carrier current and the measured total current including the contribution of the displacement current are investigated. On the basis of local detailed balance, the fluctuation theorem is shown to hold for both currents.

Nonequilibrium interfacial thermodynamics is formulated in the presence of surface reactions for the study of diffusiophoresis in isothermal systems. As a consequence of microreversibility and Onsager-Casimir reciprocal relations, diffusiophoresis, i.e., the coupling of the tangential components of the pressure tensor to the concentration gradients of solute species, has a reciprocal effect where the interfacial currents of solutes is coupled to the slip velocity. The presence of surface reactions is shown to modify the diffusiophoretic and reciprocal effects at the fluid-solid interface. The thin-layer approximation is used to describe the solution flowing near a reactive solid interface. Analytic formulas describing the diffusiophoretic and reciprocal effects are deduced in the thin-layer approximation and tested numerically for the Poiseuille flow of a solution between catalytic planar surfaces.

Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments., Comment: 11 pages, 7 figures

Janus motors with chemically active and inactive hemispheres can operate only under nonequilibrium conditions where detailed balance is broken by fluxes of chemical species that establish a nonequilibrium state. A microscopic model for reversible reactive collisions on a Janus motor surface is constructed and shown to satisfy detailed balance. The model is used to study Janus particle reactive dynamics in systems at equilibrium where generalized chemical rate laws that include time-dependent rate coefficients with power-law behavior are shown to describe reaction rates. While maintaining reversible reactions on the Janus catalytic hemisphere, the system is then driven into a nonequilibrium steady state by fluxes of chemical species that control the chemical affinity. The statistical properties of the self-propelled Janus motor in this nonequilibrium steady state are investigated and compared with predictions of a fluctuating thermodynamics theory. The model has utility beyond the examples presented here, since it allows one to explore various aspects of nonequilibrium fluctuations in systems with self-diffusiophoretic motors from a microscopic perspective.

The propulsion of active particles by self-diffusiophoresis is driven by asymmetric catalytic reactions on the particle surface that generate a mechanochemical coupling between the fluid velocity and the concentration fields of fuel and product in the surrounding solution. Because of thermal and molecular fluctuations in the solution, the motion of micrometric or submicrometric active particles is stochastic. Coupled Langevin equations describing the translation, rotation, and reaction of such active particles are deduced from fluctuating chemohydrodynamics and fluctuating boundary conditions at the interface between the fluid and the particle. These equations are consistent with microreversibility and the Onsager-Casimir reciprocal relations between affinities and currents, and provide a thermodynamically consistent basis for the investigation of the dynamics of active particles propelled by diffusiophoretic mechanisms.

Microscopic dynamical aspects of the propulsion of nanomotors by self-phoretic mechanisms are considered. Propulsion by self-diffusiophoresis relies on the mechanochemical coupling between the fluid velocity field and the concentration fields induced by asymmetric catalytic reactions on the motor surface. The consistency between the thermodynamics of this coupling and the microscopic reversibility of the underlying molecular dynamics is investigated. For this purpose coupled Langevin equations for the translational, rotational, and chemical fluctuations of self-phoretic motors are derived. A mechanochemical fluctuation theorem for the joint probability to find the motor at position r after n reactive events have occurred during the time interval t is also derived. An important result that follows from this analysis is the identification of an effect that is reciprocal to self-propulsion by diffusiophoresis, which leads to the possibility of fuel synthesis by mechanochemical coupling to external force and torque.

We present a systematic computation of the heat conductivity of the Markov jump process modeling the energy exchanges in an array of locally confined hard spheres at the conduction threshold. Based on a variational formula [Sasada M. 2016, {\it Thermal conductivity for stochastic energy exchange models}, arXiv:1611.08866], explicit upper bounds on the conductivity are derived, which exhibit a rapid power-law convergence towards an asymptotic value. We thereby conclude that the ratio of the heat conductivity to the energy exchange frequency deviates from its static contribution by a small negative correction, its dynamic contribution, evaluated to be $-0.000\,373$ in dimensionless units. This prediction is corroborated by kinetic Monte Carlo simulations which were substantially improved compared to earlier results., Comment: 33 pages, minor revisions

The kinetics and thermodynamics of free living copolymerization are studied for processes with rates depending on k monomeric units of the macromolecular chain behind the unit that is attached or detached. In this case, the sequence of monomeric units in the growing copolymer is a kth-order Markov chain. In the regime of steady growth, the statistical properties of the sequence are determined analytically in terms of the attachment and detachment rates. In this way, the mean growth velocity as well as the thermodynamic entropy production and the sequence disorder can be calculated systematically. These different properties are also investigated in the regime of depolymerization where the macromolecular chain is dissolved by the surrounding solution. In this regime, the entropy production is shown to satisfy Landauer's principle.

Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase significantly thanks to this dependence at the basis of the mechanism of exonuclease proofreading. In particular, this dependence can provide up to a hundred-fold lowering of the error probability under physiological conditions. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria., Comment: Physical Review E (2016)

A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependences on nucleotide concentrations and template sequence are explicitly taken into account. In this framework, the kinetic and thermodynamic properties of DNA replication, in particular, the mean growth velocity, the error probability, and the entropy production in terms of the rate constants and the concentrations are calculated analytically. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria., Comment: Physical Review E (2016)

Isometric fluctuation relations are deduced for the fluctuations of the order parameter in equilibrium systems of condensed-matter physics with broken discrete or continuous symmetries. These relations are similar to their analogues obtained for non-equilibrium systems where the broken symmetry is time reversal. At equilibrium, these relations show that the ratio of the probabilities of opposite fluctuations goes exponentially with the symmetry-breaking external field and the magnitude of the fluctuations. These relations are applied to the Curie-Weiss, Heisenberg, and $XY$~models of magnetism where the continuous rotational symmetry is broken, as well as to the $q$-state Potts model and the $p$-state clock model where discrete symmetries are broken. Broken symmetries are also considered in the anisotropic Curie-Weiss model. For infinite systems, the results are calculated using large-deviation theory. The relations are also applied to mean-field models of nematic liquid crystals where the order parameter is tensorial. Moreover, their extension to quantum systems is also deduced., Comment: 34 pages, 14 figures

We investigate the properties of a two-dimensional quasicrystal in the presence of a uniform magnetic field. In this configuration, the density of states (DOS) displays a Hofstadter butterfly-like structure when it is represented as a function of the magnetic flux per tile. We show that the low-DOS regions of the energy spectrum are associated with chiral edge states, in direct analogy with the Chern insulators realized with periodic lattices. We establish the topological nature of the edge states by computing the topological Chern number associated with the bulk of the quasicrystal. This topological characterization of the non-periodic lattice is achieved through a local (real-space) topological marker. This work opens a route for the exploration of topological insulating materials in a wide range of non-periodic lattice systems, including photonic crystals and cold atoms in optical lattices., Comment: 10 pages, 9 figures. Published version

A study is reported of the quantum scattering resonances of dissociating molecules using a semiclassical approach based on periodic-orbit theory. The dynamics takes place on a potential energy surface with an energy barrier separating two channels of dissociation. Above the barrier, the unstable symmetric-stretch periodic orbit may undergo a supercritical pitchfork bifurcation, leading to a classically chaotic regime. Signatures of the bifurcation appear in the spectrum of resonances, which have a shorter lifetime than classically expected. A method is proposed to evaluate semiclassically the energy and lifetime of the quantum resonances in this intermediate regime.

An overview is given of recent advances in nonequilibrium statistical mechanics about the statistics of random paths and current fluctuations. Although statistics is carried out in space for equilibrium statistical mechanics, statistics is considered in time or spacetime for nonequilibrium systems. In this approach, relationships have been established between nonequilibrium properties such as the transport coefficients, the thermodynamic entropy production, or the affinities, and quantities characterizing the microscopic Hamiltonian dynamics and the chaos or fluctuations it may generate. This overview presents results for classical systems in the escape-rate formalism, stochastic processes, and open quantum systems.

Information erasure at the molecular scale during the depolymerization of copolymers is shown to require a minimum entropy production in accordance with Landauer's principle and as a consequence of the second law of thermodynamics. This general result is illustrated with an exactly solvable model of copolymerization, which also shows that the minimum entropy production that is possible for a specific molecular mechanism of depolymerization may be larger than the minimum required by Landauer's principle.