Statistical mechanical theory for the structure of steady state systems: application to a Lennard-Jones fluid with applied temperature gradient

The constrained entropy and probability distribution are given for the structure that develops in response to an applied thermodynamic gradient, as occurs in driven steady state systems. The theory is linear but is applicable to gradients with arbitrary spatial variation. The phase space probability distribution is also given, and it is surprisingly simple with a straightforward physical interpretation. With it, all of the known methods of equilibrium statistical mechanics for inhomogeneous systems may now be applied to determining the structure of nonequilibrium steady state systems. The theory is illustrated by performing Monte Carlo simulations on a Lennard-Jones fluid with externally imposed temperature and chemical potential gradients. The induced energy and density moments are obtained, as well as the moment susceptibilities that give the rate of change of these with imposed gradient and which also give the fluctuations in the moments. It is shown that these moment susceptibilities can be written in terms of bulk susceptibilities and also that the Soret coefficient can be expressed in terms of them.     

Statistical mechanical theory for steady state systems. V. Nonequilibrium probability density

The phase space probability density for steady heat flow is given. This generalizes the Boltzmann distribution to a nonequilibrium system. The expression includes the nonequilibrium partition function, which is a generating function for statistical averages and which can be related to a nonequilibrium free energy. The probability density is shown to give the Green-Kubo formula in the linear regime. A Monte Carlo algorithm is developed based upon a Metropolis sampling of the probability distribution using an umbrella weight. The nonequilibrium simulation scheme is shown to be much more efficient for the thermal conductivity of a Lennard-Jones fluid than the Green-Kubo equilibrium fluctuation method. The theory for heat flow is generalized to give the generic nonequilibrium probability densities for hydrodynamic transport, for time-dependent mechanical work, and for nonequilibrium quantum statistical mechanics.     

Statistical mechanical theory for steady state systems. VII. Nonlinear theory

The second entropy theory for nonequilibrium thermodynamics is extended to the nonlinear regime and to systems of mixed parity (even and odd functions of molecular velocities). The steady state phase space probability density is given for systems of mixed parity. The nonlinear transport matrix is obtained and it is shown to yield the analog of the linear Onsager-Casimir reciprocal relations. Its asymmetric part contributes to the flux and to the production of second entropy. The nonlinear transport matrix is not simply expressible as a Green-Kubo fluctuation equilibrium time correlation function. However, here the first nonlinear correction to the transport coefficient is given explicitly as a type of the Green-Kubo equilibrium time correlation function. The theory is illustrated by application to chemical kinetics.     

Entropy production of a mechanically driven single oligomeric enzyme: a consequence of fluctuation theorem

In this work we have shown how an applied mechanical force affects an oligomeric enzyme kinetics in a chemiostatic condition where the statistical characteristics of random walk of the substrate molecules over a finite number of active sites of the enzyme plays important contributing factors in governing the overall rate and nonequilibrium thermodynamic properties. The analytical results are supported by the simulation of single trajectory based approach of entropy production using Gillespie’s stochastic algorithm. This microscopic numerical approach not only gives the macroscopic entropy production from the mean of the distribution of entropy production which depends on the force but also a broadening of the distribution by the applied mechanical force, a kind of power broadening. In the nonequilibrium steady state (NESS), both the mean and the variance of the distribution increases and then saturates with the rise in applied force corresponding to the situation when the net rate of product formation reaches a limiting value with an activationless transition. The effect of the system-size and force on the entropy production distribution is shown to be constrained by the detailed fluctuation theorem.     

Molecular theory of irreversibility

A generalization of the Gibbs entropy postulate is proposed based on the Bogolyubov-Born-Green-Kirkwood-Yvon hierarchy of equations as the nonequilibrium entropy for a system of N interacting particles. This entropy satisfies the basic principles of thermodynamics in the sense that it reaches its maximum at equilibrium and is coherent with the second law. By using a generalization of the Liouville equation describing the evolution of the distribution vector, it is demonstrated that the entropy production is a non-negative quantity. Moreover, following the procedure of nonequilibrium thermodynamics a transport matrix is introduced and a microscopic expression for this is derived. This framework allows one to perform the thermodynamic analysis of nonequilibrium steady states with smooth phase-space distribution functions which, as proven here, constitute the states of minimum entropy production when one considers small departures from stationarity.     

非平衡定态化学反应体系对细致平衡偏离的不可逆性之随机热力学量度

在随机描述的层次上,成功地构筑了非平衡定态化学反应体系对细致平衡偏离的不可逆性之随机热力学判据.基于Fokker-Planck方程建立了连续Markov过程系统的随机熵平衡方程,发现在随机态空间中随机熵的时间变率亦可分为源项和流项两部分贡献.对于化学反应体系,作为态空间源项的随机熵产生可作为偏离细致平衡不可逆性的合适度量,此泛函量的零值标志着细致平衡.进一步借助按系统广度量的Ω展开法,通过对随机力及共轭的随机流的分析揭示态空间中的随机熵产生仅源于状态对细致平衡的偏离,并主要来自非Poisson涨落的贡献,因而可作为随机热力学量去判别和量度化学反应体系对细致平衡的偏离.     

一个纳入活化络合非平衡效应的TST公式体系

在唯象理论的层次上评述了活化络合体系的非平衡性引起的非平衡统计问题;通过分析活化络合过程的耗散与涨落对反应速度的影响,提出了一个纳入了活化络合过程非平衡效应的TST公式体系代替活化络合平衡常数,建立了活化络合耗散函数与反应速度的关系.同时讨论了影响反应活化络合进程耗散-涨落的诸因素所导致的速度常数统计漂移     

Calculation of entropy with computer simulation methods

A new approximate method for calculating entropy with computer simulation methods is proposed. The sampling probability of an equilibrium configuration is calculated by means of the frequency of occurrence of what we call here local states (related to the state of the particle and its neighbors); hence entropy can be calculated as well. The method is applied to the Metropolis' Monte Carlo simulation for the case of the square Ising lattice. The results are in very good agreement with theory even close to the critical temperature. The method is used also to calculate non-equilibrium entropy.     

Statistical mechanical theory for steady-state systems. III. Heat flow in a Lennard-Jones fluid

A statistical mechanical theory for heat flow is developed based upon the second entropy for dynamical transitions between energy moment macrostates. The thermal conductivity, as obtained from a Green-Kubo integral of a time correlation function, is derived as an approximation from these more fundamental theories, and its short-time dependence is explored. A new expression for the thermal conductivity is derived and shown to converge to its asymptotic value faster than the traditional Green-Kubo expression. An ansatz for the steady-state probability distribution for heat flow down an imposed thermal gradient is tested with simulations of a Lennard-Jones fluid. It is found to be accurate in the high-density regime at not too short times, but not more generally. The probability distribution is implemented in Monte Carlo simulations, and a method for extracting the thermal conductivity is given.     

The energy pump and the origin of the non-equilibrium flux of the dynamical systems and the networks

The global stability of dynamical systems and networks is still challenging to study. We developed a landscape and flux framework to explore the global stability. The potential landscape is directly linked to the steady state probability distribution of the non-equilibrium dynamical systems which can be used to study the global stability. The steady state probability flux together with the landscape gradient determines the dynamics of the system. The non-zero probability flux implies the breaking down of the detailed balance which is a quantitative signature of the systems being in non-equilibrium states. We investigated the dynamics of several systems from monostability to limit cycle and explored the microscopic origin of the probability flux. We discovered that the origin of the probability flux is due to the non-equilibrium conditions on the concentrations resulting energy input acting like non-equilibrium pump or battery to the system. Another interesting behavior we uncovered is that the probabilistic flux is closely related to the steady state deterministic chemical flux. For the monostable model of the kinetic cycle, the analytical expression of the probabilistic flux is directly related to the deterministic flux, and the later is directly generated by the chemical potential difference from the adenosine triphosphate (ATP) hydrolysis. For the limit cycle of the reversible Schnakenberg model, we also show that the probabilistic flux is correlated to the chemical driving force, as well as the deterministic effective flux. Furthermore, we study the phase coherence of the stochastic oscillation against the energy pump, and argue that larger non-equilibrium pump results faster flux and higher coherence. This leads to higher robustness of the biological oscillations. We also uncovered how fluctuations influence the coherence of the oscillations in two steps: (1) The mild fluctuations influence the coherence of the system mainly through the probability flux while maintaining the regular landscape topography. (2) The larger fluctuations lead to flat landscape and the complete loss of the stability of the whole system.     

Non-equilibrium thermodynamics and kinetic theory of gas mixtures in the presence of interfaces

A broad range of the boundary value problems of the kinetic theory of gases and gas mixtures is considered based on kinetic theory and non-equilibrium thermodynamics. The interrelation of the kinetic theory and non-equilibrium thermodynamics is discussed. The balance equations at the interface are obtained for the case of the boundary layers with peculiar properties. Procedures for deriving the boundary conditions for slightly rarefied gas mixtures are outlined. The problems of calculating slip coefficients are discussed. The specificity of the kinetic effects in the boundary conditions is shown. A set of general relations related to gas mixture flows in capillaries is deduced. The possibility of non-equilibrium kinetic effects in the form of a paradoxical distribution of non-equilibrium temperature is shown. Methods of non-equilibrium thermodynamics are used to obtain the phenomenological equations describing the thermophoresis and diffusiophoresis of particles and cross phenomena. The growth and evaporation of droplets is considered based on kinetic theory and non-equilibrium thermodynamics.     

Potential and flux decomposition for dynamical systems and non-equilibrium thermodynamics: curvature, gauge field, and generalized fluctuation-dissipation theorem

The driving force of the dynamical system can be decomposed into the gradient of a potential landscape and curl flux (current). The fluctuation-dissipation theorem (FDT) is often applied to near equilibrium systems with detailed balance. The response due to a small perturbation can be expressed by a spontaneous fluctuation. For non-equilibrium systems, we derived a generalized FDT that the response function is composed of two parts: (1) a spontaneous correlation representing the relaxation which is present in the near equilibrium systems with detailed balance and (2) a correlation related to the persistence of the curl flux in steady state, which is also in part linked to a internal curvature of a gauge field. The generalized FDT is also related to the fluctuation theorem. In the equal time limit, the generalized FDT naturally leads to non-equilibrium thermodynamics where the entropy production rate can be decomposed into spontaneous relaxation driven by gradient force and house keeping contribution driven by the non-zero flux that sustains the non-equilibrium environment and breaks the detailed balance. On any particular path, the medium heat dissipation due to the non-zero curl flux is analogous to the Wilson lines of an Abelian gauge theory.     

Statistical mechanics and fluid structure

In the axiomatic approach to the derivation of statistical mechanics the theory is based upon the equations of motions of classical mechanics (Hamilton equations). Since these equations are unstable with respect to initial conditions, in the time τ ≈ 10^?12 s they generate chaos in the system of atoms and molecules. This chaos can be described by only probability theory laws. The laws of this theory are introduced into statistical mechanics as the second postulate. However, for both postulates (i.e., Hamilton equations and probability theory laws) to be compatible with each other, about one and a half ten of additional requirements defining in detail the matter model underlying the theory must be imposed on the system. This report analyzes only the restrictions imposed by probability theory. The main of them are: a transition to the thermodynamic limit, the condition of correlation attenuation, and a short-range character of the interaction potential. The matter model formulated based on these restrictions is a continuous medium in which a correlation sphere with a small radius R ≈ 10^?7 cm (physical point) is submerged. It is submerged in an infinite thermostat, the particles of which behave as the ideal gas relative to the particles forming the correlation sphere. Here all macroscopic parameters of matter in this physical point are determined by the state of the correlation sphere. Thus formulated model determines the macro- and microscopic structure of matter, and finally, results in thermodynamic and hydrodynamic equations.     

Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: an index of cooperativity

Here we have systematically studied the cooperative binding of substrate molecules on the active sites of a single oligomeric enzyme in a chemiostatic condition. The average number of bound substrate and the net velocity of the enzyme catalyzed reaction are studied by the formulation of stochastic master equation for the cooperative binding classified here as spatial and temporal. We have estimated the entropy production for the cooperative binding schemes based on single trajectory analysis using a kinetic Monte Carlo technique. It is found that the total as well as the medium entropy production shows the same generic diagnostic signature for detecting the cooperativity, usually characterized in terms of the net velocity of the reaction. This feature is also found to be valid for the total entropy production rate at the non-equilibrium steady state. We have introduced an index of cooperativity, C, defined in terms of the ratio of the surprisals or equivalently, the stochastic system entropy associated with the fully bound state of the cooperative and non-cooperative cases. The criteria of cooperativity in terms of C is compared with that of the Hill coefficient of some relevant experimental result and gives a microscopic insight on the mechanism of cooperative binding of substrate on a single oligomeric enzyme which is usually estimated from the macroscopic reaction rate.     

Transport properties of 2F <==> F2 in a temperature gradient as studied by molecular dynamics simulations

We calculate transport properties of a reacting mixture of F and F(2) from results of non-equilibrium molecular dynamics simulations. The reaction investigated is controlled by thermal diffusion and is close to local chemical equilibrium. The simulations show that a formulation of the transport problem in terms of classical non-equilibrium thermodynamics theory is sound. The chemical reaction has a large effect on the magnitude and temperature dependence of the thermal conductivity and the interdiffusion coefficient. The increase in the thermal conductivity in the presence of the chemical reaction, can be understood as a response to an imposed temperature gradient, which reduces the entropy production. The heat of transfer for the Soret stationary state was more than 100 kJ mol(-1), meaning that the Dufour and Soret effects are non-negligible in reacting mixtures. This sheds new light on the transport properties of reacting mixtures.     

On the Statistical Mechanics of Non-Hamiltonian Systems: The Generalized Liouville Equation, Entropy, and Time-Dependent Metrics

Several questions in the statistical mechanics of non-Hamiltonian systems are discussed. The theory of differential forms on the phase space manifold is applied to provide a fully covariant formulation of the generalized Liouville equation. The properties of invariant volume elements are considered, and the nonexistence in general of smooth invariant measures noted. The time evolution of the generalized Gibbs entropy associated with a given choice of volume form is studied, and conditions under which the entropy is constant are discussed. For non-Hamiltonian systems on manifolds with a metric tensor compatible with the flow, it is shown that the associated metric factor is in general a time-dependent solution of the generalized Liouville equation.     

A model for energy transfer in inelastic molecular collisions applicable at steady state or non-steady state and for an arbitrary distribution of collision energies

A new model for energy exchange between translational and internal degrees of freedom in atom-molecule collisions has been developed. It is suitable for both steady state conditions (e.g., a large number of collisions with thermal kinetic energies) and non-steady state conditions with an arbitrary distribution of collision energies (e.g., single high-energy collisions). In particular, it does not require that the collision energies be characterized by a quasi-thermal distribution, but nevertheless it is capable of producing a Boltzmann distribution of internal energies with the correct internal temperature under quasi-thermal conditions. The energy exchange is described by a transfer probability density that depends on the initial relative kinetic energy, the internal energy of the molecule, and the amount of energy transferred. The probability density for collisions that lead to excitation is assumed to decrease exponentially with the amount of transferred energy. The probability density for de-excitation is obtained from microscopic reversibility. The model has been implemented in the ion trap simulation program ITSIM and coupled with an Rice-Rampsberger-Kassel-Marcus (RRKM) algorithm to describe the unimolecular dissociation of populations of ions. Monte Carlo simulations of collisional energy transfer are presented. The model is validated for non-steady state conditions and for steady state conditions, and the effect of the kinetic energy dependence of the collision cross-section on internal temperature is discussed. Applications of the model to the problem of chemical mass shifts in RF ion trap mass spectrometry are shown.     

Free Energies in the Landau and Molecular Field Approaches

An expression for the entropy as a power series in the order parameter is derived in the context of molecular field theory. The expression is valid both at and away from equilibrium. It is a unique generalization of molecular field theory to non-equilibrium situations. Discrepancies with certain expressions which have appeared in the literature are resolved. Analysis of the radius of convergence of the power series indicates that in certain cases, including the Maier-Saupe model of liquid crystals, molecular field theory and Landau theory cannot be made to agree over the entire range of possible values of the order parameter.