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.     

Statistical mechanical theory for steady state systems. IV. Transition probability and simulation algorithm demonstrated for heat flow

Two microscopic transition theorems are given for the probability of nonequilibrium work performed on a subsystem of a thermal reservoir along the trajectory in phase space of the subsystem. The resultant transition probability is applied to the case of heat flow down an applied temperature gradient. A combined molecular dynamics and Monte Carlo algorithm is given for such a nonequilibrium steady state. Results obtained for the thermal conductivity are in good agreement with previous Green-Kubo and nonequilibrium molecular dynamics results.     

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.     

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.     

Equilibrium and nonequilibrium molecular dynamics simulations of the thermal conductivity of molten alkali halides

The thermal conductivity of molten NaCl and KCl was calculated through the Evans-Gillan nonequilibrium molecular dynamics (NEMD) algorithm and Green-Kubo equilibrium molecular dynamics (EMD) simulations. The EMD simulations were performed for a "binary" ionic mixture and the NEMD simulations assumed a pure system for reasons discussed in this work. The cross thermoelectric coefficient obtained from Green-Kubo EMD simulations is discussed in terms of the homogeneous thermoelectric power or Seebeck coefficient of these materials. The thermal conductivity obtained from NEMD simulations is found to be in very good agreement with that obtained through Green-Kubo EMD simulations for a binary ionic mixture. This result points to a possible cancellation between the neglected "partial enthalpy" contribution to the heat flux associated with the interdiffusion of one species through the other and that part of the thermal conductivity related to the coupled fluxes of charge and heat in "binary" ionic mixtures.     

Theory for non-equilibrium statistical mechanics

This paper reviews a new theory for non-equilibrium statistical mechanics. This gives the non-equilibrium analogue of the Boltzmann probability distribution, and the generalization of entropy to dynamic states. It is shown that this so-called second entropy is maximized in the steady state, in contrast to the rate of production of the conventional entropy, which is not an extremum. The relationships of the new theory to Onsager's regression hypothesis, Prigogine's minimal entropy production theorem, the Langevin equation, the formula of Green and Kubo, the Kawasaki distribution, and the non-equilibrium fluctuation and work theorems, are discussed. The theory is worked through in full detail for the case of steady heat flow down an imposed temperature gradient. A Monte Carlo algorithm based upon the steady state probability density is summarized, and results for the thermal conductivity of a Lennard-Jones fluid are shown to be in agreement with known values. Also discussed is the generalization to non-equilibrium mechanical work, and to non-equilibrium quantum statistical mechanics. As examples of the new theory two general applications are briefly explored: a non-equilibrium version of the second law of thermodynamics, and the origin and evolution of life.     

Nonequilibrium potential function of chemically driven single macromolecules via Jarzynski-type Log-Mean-Exponential Heat

Applying the method from recently developed fluctuation theorems to the stochastic dynamics of single macromolecules in ambient fluid at constant temperature, we establish two Jarzynski-type equalities: (1) between the log-mean-exponential (LME) of the irreversible heat dissiption of a driven molecule in nonequilibrium steady-state (NESS) and ln P(ness)(x) and (2) between the LME of the work done by the internal force of the molecule and nonequilibrium chemical potential function mu(ness)(x) identical with U(x) + k(B)T ln P(ness)(x), where P(ness)(x) is the NESS probability density in the phase space of the macromolecule and U(x) is its internal potential function. Psi = integral mu(ness)(x) P(ness)(x) dx is shown to be a nonequilibrium generalization of the Helmholtz free energy and DeltaPsi = DeltaU - TDeltaS for nonequilibrium processes, where S = - kB integralP(x) ln P(x) dx is the Gibbs entropy associated with P(x). LME of heat dissipation generalizes the concept of entropy, and the equalities define thermodynamic potential functions for open systems far from equilibrium.     

Maximum Caliber: a variational approach applied to two-state dynamics

We show how to apply a general theoretical approach to nonequilibrium statistical mechanics, called Maximum Caliber, originally suggested by E. T. Jaynes [Annu. Rev. Phys. Chem. 31, 579 (1980)], to a problem of two-state dynamics. Maximum Caliber is a variational principle for dynamics in the same spirit that Maximum Entropy is a variational principle for equilibrium statistical mechanics. The central idea is to compute a dynamical partition function, a sum of weights over all microscopic paths, rather than over microstates. We illustrate the method on the simple problem of two-state dynamics, A<-->B, first for a single particle, then for M particles. Maximum Caliber gives a unified framework for deriving all the relevant dynamical properties, including the microtrajectories and all the moments of the time-dependent probability density. While it can readily be used to derive the traditional master equation and the Langevin results, it goes beyond them in also giving trajectory information. For example, we derive the Langevin noise distribution rather than assuming it. As a general approach to solving nonequilibrium statistical mechanics dynamical problems, Maximum Caliber has some advantages: (1) It is partition-function-based, so we can draw insights from similarities to equilibrium statistical mechanics. (2) It is trajectory-based, so it gives more dynamical information than population-based approaches like master equations; this is particularly important for few-particle and single-molecule systems. (3) It gives an unambiguous way to relate flows to forces, which has traditionally posed challenges. (4) Like Maximum Entropy, it may be useful for data analysis, specifically for time-dependent phenomena.     

Information theory and electron density

The intriguing concept of inherent uncertainty of probability schemes in information theory and statistical inference is applied to the molecular electron density. The electron density function is treated as a multimodal, three-dimensional probability density function describing the distribution of the electrons of a molecule in real space. A simple theory is proposed to introduce the amount of information associated with perturbations of the nuclear geometry such as molecular vibrations and reaction paths, in particular. It is shown by computations that the amount of information associated with the normal modes of vibration is related to the reduced mass. The proposed theory also suggests a novel Riemannian nuclear configuration space which is completely defined by the observable electron density of a molecular system.     

A simple and effective boundary model in nonequilibrium molecular dynamics method

We propose a simple and effective boundary model in a nonequilibrium molecular dynamics (NEMD) simulation to study the out-of-equilibrium dynamics of polymer fluids. The present boundary model can effectively weaken the depletion effect and the slip effect near the boundary, and remove the unwanted heat instantly. The validity of the boundary model is checked by investigating the flow behavior of dilute polymer solution driven by an external force. Reasonable density distributions of both polymer and solvent particles, velocity profiles of the solvent and temperature profiles of the system are obtained. Furthermore, the studied polymer chain shows a cross-streaming migration towards center of the tube, which is consistent with that predicted in previous literatures. These numerical results give powerful evidences for the validity of the present boundary model. Besides, the boundary model can also be used in other flows in addition to the Poiseuille flow.     

On calculation of thermal conductivity from Einstein relation in equilibrium molecular dynamics

In equilibrium molecular dynamics, Einstein relation can be used to calculate the thermal conductivity. This method is equivalent to Green-Kubo relation and it does not require a derivation of an analytical form for the heat current. However, it is not as commonly used as Green-Kubo relationship. Its wide use is hindered by the lack of a proper definition for integrated heat current (energy moment) under periodic boundary conditions. In this paper, we developed an appropriate definition for integrated heat current to calculate thermal conductivity of solids under periodic conditions. We applied this method to solid argon and silicon based systems; compared and contrasted with the Green-Kubo approach.     

Phoretic forces on convex particles from kinetic theory and nonequilibrium thermodynamics

In this article we derive the phoretic forces acting on a tracer particle, which is assumed to be small compared to the mean free path of the surrounding nonequilibrium gas, but large compared to the size of the surrounding gas molecules. First, we review and extend the calculations of Waldmann [Z. Naturforsch. A 14A, 589 (1959)] using half-sphere integrations and an accommodation coefficient characterizing the collision process. The presented methodology is applied to a gas subject to temperature, pressure, and velocity gradients. Corresponding thermophoretic, barophoretic, and rheophoretic forces are derived, and explicit expressions for spherical particles are compared to known results. Second, nonequilibrium thermodynamics is used to join the diffusion equation for the tracer particle with the continuum equations of nonisothermal hydrodynamics of the solvent. So doing, the distinct origin of the thermophoretic and barophoretic forces is demonstrated. While the latter enters similarly to an interaction potential, the former is given by flux-flux correlations in terms of a Green-Kubo relation, as shown in detail.     

Molecular thermodynamic model for equilibria in solution II. Statistical microscopic properties of ensembles

A statistical thermodynamic model for the interpretation of the equilibria in solution is based on the principle that the representative statistical ensembles can be characterized by two types of molecular distribution, one for non-reacting systems and another for reacting ones, respectively. Non-reacting and reacting ensembles correspond at the molecular level to one or a couple of potential curves, respectively. The properties of the thermodynamic model for solutions can be set up following some rules. These concern the statistical extension of the microscopic model to the whole ensemble and the successive averaging to get a mean partition function. The mean partition function is linked to the experimental domain of concentrations, dilutions and equilibrium constants (probability space) and to that of calorimetry, chemical work, and potentiometry (thermodynamics space). The formal connection between probability and thermodynamic space and the conformity of thermal equivalent dilution with the formulations of statistical thermodynamics are also shown.     

Photonic superdiffusive motion in resonance radiation trapping

In this work we consider the relation between the jump length probability density function and the line shape function in resonance radiation trapping in atomic vapors. The two-sided jump length probability density function suitable for a unidimensional formulation of radiative transfer is also derived. As a side result, a procedure to obtain the Maxwell distribution of velocities from the Maxwell-Boltzmann distribution of speeds was obtained. General relations that give the asymptotic jump length behavior and the Levy flight parameter mu for any line shape are obtained. The results are applied to generalized Doppler, generalized Lorentz, and Voigt line shape functions. It is concluded that the lighter the tail of the line shape function, the less heavy the tail of the jump length probability density function, although this tail is always heavy, with mu < or =1.     

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.