Equilibrium Ensemble Averages Research Articles

Memory effects in a random walk description of protein structure ensembles.

In this paper, we show that ensembles of well-structured and unstructured proteins can be distinguished by borrowing concepts from non-equilibrium statistical mechanics. For this purpose, we represent proteins by two different polymer models and interpret the resulting polymer configurations as random walks of a diffusing particle in space. The first model is the trace of the Cα-atoms along the protein main chain, and the second is their projections onto the protein axis. The resulting trajectories are subsequently analyzed using the theory of the generalized Langevin equation. Velocities are replaced by displacements relating consecutive points on the discrete protein axes and equilibrium ensemble averages by averages over appropriate protein structure ensembles. The resulting displacement autocorrelation functions resemble those of the velocity autocorrelation functions of simple liquids and display a minimum, which can be related to the lengths of secondary structure elements. This minimum is clearly more pronounced for well-structured proteins than for unstructured ones, and the corresponding memory function displays a slower decay, indicating a stronger "folding memory."

Free Energies of Quantum Particles: The Coupled-Perturbed Quantum Umbrella Sampling Method.

We introduce a new simulation method called Coupled-Perturbed Quantum Umbrella Sampling that extends the classical umbrella sampling approach to reaction coordinates involving quantum mechanical degrees of freedom. The central idea in our method is to solve coupled-perturbed equations to find the response of the quantum system's wave function along a reaction coordinate of interest. This allows for propagation of the system's dynamics under the influence of a quantum biasing umbrella potential and provides a method to rigorously undo the effects of the bias to compute equilibrium ensemble averages. In this way, one can drag electrons into regions of high free energy where they would otherwise not go, thus enabling chemistry by fiat. We demonstrate the applicability of our method for two condensed-phase systems of interest. First, we consider the interaction of a hydrated electron with an aqueous sodium cation, and we calculate a potential of mean force that shows that an e(-):Na(+) contact pair is the thermodynamically favored product starting from either a neutral sodium atom or the separate cation and electron species. Second, we present the first determination of a hydrated electron's free-energy profile relative to an air/water interface. For the particular model parameters used, we find that the hydrated electron is more thermodynamically stable in the bulk rather than at the interface. Our analysis suggests that the primary driving force keeping the electron away from the interface is the long-range electron-solvent polarization interaction rather than the short-range details of the chosen pseudopotential.

Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: Theory and application to free energies, moments, and thermodynamic length in single-molecule pulling experiments

Recently discovered identities in statistical mechanics have enabled the calculation of equilibrium ensemble averages from realizations of driven nonequilibrium processes, including single-molecule pulling experiments and analogous computer simulations. Challenges in collecting large data sets motivate the pursuit of efficient statistical estimators that maximize use of available information. Along these lines, Hummer and Szabo developed an estimator that combines data from multiple time slices along a driven nonequilibrium process to compute the potential of mean force. Here, we generalize their approach, pooling information from multiple time slices to estimate arbitrary equilibrium expectations. Our expression may be combined with estimators of path-ensemble averages, including existing optimal estimators that use data collected by unidirectional and bidirectional protocols. We demonstrate the estimator by calculating free energies, moments of the polymer extension, the thermodynamic metric tensor, and the thermodynamic length in a model single-molecule pulling experiment. Compared to estimators that only use individual time slices, our multiple time-slice estimators yield substantially smoother estimates and achieve lower variance for higher-order moments.

Probing subglass relaxation in polymers via a geometric representation of probabilities, observables, and relaxation modes for discrete stochastic systems

The dynamics of many physical, chemical, and biological systems can be reduced to a succession of infrequent transitions in a network of discrete states representing low energy regions in configuration space. This enables accessing long-time dynamics and predicting macroscopic properties. Here we develop a new, perfectly general statistical mechanical/geometric formulation that expresses both state probabilities and all observables in the same Euclidean space, spanned by the eigenvectors of the symmetrized time evolution operator. Our formalism leads to simple expressions for nonequilibrium and equilibrium ensemble averages, variances, and time correlation functions of any observable and allows a rigorous decomposition of the dynamics into relaxation modes. Applying it to subglass segmental relaxation in atactic polystyrene up to times on the order of 10 micros, we probe the molecular mechanism of the gamma and delta processes and unequivocally identify the delta process with rotation of a single phenyl group around its stem.

Memory functions for transport fluxes: Explicit formulae for high order memory kernels

Abstract Memory kernels of the fourth order and fifth order in Mori's continued fraction representation of time correlation functions are derived here explicitly in terms of the transport fluxes and their time derivatives. Collective modes and mode-mode coupling effects are included in the basic dynamic variable set. It is observed that the damping matrix terms in the continued fraction, are equilibrium ensemble averages of the transport fluxes and are thus amenable to computer simulation calculations. Since equilibrium ensemble averages can be obtained with less numerical uncertainties than dynamic time correlations, the expressions presented for K 4 (0) and K 5 (0) are useful in numerical works.

Classical Green's Functions in Response Theory

The present paper is concerned with the retarded many-time thermodynamic Green's function method in classical statistical mechanics. In the formulation of the nonlinear response of a dynamical variable, unaveraged Green's functions are specified and used to discuss the physical meaning of many-time Poisson-bracket nests. Equilibrium ensemble averages of these Green's functions are relevant to the classical Kubo response theory, the latter of which is interpreted from the viewpoints of both the classical ``Heisenberg'' and ``Schrödinger'' pictures. A method for evaluating the many-time thermodynamic Green's functions based on their definition in terms of the resolvent operator is suggested and discussed in relation to the linear dielectric function and the anharmonic oscillator. The many-time Green's function equations of motion are shown to be equivalent to identities based on the resolvent operator. It is shown how microscopic equations of motion can be used to derive the Bogoliubov-Sadovnikov (B-S) hierarchy from the lowest-order many-time Green's function equation of motion.

Model Approach to Nonadiabatic Reaction Processes

A transport theory of reactive flux is developed on the basis of a model potential-energy surface with an unbranched reaction path and many harmonic vibrations perpendicular to this path. Coriolis forces are ignored and the vibrational spectrum is assumed to be slowly varying with the reaction coordinate ξ. An interaction between translational and vibrational motion on the potential-energy surface, similar to the one in the Fröhlich Hamiltonian, is derived. The method of equations of motion is employed to calculate Green's functions. With the assumption of equilibrium for the bound degrees of freedom, Green's functions containing higher correlations can be expressed exactly in terms of Green's functions of lower order. Solutions of the integral equations are given for physically relevant energy regions. Explicit account is taken of the internal linewidth and the effects of reactive resonance scattering. The results are expressed in terms of equilibrium ensemble averages and reaction rates.

The heats of transport and the time correlation formalism

Formal expressions for the heats of transport, Q*, in a multicomponent system have been derived. The starting point is the well-known time correlation expressions for the phenomenological coefficients in the equations which express each flux of matter and the heat flux as linear functions of all the conjugate forces. Each Q* is the sum of a part involving only equilibrium ensemble averages and a time correlation part. The equilibrium part is identical to that of the Kirkwood transport theory. The properties of the non-equilibrium part are briefly discussed and an alternative form derived which expands it as a linear function of the isothermal friction constants, the coefficients of proportionality being a different set of time correlation functions.

Theory of the Influence of Environment on the Angular Distribution of Nuclear Radiation

The effect of electronic relaxation processes on the angular correlation and on the angular distribution of radiation from oriented nuclei is investigated. The influence of the environment on the radioactive nuclei is taken into account by reducing the density operator for the total system (nucleus and surroundings mutually interacting) to a density operator for the nucleus alone. Elimination of the unobserved bath variables is performed with the help of Zwanzig's projection-operator technique. The Liouville formalism is used throughout. The (initially unspecified) properties of the environment enter the theory via second-order correlation functions, which are defined in terms of equilibrium ensemble averages of certain bath operators, like, e.g., the hyperfine-field operator. The matrix elements of the nuclear-evolution operator (which is a superoperator in Liouville space) with respect to a complete orthonormal set of multipole operators are just the usual perturbation factors ${{G}_{k{k}^{\ensuremath{'}}}}^{q{q}^{\ensuremath{'}}}$ of perturbed-angular-correlations theory. The consequent use of the multipole representation yields immediately the final formulas needed in the expression for both the angular distribution of radiation from oriented nuclei and the angular correlation function. The general theory includes relaxation processes due to magnetic and quadrupole interactions. The important case of purely magnetic interactions is discussed in more detail. Specialization to relaxation caused by randomly fluctuating fields yields a formula which contains both the Abragam-Pound result for time-fluctuating quadrupole interaction and Micha's extension to randomly time-varying magnetic fields in multidomain ferromagnets. Exact high-temperature solutions are presented for single crystals in a static magnetic field and with magnetic-type relaxation processes (axially symmetric case). For nuclei with spin $I=1$, the extension to arbitrary temperatures has been considered. The application of the present theory to the problem of multipole relaxation (which arises, e.g., in spin-lattice relaxation measurements with NMR/ON technique) is discussed.