Ensemble Of Microstates Research Articles

Microscopically Reversible Pathways with Memory

Statistical mechanics is a physics theory that deals with ensembles of microstates of a system compatible with environmental constraints and that on average define a thermodynamic state. The evolution of a small system is normally subjected to changing constraints, as set by a protocol, and involves a stochastic dependence on previous events. Here, we generalize the dynamic trajectories described by a realization of a physical system without dissipation to include those in which the history of previous events is necessary to understand its future. This framework is then used to characterize the processes experienced by the stochastic system, as derived from ensemble averages over the available pathways. We find that the pathways that the system traces in the presence of a protocol entail different statistics from those in its absence and prove that both types of pathways are equivalent in the limit of independent events. Such equivalence implies that a thermodynamic system cannot evolve away from equilibrium in the absence of memory. These results are useful to interpret single-molecule experiments in biophysics and other fields in nanoscience, as well as an adequate platform to describe non-equilibrium processes.

Thermodynamics Property of Electron-Phonon Interaction in Superconducting State

Abstract The purpose of this research was to investigate thermodynamics property of the electron-phonon interactions lead to generate Cooper pairs in superconducting state which was entropy. Entropy was a fundamental physical quantity of significant importance for the quantum phase transition. Normally, this property well known of the quasiparticles system in BCS theory but never theoretical research explain about statement of the background for this property. For this reason, by using atomistic microscopic of matter to definitions of the microcanonical ensemble of microstates, we assumed that density of the positive charged lattice ions was perturbed as a result of the electron motion deform the lattice. Our main result shows that the function of entropy from the microcanonical ensemble of microstates sense corresponds to the function of entropy and the Fermi distribution function of the quasiparticles system in BCS theory. Although, the entropy was absolute value can’t be directly measured but the function of entropy could be used as a part of calculation to found the specific heat jump of superconductor. To illustrate the effectiveness of this research, we investigated the situation involving the specific heat jump of hybridized two-band superconductor and the effect of hybridization coefficient on the specific heat jump was investigated.

Effects of hydrostatic pressure on the conformational equilibrium of tryptophan synthase from Salmonella typhimurium

A wide range of parameters influence allosteric communications between the alpha- and beta-subunits of the Trp synthase alpha(2)beta(2) multienzyme complex with L-Ser, including monovalent cations, pH, temperature, ligands, organic solvents, and hydrostatic pressure. The conformational change from closed to open can be monitored either by absorbance at 423 nm or fluorescence at 495 nm from the pyridoxal-5'-phosphate-L-Ser complex. Pressure perturbation was used to quantify the effects of monovalent cations, ligands, and mutations on the conformational equilibrium of Trp synthase. P-jump kinetics in the presence of Na(+), NH(4) (+), and Na(+) together with benzimidazole were also examined. The plots of lnk versus P are nonlinear and require a compressibility (beta(double dagger) (o)) term to obtain a good fit. beta(double dagger) (o) is positive for the Na(+) enzyme but negative for NH(4) (+) and Na(+) with benzimidazole. These results suggest that there is a large contribution of solvation to the kinetics of the conformational change of Trp synthase. The relaxation kinetics are also different if the P-jumps are made by increasing or decreasing pressure, suggesting that the enzyme conformations are ensembles of microstates.

The sodium/galactose symporter crystal structure is a dynamic, not so occluded state

The recent elucidation of the sodium/galactose symporter structure from the Vibrio parahaemolyticus bacterium, vSGLT, has revealed a similarity in the core architecture with transporters from different gene families, including the leucine transporter (LeuT). Even though several transporters sharing this core have been structurally determined over the past few years, vSGLT is the only one crystallized in the substrate-bound inward-facing conformation so far. In this study, we report the first insight into the dynamics and coordination of the galactose (Gal) and proposed Na+ ion in vSGLT using a series of molecular dynamics simulations with a total time of about 0.1 micros. Our study reveals new residues, not observed in the crystal structure, which closely interact with the Na(+) ion or the substrate for extended times, and shows that in the crystallized conformation, a Na+ ion placed at the site equivalent to Na2 in LeuT can escape into the intracellular (IC) space in the absence of external forces. We have identified the highly conserved Asp189 as a likely binding residue on the pathway of Na(+) into the IC cavity. The release of Gal, on the other hand, requires the rotation of the side chain of the inner hydrophobic gate, Tyr263, without a significant change in vSGLT backbone conformation. Our simulations further show that the crystal structure represents but one accessible binding pose of Gal and Na+ among an ensemble of microstates, and that the Gal undergoes versatile alternate interactions at the binding pocket.

STATES AND MICROSTATES IN A MEAN-FIELD APPROACH TO THE MINORITY GAME AND ITS GENERALIZATIONS

We developed a mean-field approach to the Minority Game, that allows us to reproduce the behavior of the model in the phase in which a so-called "dynamics of period two" is present. This dynamics describes the situation where the model is controlled by the presence of crowds of agents participating in the game. Our approach is based on the hypothesis that we can introduce states representative of the system, in such a form that averages over time can be replaced by averages over those states. The main idea is to work with virtual agents, rather than working with the actual set of agents of a particular game. Virtual agents are built from all the possible pairs of the strategies available in the model (the Full Strategy Space FSS). Moreover, we define an ensemble of microstates and, thereafter, states compatible with the specifications of the game. In this work we explain in detail how to introduce these elements, and how to actually calculate the ensemble of states and microstates. We have developed one generalization of the Minority Game as an attempt to make the model more realistic, by introducing interactions among the agents. We also discuss and explain the adequate ensemble of states and microstates for that generalization.

Entropy and Granular Materials: Model

The macrostructure of a granular material is treated as an ensemble of microstates of like spheres where each microstate is identified by a coordination number and a corresponding porosity. The probability of occurrence of these finite numbers of microstates is constrained by measurable information concerning the macrostate and described by maximizing the information entropy subject to these constraints and the axioms of probability theory. The macrostate behavior is then deduced from the probabilities of occurrence of the microstates and their mechanical performance. Existing observations of phenomena in granular media as related to soils and liquids are discussed and explained in light of the proposed entropy maximization scheme. Critical tests to examine the viability of the entropy model are proposed.

Determination of thermodynamic functions from scanning calorimetry data

AbstractWe present a theoretical basis and new methods for the determination of thermodynamic functions from scanning calorimetry data. A thermodynamic state is defined here as an ensemble of microstates in the system, and it can be defined only through assumptions of its heat capacity function and the two integral constants. With these assumptions, scanning calorimetry data can be analyzed using the single or double (or multi‐) deconvolution presented here. New equations to calculate the van't Hoff enthalpy function and the calorimetric enthalpy function are presented. We prove that the agreement of these two functions is a necessary and sufficient factor for the condition that the system can be described with the assumed two‐state model.