This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration data, i.e., slope of free energy with respect to the switching variable lambda. We employ linear regression to construct a polynomial that optimally fits the thermodynamic integration data, and thus reduces the bias and uncertainty of the resulting free energy est...

an analytical equation of state is applied to calculate the thermodynamic properties for argon. theequation of state is that of song and mason. it is based on a statistical-mechanical perturbation theory ofhard convex bodies and can be written as fifth-order polynomial in the density. there exist three temperaturedependentparameters: the second virial coefficient, an effective molecular volume,...

We describe the origin and significance of electrical and mechanical observations on nerves. To this end, we compare two models for neural activity, which are the established Hodgkin–Huxley model and the more recent soliton theory, respectively. While the Hodgkin–Huxley model focuses particularly on the electrical aspects of the neural membranes, the soliton model is based on hydrodynamic and t...

Numerous cellular cosolutes significantly impact the way that proteins and other biomacromolecules act and interact. We have followed the thermodynamic effect of several cosolute classes, including polymers, cellular osmolytes, and inorganic salts, on the stability of biomolecular folding and complexation. By comparing changes in free energy, enthalpy, and entropy upon cosolutes addition for th...

Thermodynamic and dynamic analyses of a variable speed reciprocating compressor have been conducted to investigate performance changes and some data related to the reliability problems such as valve velocity, PV value, bearing loci, Sommerfeld number, minimum film thickness etc. The first law of thermodynamics, continuity equations, valve dynamic equations and Helmholtz resonator method were us...

Using the Thermodynamic Formalism, we introduce a Gibbsian model for the identification of regular grammars based only on positive evidence. This model mimics the natural language acquisition procedure driven by prosody which is here represented by the thermodynamic potential. The statistical question we face is how to estimate the incidence matrix of a sub-shift of finite type from a sample pr...

We analyze numerically thermal fluctuations of the static overlap between equilibrium configurations in a glass-forming liquid approaching the glass transition. We find that the emergence of slow dynamics near the onset temperature correlates with the development of non-Gaussian probability distributions of overlap fluctuations, measured using both annealed and quenched definitions. Below a cri...

Calorimetric heat effects and structural rearrangements accompanying the immersion of dry solid bovine pancreatic α-chymotrypsin in anhydrous organic solvents and water were measured at 298 K. It was found that the enthalpy and IR-absorbance changes being put together obey good linear correlation. According to the extent of their influence on the protein structure and thermodynamic state the so...

“Umbrella samplmg” has been incorporated in the thermodynamic integration method to obtain a potential of mean force by slow growth molecular-dynamics simulations. The method was tested for liquid argon, for which good agreement was obtained with a standard potential of mean force, as derived from the radial pair-correlation function. For a sodium chloride ion-pair in aqueous solution the calcu...

The aim of thermodynamic integration is to compute the difference in a thermodynamic property (usually the free energy) of the system between some reference state and the state of interest. To measure the free energy change from initial to final state, thermodynamic parameters characterizing the system are changed infinitely slowly so that at each stage along the path the system is in equilibri...