When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entro...

Accurate computation of free energy changes upon molecular binding remains a challenging problem, and changes in configurational entropy are especially difficult due to the potentially large numbers of local minima, anharmonicity, and high-order coupling among degrees of freedom. Here we propose a new method to compute molecular entropies based on the maximum information spanning tree (MIST) ap...

The free energy of binding of a ligand to a macromolecule is here formally decomposed into the (effective) energy of interaction, reorganization energy of the ligand and the macromolecule, conformational entropy change of the ligand and the macromolecule, and translational and rotational entropy loss of the ligand. Molecular dynamics simulations with implicit solvation are used to evaluate thes...

‎In this short note‎, ‎we present some inequalities for relative operator entropy which are generalizations of some results obtained by Zou [Operator inequalities associated with Tsallis relative operator entropy‎, ‎{em Math‎. ‎Inequal‎. ‎Appl.}‎ ‎{18} (2015)‎, ‎no‎. ‎2‎, ‎401--406]‎. ‎Meanwhile‎, ‎we also show some new lower and upper bounds for relative operator entropy and Tsallis relative o...

To better understand the interplay between protein-protein binding and protein dynamics, we analyzed molecular dynamics simulations of 17 protein-protein complexes and their unbound components. Complex formation does not restrict the conformational freedom of the partner proteins as a whole, but, rather, it leads to a redistribution of dynamics. We calculate the change in conformational entropy...

Isothermal titration calorimetry is able to provide accurate information on the thermodynamic contributions of enthalpy and entropy changes to free energies of binding. The Structure/Calorimetry of Reported Protein Interactions Online database of published isothermal titration calorimetry studies and structural information on the interactions between proteins and small-molecule ligands is used ...

A numerical investigation of entropy generation in laminar forced convection of gas flow over a backward facing step in a horizontal duct under bleeding condition is presented. For calculation of entropy generation from the second law of thermodynamics in a forced convection flow, the velocity and temperature distributions are primary needed. For this purpose, the three-dimensional Cartesian co...

abstract   background: the survival curves generally have been used for analysis of cell survival under stress conditions. they depict the relationship between the fraction of cells retaining their reproductive integrity and the absorbed dose. the median lethal dose, lethal concentration, 50% (lc 50 ) of a  toxin ,  radiation , or  pathogen  is the  dose required to kill half the members of a t...

 Casimir entropy is an important aspect of casimir effect and at the nanoscale is visible. In this paper, we employ the path integral method to ‎obtain a‎ ‎general‎ relation for casimir entropy and ‎i‎nternal energy of arbitrary shaped objects in the presence of two, three and four dimension scalar fields and ‎the‎ electromagnetic field. For this purpose, using Lagrangian and based on a perturb...

Let $G$ be a finite simple graph whose vertices and edges are weighted by two functions. In this paper we shall define and calculate entropy of a dynamical system on weights of the graph $G$, by using the weights of vertices and edges of $G$. We examine the conditions under which entropy of the dynamical system is zero, possitive or $+infty$. At the end it is shown that, for $rin [0,+infty]$, t...