Related papers: Computing spatially resolved rotational hydration …
This paper determines the excess free energy associated with the formation of a spherical cavity in a hard sphere fluid. The solvation free energy can be calculated by integration of the structural changes induced by inserting the cavity…
This article deals with the error estimates for numerical approximations of the entropy solutions of coupled systems of nonlocal hyperbolic conservation laws. The systems can be strongly coupled through the nonlocal coefficient present in…
We present a novel discontinuous Galerkin finite element method for numerical simulations of the rotating thermal shallow water equations in complex geometries using curvilinear meshes, with arbitrary accuracy. We derive an entropy…
We combine molecular dynamics simulations with experiments to estimate solubilities of organic salts in complex growth environments. We predict the solubility by simulations of the growth and dissolution of ions at the crystal surface kink…
We present a molecular dynamics simulation method for the computation of the solubility of organic crystals in solution. The solubility is calculated based on the equilibrium free energy difference between the solvated solute and its…
Modeling electronic systems is an important application for quantum computers. In the context of materials science, an important open problem is the computational description of chemical reactions on surfaces. In this work, we outline a…
We consider the numerical solution of coupled volume-surface reaction-diffusion systems having a detailed balance equilibrium. Based on the conservation of mass, an appropriate quadratic entropy functional is identified and an…
Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global…
The temperature-dependent behavior of defect densities within a crystalline structure is intricately linked to the phenomenon of vibrational entropy. Traditional methods for evaluating vibrational entropy are computationally intensive,…
The two-phase thermodynamic (2PT) model {[}J. Chem. Phys., \textbf{119}, 11792 (2003){]} provides a promising paradigm to efficiently determine the ionic entropies of liquids from molecular dynamics (MD). In this model, the vibrational…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
We demonstrate the accurate calculation of entropies and free energies for a variety of liquid metals using an extension of the two phase thermodynamic (2PT) model based on a decomposition of the velocity autocorrelation function into…
Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for ligand binding and recognition. Therefore, identifying the…
We discuss the simple microscopic derivation of a hydrophobic effect. Our approach is based on the standard functional representation of the partition function of interacting classical particles and subsequent passage to collective…
This study proposes a novel spatial discretization procedure for the compressible Euler equations which guarantees entropy conservation at a discrete level when an arbitrary equation of state is assumed. The proposed method, based on a…
Stable numerical simulations for a hyperbolic system of conservation laws of relaxation type but not in divergence form are obtained by incorporating the physical entropy into the simulations. The entropy balance is utilized as an…
Molecular dynamics simulations of water, liquid beryllium fluoride and silica melt are used to study the accuracy with which the entropy of ionic and molecular liquids can be estimated from atom-atom radial distribution function data. All…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…
We calculate the entanglement entropy for a sphere and a massless scalar field in any dimensions. The reduced density matrix is expressed in terms of the infinitesimal generator of conformal transformations keeping the sphere fixed. The…
In the free energy of hydration of a solute, the chemical contribution is given by the free energy required to expel water molecules from the coordination sphere and the packing contribution is given by the free energy required to create…