Search results for "thermodynamic integration"
showing 8 items of 18 documents
Computing absolute free energies of disordered structures by molecular simulation
2009
We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from a configuration which is representative for the state of interest. The method can be applied to lattice models (e.g., the Ising model) as well as off-lattice molecular models. We focus mainly on the more challenging off-lattice case. We propose a Monte Carlo algorithm, by which the thermodynamic integration path can be sampled efficiently. At the examples of the hard sphere liquid and a hard disk solid with a defect, we discuss several properties of the …
Bimodal Acidity at the Amorphous Silica/Water Interface
2015
International audience; Understanding the microscopic origin of the acid base behavior of mineral surfaces in contact with water is still a challenging task, for both the experimental and the theoretical communities. Even for a relatively simple material, such as silica, the origin of the bimodal acidity behavior is still a debated topic. In this contribution we calculate the acidity of single sites on the humid silica surface represented by a model for the hydroxylated amorphous surface. Using a thermodynamic integration approach based on ab initio molecular dynamics, we identify two different acidity values. In particular, some convex geminals and some type of vicinals are very acidic (pK…
Transitions between imperfectly ordered crystalline structures: A phase switch Monte Carlo study
2012
A model for two-dimensional colloids confined laterally by ``structured boundaries'' (i.e., ones that impose a periodicity along the slit) is studied by Monte Carlo simulations. When the distance $D$ between the confining walls is reduced at constant particle number from an initial value ${D}_{0}$, for which a crystalline structure commensurate with the imposed periodicity fits, to smaller values, a succession of phase transitions to imperfectly ordered structures occur. These structures have a reduced number of rows parallel to the boundaries (from $n$ to $n\ensuremath{-}1$ to $n\ensuremath{-}2$, etc.) and are accompanied by an almost periodic strain pattern, due to ``soliton staircases'' …
Does Young's equation hold on the nanoscale? A Monte Carlo test for the binary Lennard-Jones fluid
2010
When a phase-separated binary ($A+B$) mixture is exposed to a wall, that preferentially attracts one of the components, interfaces between A-rich and B-rich domains in general meet the wall making a contact angle $\theta$. Young's equation describes this angle in terms of a balance between the $A-B$ interfacial tension $\gamma_{AB}$ and the surface tensions $\gamma_{wA}$, $\gamma_{wB}$ between, respectively, the $A$- and $B$-rich phases and the wall, $\gamma _{AB} \cos \theta =\gamma_{wA}-\gamma_{wB}$. By Monte Carlo simulations of bridges, formed by one of the components in a binary Lennard-Jones liquid, connecting the two walls of a nanoscopic slit pore, $\theta$ is estimated from the inc…
Simulation of binary fluids exposed to selectively adsorbing walls: a method to estimate contact angles and line tensions
2011
For an understanding of interfacial phenomena of fluids on the nanoscale a detailed knowledge of the excess free energies of fluids due to walls is required, as well as of the interfacial tension between coexisting fluid phases. A description of simulation approaches to solve this task is given for a suitable model binary (A + B) fluid. Sampling the order parameter distribution of the system without walls, the curvature dependent and flat interfacial tensions of coexisting ‘bulk’ phases is extracted. In a thin film geometry, the difference in wall free energies is found via a new thermodynamic integration method. Thus the contact angle θ of macroscopic droplets is estimated from Young's equ…
Absolute acidity of clay edge sites from ab-initio simulations
2012
International audience; We provide a microscopic understanding of the solvation structure and reactivity of the edges of neutral clays. In particular we address the tendency to deprotonation of the different reactive groups on the (0 1 0) face of pyrophyllite. Such information cannot be inferred directly from titration experiments, which do not discriminate between different sites and whose interpretation resorts to macroscopic models. The determination of the corresponding pKa then usually relies on bond valence models, sometimes improved by incorporating some structural information from ab-initio simulations. Here we use density functional theory based molecular dynamics simulations, comb…
Evaluating Thermal Corrections for Adsorption Processes at the Metal/Gas Interface
2019
International audience; Adsorption and desorption steps are key for active catalysts and rely on a subtle balance between enthalpic and entropic terms. While the enthalpic term is becoming ever more accurate through density functional development, the entropic term remains underrated and its precise determination a great challenge. In this work, we have performed extensive first principles thermodynamic integration (TI) simulations for the 1 adsorption of small (e.g., CO) to larger (e.g., phenol) molecules at metallic surfaces and compared their adsorption free energies to the values obtained by vertical, static statistical mechanics approximations to thermal corrections invoking three diff…
Estudio del mecanismo de reacción e inhibición de cisteína proteasas mediante métodos multiescala
2022
En esta tesis doctoral se realizaron estudios computacionales para las enzimas caspasa-1 y la 3CLpro del SARS-CoV-2. Estas enzimas pertenecen a la familia de las cisteína proteasas, las cuales hidrolizan sus respectivos sustratos rompiendo un enlace peptídico en particular. En esta reacción interviene una diada catalítica conformada por un par Cis-His. La caspasa-1 fue seleccionada debido a su importancia farmacológica en la enfermedad de Alzheimer, y la enzima 3CLpro del SARS-CoV-2 por estar involucrada en el proceso de replicación del virus responsable de la enfermedad del COVID-19. Para ambas se realizaron estudios que ayudaron a racionalizar el mecanismo de reacción con su sustrato natu…