Search results for "thermodynamic integration"
showing 10 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 …
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…
Monte Carlo calculation of free energy for a fcc lattice-gas model
1990
A face-centered-cubic Ising lattice-gas model with nearest- and next-nearest-neighbor interactions is studied, and an accurate determination of the transition temperature for the discontinuous order-disorder transition is obtained. This model is of interest in the studies of phase diagrams for metallic alloys. The location of the transition was previously not known accurately, and its estimation has a number of applications. Very accurate absolute free-energy densities for the two coexisting phases have been obtained from a combination of the standard thermodynamic integration method and the method of sampling finite-size dependence. The latent-heat also is calculated with good precision.
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…
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…
MONTE CARLO METHODS FOR FIRST ORDER PHASE TRANSITIONS: SOME RECENT PROGRESS
1992
This brief review discusses methods to locate and characterize first order phase transitions, paying particular attention to finite size effects. In the first part, the order parameter probability distribution and its fourth-order cumulant is discussed for thermally driven first-order transitions (the 3-state Potts model in d=3 dimensions is treated as an example). First-order transitions are characterized by a minimum of the cumulant, which gets very deep for large enough systems. In the second part, we discuss how to locate first order phase boundaries ending in a critical point in a large parameter space. As an example, the study of the unmixing transition of asymmetric polymer mixtures…
Intrinsic Acidity of Surface Sites in Calcium Silicate Hydrates and Its Implication to Their Electrokinetic Properties
2014
Calcium Silicate Hydrates (C–S–H) are the major hydration products of portland cement paste. The accurate description of acid–base reactions at the surface of C–S–H particles is essential for both understanding the ion sorption equilibrium in cement and prediction of mechanical properties of the hardened cement paste. Ab initio molecular dynamics simulations at the density functional level of theory were applied to calculate intrinsic acidity constants (pKa’s) of the relevant ≡SiOH and ≡CaOH2 groups on the C–S–H surfaces using a thermodynamic integration technique. Ion sorption equilibrium in C–S–H was modeled applying ab initio calculated pKa’s in titrating Grand Canonical Monte Carlo simu…
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…
The ensemble switch method for computing interfacial tensions
2015
We present a systematic thermodynamic integration approach to compute interfacial tensions for solid-liquid interfaces, which is based on the ensemble switch method. Applying Monte Carlo simulations and finite-size scaling techniques, we obtain results for hard spheres, which are in agreement with previous computations. The case of solid-liquid interfaces in a variant of the effective Asakura-Oosawa model and of liquid-vapor interfaces in the Lennard-Jones model are discussed as well. We demonstrate that a thorough finite-size analysis of the simulation data is required to obtain precise results for the interfacial tension.