Related papers: Temperature Integration: an efficient procedure fo…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
Jarzynski Equality (JE) and the thermodynamic integration method are conventional methods to calculate free energy difference (FED) between two equilibrium states with constant temperature of a system. However, a number of ensemble samples…
Thermodynamic integration (TI) offers a rigorous method for estimating free-energy differences by integrating over a sequence of interpolating conformational ensembles. However, TI calculations are computationally expensive and typically…
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 present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and…
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a polynomial that optimally fits the thermodynamic integration…
We propose an approach for computing the Gibbs free energy difference between phases of a material. The method is based on the determination of the average force acting on interfaces that separate the two phases of interest. This force,…
The calculation of the interfacial free energy between two thermodynamic phases is crucial across various fields, including materials science, chemistry, and condensed matter physics. In this study, we apply an existing thermodynamic…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
This work proposes an extension of phase change and latent heat models for the simulation of metal powder bed fusion additive manufacturing processes on the macroscale and compares different models with respect to accuracy and numerical…
The influence of temperature is a major problem in Structural Health Monitoring diagnosis using guided waves. In this article, two methods for temperature compensation are used to evaluate the temperature of a structure monitored by…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…
We demonstrate an efficient and accurate, general-purpose first-principles blueprint for calculating anharmonic vibrational free energy and predicting structural phase transition temperatures of solids. Thermodynamic integration is…
This report details an approach to improve the accuracy and precision of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable lambda) and its application to…
We apply estimation theory to a system formed by two interacting trapped ions. By using the Fisher matrix formalism, we introduce a simple scheme for estimation of the temperature of the longitudinal vibrational modes of the ions. We use…
Phase diagrams serve as a highly informative tool for materials design, encapsulating information about the phases that a material can manifest under specific conditions. In this work, we develop a method in which Bayesian inference is…
We propose a new approach, "structure integration", enabling direct evaluation of configurational free energy for large systems. The present approach is based on the statistical information of lattice. Through first-principles-based…
The microscopic approach to calculating the free energy of a three-dimensional Ising-like system in a homogeneous external field is developed in the higher non-Gaussian approximation (the $\rho^6$ model) at temperatures above the critical…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…