Related papers: Accurate Estimation of Solvation Free Energy Using…
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 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…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
Solvation free energy is an important design parameter in reaction kinetics and separation processes, making it a critical property to predict during process development. In previous research, directed message passing neural networks…
In the era of big data, we first need to manage the data, which requires us to find missing data or predict the trend, so we need operations including interpolation and data fitting. Interpolation is a process to discover deducing new data…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
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 perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethane<->methanol transformation. The results suggest that extrapolation can greatly reduce the systematic…
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…
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their…
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…
Solvation free energies are efficiently predicted by molecular density functionnal theory (MDFT) if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [Sergiievskyi et al.,…
The combination of a recently proposed linear interpolation method (LIM) [Senjean et al., Phys. Rev. A 92, 012518 (2015)], which enables the calculation of weight-independent excitation energies in range-separated ensemble…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
The interfacial free energy between a crystal and a fluid, {\gamma} cf, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring {\gamma} cf experimentally, computer…
We develop a method to fit high-temperature Gibbs free energy data for the development of interatomic potentials for atomic systems. The approach is based on Hamiltonian thermodynamic integration, enabling the identification of suitable…