Related papers: An ab initio approach to free-energy reconstructio…
Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…
Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics…
Inspired by thermodynamic integration, we propose a method for the calculation of time-independent free energy profiles from history-dependent biased simulations via Mean Force Integration (MFI). MFI circumvents the need for computing the…
Free energy profiles serve as a fundamental bridge between microscopic atomic fluctuations and macroscopic thermodynamic observables. Estimating the free energy profile along a reaction coordinate, referred to as the potential of mean force…
We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core…
The stationary functional of the all-electron density functional plus dynamical mean field theory (DFT+DMFT) formalism to perform free energy calculations and structural relaxations is implemented for the first time. Here, the first order…
We propose a method to compute free-energy differences from nonadiabatic alchemical transformations using flow-based generative models. The method, nonadiabatic force matching, hinges on estimating the dissipation along an alchemical…
The phase field crystal (PFC) method has emerged as a promising technique for modeling materials with atomistic resolution on mesoscopic time scales. The approach is numerically much more efficient than classical density functional theory…
Within the framework of density functional theory (DFT), the total energy of crystal structures is calculated at zero temperature. Herein, we briefly discuss the DFT-based lattice-dynamics approach for computing crystal free energy, the…
The formally exact framework of equilibrium Density Functional Theory (DFT) is capable of simultaneously and consistently describing thermodynamic and structural properties of interacting many-body systems in arbitrary external potentials.…
We present a new method that combines alchemical transformation with physical pathway to accurately and efficiently compute the absolute binding free energy of receptor-ligand complex. Currently, the double decoupling method (DDM) and the…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
A general set of methods is presented for calculating chemical potentials in solid and liquid mixtures using {\em ab initio} techniques based on density functional theory (DFT). The methods are designed to give an {\em ab initio} approach…
Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at…
In this paper, we show how to calculate analytical atomic forces within self-consistent density functional theory + dynamical mean-field theory (DFT+DMFT) approach in the case when ultra-soft or norm-conserving pseudopotentials are used. We…
Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach,…
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,…