Related papers: Best Practices for Alchemical Free Energy Calculat…
The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with…
The computational modelling of reactions is simple in theory but can be quite tricky in practice. This article aims at the purpose of providing an assistance to a proper way of describing reactions theoretically and provides rough…
Predicting crystal nucleation is among the most significant long--standing challenges in condensed matter. In the system most studied (hard sphere colloids), the comparison between experiments performed using static light scattering and…
We consider the thermodynamics of chemical coupling from the viewpoint of free energy transduction efficiency. In contrast to an external parameter-driven stochastic energetics setup, the dynamic change of the equilibrium distribution…
Despite the strength of Molecular Dynamics simulations in providing insights into the microscopic details of phenomenon in many fields in materials science, physics and biology, the biggest barrier is its limited timescale which is several…
We propose a formulation of adaptive computation of free energy differences, in the ABF or nonequilibrium metadynamics spirit, using conditional distributions of samples of configurations which evolve in time. This allows to present a truly…
It has recently been shown that the Helmholtz free energy difference between two equilibrium configurations of a system may be obtained from an ensemble of finite-time (nonequilibrium) measurements of the work performed in switching an…
Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems…
Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic…
We have derived several relations, which allow the evaluation of the system free energy changes in the leading order in $\hbar^{2}$ along classically generated trajectories. The results are formulated in terms of purely classical…
Machine-learning potentials are usually trained on the ground-state, Born-Oppenheimer energy surface, which depends exclusively on the atomic positions and not on the simulation temperature. This disregards the effect of thermally-excited…
Recent years have witnessed major advances in our understanding of nonequilibrium processes. The Jarzynski equality, for example, provides a link between equilibrium free energy differences and finite-time, nonequilibrium dynamics. We…
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…
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…
We introduce an orbital free electron density functional approximation based on alchemical perturbation theory. Given convergent perturbations of a suitable reference system, the accuracy of popular self-consistent Kohn-Sham density…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…
The key problem of statistical physics standing over one hundred years is how to exactly calculate the partition function (or free energy) of many-body interaction systems, which severely hinders application of the theory for realistic…
In this thesis a new model for calculating the total energy of atomic and solid systems is presented. The model is used to study the properties of the Si(100) surface and dislocation dynamics in the diamond structure. For the Si(100)…
As minimal cells or protocells are dramatically simpler than modern unicells it is possible to quantitatively estimate free energy changes for every process in the lifecycle of a protocell and compare these with estimates of the free energy…
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…