Related papers: An ab initio approach to free-energy reconstructio…
We present a unique derivation of metadynamics. The starting point for the derivation is an on-the-fly reweighting scheme but through an approximation we recover the standard metadynamics and the well-tempered metadynamics in a general form…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
In this study, we carried out equilibrium molecular dynamics (EMD) simulations of the liquid-liquid interface between two different Lennard-Jones components with varying miscibility, where we examined the relation between the interfacial…
We present a novel methodology to compute relaxed dislocations core configurations, and their energies in crystalline metallic materials using large-scale \emph{ab-intio} simulations. The approach is based on MacroDFT, a coarse-grained…
The dynamics of low-energy induced fission is explored using a consistent microscopic framework that combines the time-dependent generator coordinate method (TDGCM) and time-dependent nuclear density functional theory (TDDFT). While the…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
We present a real-space formulation and higher-order finite-difference implementation of periodic Orbital-free Density Functional Theory (OF-DFT). Specifically, utilizing a local reformulation of the electrostatic and kernel terms, we…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
Dynamic density functional theory (DDFT) is a promising approach for predicting the structural evolution of a drying suspension containing one or more types of colloidal particles. The assumed free-energy functional is a key component of…
For the theoretical understanding of the reactivity of complex chemical systems accurate relative energies between intermediates and transition states are required. Despite its popularity, density functional theory (DFT) often fails to…
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…
The solid-liquid interface free energy \gamma sl is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous…
We present an approach to the estimate of the potential of mean force along a generic reaction coordinate based on maximum likelihood methods and path-ensemble averages in systems driven far from equilibrium. Following similar arguments,…
Density functional theory (DFT) is an efficient instrument for describing a wide range of nanoscale phenomena: wetting transition, capillary condensation, adsorption, etc. In this paper, we suggest a method for obtaining the equilibrium…
We present an accurate implementation of total energy calculations into the local density approximation plus dynamical mean-field theory (LDA+DMFT) method. The electronic structure problem is solved through the full potential linear…
Classical density functional theory (DFT) is a powerful framework to study inhomogeneous fluids. Its standard form is based on the knowledge of a generating free energy functional. If this is known exactly, then the results obtained by…
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…
The impact of leading collective electronic fluctuations on a free energy of a prototype 1D model for molecular systems is considered within the recently developed Fluctuating Local Field (FLF) approach. The FLF method is a non-perturbative…
The derivation of electromagnetic gyrofluid equations is made systematic by using the Hermite polynomial form of the underlying delta-f gyrokinetic distribution function. The gyrokinetic free-energy functional is explicitly used to set up…
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…