Related papers: An ab initio approach to free-energy reconstructio…
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof…
Steered molecular dynamics (SMD) simulations for the calculation of free energies are well suited for high-throughput molecular simulations on a distributed infrastructure due to the simplicity of the setup and parallel granularity of the…
Smooth, highly accurate analytical representations of Fermi-Dirac (FD) integral combinations important in free-energy density functional calculations are presented. Specific forms include those that occur in the local density approximation…
Density functional theory (DFT) serves as the basis for computational discovery in materials science and chemistry, yet each calculation demands extensive human effort: adjusting algorithms when convergence stalls, revising plans when…
Free energy functionals of Ginzburg-Landau type lie at the heart of a broad class of continuum dynamical models, such as the Cahn-Hilliard and Swift-Hohenberg equations. Despite the wide use of such models, the assumptions embodied in the…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on \emph{ab initio} molecular dynamics followed by a mapping onto a model…
A linear response function (LRF) determines the mean-response of a nonlinear climate system to weak imposed forcings, and an eddy flux matrix (EFM) determines the eddy momentum and heat flux responses to mean-flow changes. Neither LRF nor…
Comparison of free energies between different phases and different compositions underlies the prediction of alloy phase diagrams. To allow direct comparison, consistent reference points for the energies or enthalpies are required, and the…
Recently we introduced a new technique for computing the average free energy of a system with quenched randomness. The basic tool of this technique is a distributional zeta-function. The distributional zeta-function is a complex function…
Ab initio modeling of dynamic structure factors (DSF) and related density response properties in the warm dense matter (WDM) regime is a challenging computational task. The DSF, convolved with a probing X-ray beam and instrument function,…
We test Laplacian-level meta-generalized gradient approximation (meta-GGA) non-interacting kinetic energy functionals based on the fourth-order gradient expansion (GE4). We consider several well known Laplacian-level meta-GGAs from…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
We present a framework for computing the shock Hugoniot using on-the-fly machine learned force field (MLFF) molecular dynamics simulations. In particular, we employ an MLFF model based on the kernel method and Bayesian linear regression to…
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…
Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
The potential of mean force (PMF) between two nano crystals (NCs) represents an effective interaction potential that can be used to study the assembly of NCs to various superstructures. For a given temperature, the effective interaction is…
The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…
We prove the existence of the exact density-functional theory formalism for open electronic systems, and develop subsequently an exact time-dependent density-functional theory (TDDFT) formulation for the dynamic response. The TDDFT…