Related papers: Computing chemical potentials of solutions from st…
The structure of aqueous CsCl solutions was investigated by classical molecular dynamics simulations (MD) at three salt concentrations (1.5, 7.5, and 15 mol %). Thirty interatomic potential sets, based on the 12-6 Lennard-Jones model,…
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…
Two machine learning-aided thermodynamic integration schemes to compute the chemical potentials of atoms and molecules have been developed and compared. One is the particle insertion method, and the other combines particle insertion with…
Computational exploration of the compositional spaces of materials can provide guidance for synthetic research and thus accelerate the discovery of novel materials. Most approaches employ high-throughput sampling and focus on reducing the…
The phenomenon of solidification of a substance from its liquid phase is of the greatest practical and theoretical importance, and atomistic simulations can provide precious information towards its understanding and control. Unfortunately,…
Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I…
We use the ``isoconfigurational ensemble'' [Phys. Rev. Lett. {\bf 93}, 135701 (2004)] to analyze both dynamical and structural properties in simulations of a glass forming molecular liquid. We show that spatially correlated clusters of low…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
We compute the phase separation of the immiscible liquid alloy Fe-Cu-Ni. Our computational approach uses a virtual semigrand canonical Widom approach to determine differences in excess chemical potentials between different species. Using an…
In this tutorial we discuss the chemical potential of ions in water (i.e., in a salt solution, in an electrolyte phase) and inside (charged) nanoporous materials such as porous membranes. In water treatment, such membranes are often used to…
Molecular crystals often exist in multiple competing polymorphs, showing significantly different physico-chemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful…
The modeling of solute chemistry at low-symmetry defects in materials is historically challenging, due to the computation cost required to evaluate thermodynamic properties from first principles. Here, we offer a hybrid multiscale approach…
Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal…
We propose a new scheme to parameterize effective potentials that can be used to simulate atomic systems such as oxide glasses. As input data for the optimization, we use the radial distribution functions of the liquid and the vibrational…
We evaluate the grand potential of a cluster of two molecular species, equivalent to its free energy of formation from a binary vapour phase, using a nonequilibrium molecular dynamics technique where guide particles, each tethered to a…
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…
Many references exist in the density functional theory (DFT) literature to the chemical potential of the electrons in an atom or a molecule. The origin of this notion has been the identification of the Lagrange multiplier $\mu = \partial…
Temperature and baryon, charge, and strangeness chemical potentials characterize QCD matter under extreme conditions. Differences between these chemical potentials and their ratios probe conserved-charge correlations and the system's…
The Lennard-Jones (LJ) Potential Energy Problem is to construct the most stable form of $N$ atoms of a molecule with the minimal LJ potential energy. This problem has a simple mathematical form $f(x) = 4\sum_{i=1}^N \sum_{j=1,j<i}^N…
We introduce an approach to exploit the existence of multiple levels of description of a physical system to radically accelerate the determination of thermodynamic quantities. We first give a proof of principle of the method using two…