Comparison of the Performance of Machine Learning Models in Representing High-Dimensional Free Energy Surfaces and Generating Observables.

Free energy surfaces of chemical and physical systems are often generated using a popular class of enhanced sampling methods that target a set of collective variables (CVs) chosen to distinguish the characteristic features of these surfaces. While some of these approaches are typically limited to low (∼1-3)-dimensional CV subspaces, methods such as driven adiabatic free-energy dynamics/temperature-accelerated molecular dynamics have been shown to be capable of generating free energy surfaces of quite high dimension by sampling the associated marginal probability distribution via full sweeps over the CV landscape. These approaches repeatedly visit conformational basins, producing a scattering of points within the basins on each visit.

An open-chain imaginary-time path-integral sampling approach to the calculation of approximate symmetrized quantum time correlation functions.

We introduce a scheme for approximating quantum time correlation functions numerically within the Feynman path integral formulation. Starting with the symmetrized version of the correlation function expressed as a discretized path integral, we introduce a change of integration variables often used in the derivation of trajectory-based semiclassical methods. In particular, we transform to sum and difference variables between forward and backward complex-time propagation paths.

Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates.

Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H and D diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H and D as a function of temperature.

The Surface Potential of the Water-Vapor Interface from Classical Simulations.

The electrochemical surface potential across the water-vapor interface provides a measure of the orientation of water molecules at the interface. However, the large discrepancies between surface potentials calculated from ab initio (AI) and classical molecular dynamics (MD) simulations indicate that what is being calculated may be relevant to different test probes. Although a method for extracting the electrochemical surface potential from AIMD simulations has been given, methods for MD simulations have not been clarified.

Hydrophobic hydration and the anomalous partial molar volumes in ethanol-water mixtures.

The anomalous behavior in the partial molar volumes of ethanol-water mixtures at low concentrations of ethanol is studied using molecular dynamics simulations. Previous work indicates that the striking minimum in the partial molar volume of ethanol VE as a function of ethanol mole fraction XE is determined mainly by water-water interactions. These results were based on simulations that used one water model for the solute-water interactions but two different water models for the water-water interactions.

The molecular charge distribution, the hydration shell, and the unique properties of liquid water.

The most essential features of a water molecule that give rise to its unique properties are examined using computer simulations of different water models. The charge distribution of a water molecule characterized by molecular multipoles is quantitatively linked to the liquid properties of water via order parameters for the degree (S(2)) and symmetry (ΔS(2)) of the tetrahedral arrangement of the nearest neighbors, or "hydration shell." ΔS(2) also appears to determine the long-range tetrahedral network and interfacial structure.

Effects of microcomplexity on hydrophobic hydration in amphiphiles.

Hydrophobic hydration is critical in biology as well as many industrial processes. Here, computer simulations of ethanol/water mixtures show that a three-stage mechanism of dehydration of ethanol explains the anomalous concentration dependence of the thermodynamic partial molar volumes, as well as recent data from neutron diffraction and Raman scattering. Moreover, the simulations show that the breakdown of hydrophobic hydration shells, whose structure is determined by the unique molecular properties of water, is caused by the microcomplexity of the environment and may be representative of early events in protein folding and structure stabilization in aqueous solutions.