Using the simple point charge/extended water model, we performed molecular dynamics simulations of homogeneous vapor-liquid nucleation at various values of temperature T and supersaturation S, from which the nucleation rate J, critical nucleus size n(*), and the cluster formation free energy DeltaG were derived. As well as providing lots of simulation data, the results were compared with theories on homogeneous nucleation, including the classical, semi-phenomenological, and scaled models, but none of these gave a satisfactory explanation for our results. It was found that two main factors made the theories fail: (1) The average cluster structure including the nonspherical shape and the core structure that is not like the bulk liquid and (2) the forward rate which is larger than assumed by the theories by about one order of magnitude. The quantitative evaluation of these factors is left for future investigations.

Although the computation of heat flux and thermal conductivity either via Fourier's law or the Green-Kubo relation has become a common task in molecular dynamics simulation, contributions of three-body and larger many-body interactions have always proved problematic to compute. In recent years, due to the success when applying to pressure tensor computation, atomic stress approximation has been widely used to calculate heat flux, where the LAMMPS molecular dynamics package is the most prominent propagator. We demonstrated that the atomic stress approximation, while adequate for obtaining pressure, produces erroneous results in the case of heat flux when applied to systems with many-body interactions, such as angle, torsion, or improper potentials. This also produces incorrect thermal conductivity values. To remedy this deficiency, by starting from a strict formulation of heat flux with many-body interactions, we reworked the atomic stress definition which resulted in only a simple modification. We modified the LAMMPS package accordingly to demonstrate that the new atomic stress approximation produces excellent results close to that of a rigid formulation.

We used molecular dynamics simulations to study the structure and shear dynamics of two ionic liquids (ILs) featuring the same cation 1-butyl-3-methyl-imidazolium or [BMIM], paired with bis(trifluoromethanesulphonyl)amide [NTF2] and tetrafluoroborate [BF4] anions, confined between two hydroxylated silica surfaces. The results demonstrate how the shape of IL molecules affects their layering structure at hydroxylated silica surfaces and how the layered structure of nanoconfined liquids determines their dynamical properties at the molecular level. When [BMIM][NTF2] is sheared, larger molecular fluctuations in the inner layers are required to stabilise the system, and the resulting dynamics is irregular. The alternating charged layers in [BMIM][BF4] allow the system to stabilise through smaller oscillations, and the layers appear to shear on top of each other in a laminar fashion. The simulated dynamics explains qualitatively the relative change in viscosity that the two ILs exhibit when confined, as has been observed in previous experiments.

With the aid of molecular dynamics simulation, we consider why the diffusivity of liquid becomes slower as the liquid is confined to a narrower space. The diffusion coefficient of octamethylcyclotetrasiloxane liquid confined between two mica surfaces was calculated for a range of surface separations from 64 to 23 Å. The resulting separation dependence of the diffusion coefficient can be explained by considering that the molecular diffusion is an activated process. In particular, we find that the increase in the activation energy is closely correlated with the decrease of the potential energy per molecule, from which we propose a molecular-level mechanism of this confined-induced diffusion slowdown.