Thermodynamics and the potential energy landscape: case study of small water clusters

We investigated the structure and the thermodynamic properties of small water clusters with the nested sampling computational technique, using two different water models, the coarse-grained mW (up to 25 molecules) and the flexible version of the TIP3P (up to 16 molecules). With mapping the entire potential energy landscape of the clusters, we calculated the heat capacity curves, located the structural transitions and identified those local minima basins which contribute the most to the total partition function. We found that in case of the mW model, trends in first-order-like and continuous-like transitions can be very well matched to the characteristics of the landscape: cluster sizes with fewer and narrower local minima basins show a sharper ’melting’ peak on the heat capacity curve. Trends in case of the TIP3P model were not easily assigned to changing occupation of basins, and the contribution of local minima were negligible, except for n = 7, 15 and 16

On the performance of interatomic potential models of iron: comparison of the phase diagrams

In order to study the performance of interatomic potentials and their reliability at higher pressures, the phase diagram of four different embedded-atom type potential models of iron is compared. The calculations were done by the nested sampling technique in the pressure range 0.1 GPa–100 GPa. The low pressure stable structure is found to be the body- centred cubic in all cases, but the higher pressure phases show a great variation, being face-centred cubic, hexagonal close-packed and – at very low temperatures – different body-centred tetragonal phases are observed as well. The melting line is overestimated considerably for three of the models, but for the one where liquid properties had been taken into account during the potential fitting process, the agreement with experimental results is good, even at very high pressures

Stability of the high-density Jagla liquid in 2D : sensitivity to parameterisation

We computed the pressure-temperature phase diagram of the hard-core two-scale ramp potential in two-dimensions, with the parameterisation originally suggested by Jagla[E. A. Jagla, Phys. Rev. E 63, 061501 (2001)], as well as with a series of systematically modified variants of the model to reveal the sensitivity of the stability of phases. The nested sampling method was used to explore the potential energy landscape, allowing the identification of thermodynamically relevant phases, such as low- and high-density liquids and various crystalline forms, some of which have not been reported before. We also proposed a smooth version of the potential, which is differentiable beyond the hard-core. This potential reproduces the density anomaly, but forms a dodecahedral quasi-crystal structure at high pressure. Our results allow to hypothesise on the necessary modifications of the original model in order to improve the stability of the metastable high density liquid phase in 3D

Simulation study of micelle formation by bile salts

We report coarse-grained, implicit-solvent simulations of aqueous solutions of bile salts. The parameters in our model were optimized to reproduce some of the experimentally known behavior of dihydroxy bile salts at “physiological” temperature and counterion concentration. We find that micelle formation in dihydroxy and trihydroxy bile salts is only weakly cooperative in the sense that there is barely a free energy barrier that stabilizes these micelles against disassembly. Bile molecules are found to pack in many different orientations in pure bile micelles. Both features may be physiologically relevant: the ability to pack in different orientations may be necessary to form mixed micelles with nutrients of a wide range of molecular lengths and shapes, and the reduced micelle stability may facilitate nutrient release once the mixed micelles reach the intestinal wall.FOM Institute-Scientific Research (NWO). Senter-Novem -Dutch Ministry of Economic; Affairs through the Food & Nutrition Delta 2 Program -grant DFN0642300; Royal Society of London (Wolfson Merit Award) and from the ERC (Advanced Grant agreement 227758)

Poissonian and non Poissonian Voronoi Diagrams with application to the aggregation of molecules

The distributions that regulate the spatial domains of the Poissonian Voronoi Diagrams are discussed adopting the sum of gamma variate of argument two. The distributions that arise from the product and quotient of two gamma variates of argument two are also derived. Three examples of non Poissonian seeds for the Voronoi Diagrams are discussed. The developed algorithm allows the simulation of an aggregation of methanol and water.Comment: 18 pages 10 Figure

Percolation transition of hydration water at hydrophilic surfaces

An analysis of water clustering is used to study the quasi-2D percolation transition of water adsorbed at planar hydrophilic surfaces. Above the critical temperature of the layering transition (quasi-2D liquid-vapor phase transition of adsorbed molecules) a percolation transition occurs at some threshold surface coverage, which increases with increasing temperature. The location of the percolation line is consistent with the existence of a percolation transition at the critical point. The percolation threshold at a planar surface is weakly sensitive to the size of the system when its lateral dimension increases from 80 to 150 A. The size distribution of the largest water cluster shows a specific two-peaks structure in a wide range of surface coverage : the lower- and higher-size peaks represent contributions from non-spanning and spanning clusters, respectively. The ratio of the average sizes of spanning and non-spanning largest clusters is about 1.8 for all studied planes. The two-peak structure becomes more pronounced with decreasing size of the planar surface and strongly enhances at spherical surfaces.Comment: 17 pages, 11 figure

Instantaneous Liquid Interfaces

We describe and illustrate a simple procedure for identifying a liquid interface from atomic coordinates. In particular, a coarse grained density field is constructed, and the interface is defined as a constant density surface for this coarse grained field. In applications to a molecular dynamics simulation of liquid water, it is shown that this procedure provides instructive and useful pictures of liquid-vapor interfaces and of liquid-protein interfaces.Comment: 15 pages, 4 figure

Dataset to support : Phase properties of the finite range Wang-Frenkel potential

In the current work we revisit the potential proposed by Wang et al. as a well defined finite-range alternative to the widely used Lennard-Jones interaction model. The advantage of the proposed Wang-Frenkel potential is that it not only goes smoothly to zero at the cutoff distance, hence eliminating inconsistencies caused by different treatments of the truncation, but with changing the range of the potential, it is capable of describing soft matter-like behaviour as well as traditional "Lennard-Jones-like" properties. We use the nested sampling method to perform an unbiased sampling of the potential energy surface, and map the pressure-temperature phase diagram of a range of truncation distances. We discuss the relatively small change in the melting line and the appearance of the liquid-vapour co-existence line and critical point at longer interaction ranges. We also present the ground state diagram, demonstrating that different polytypic phases appear to be global minima for the model at different pressures and cutoff values, similar to what had been shown in case of the Lennard-Jones model. Finally, we compare the lowest energy structure of some of the $N<60$ clusters to that of the known minima of Lennard-Jones and Morse potential, using different cutoff values, revealing a behaviour closely resembling that of the Morse clusters