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Register a new userCharacterizing Solvent Density Fluctuations in Dynamical Observation Volumes
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Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to important insights into these processes. Although techniques such as the indirect umbrella sampling (INDUS) method (Patel et al. J. Stat. Phys. 2011, 145, 265-275) can be used to characterize solvent fluctuations in static observation volumes of various sizes and shapes, characterizing how the solvent mediates inherently dynamic processes, such as self-assembly or conformational change, remains a challenge. In this work, we generalize the INDUS method to facilitate the enhanced sampling of solvent fluctuations in dynamical observation volumes, whose positions and shapes can evolve. We illustrate the usefulness of this generalization by characterizing water density fluctuations in dynamic volumes pertaining to the hydration of flexible solutes, the assembly of small hydrophobes, and conformational transitions in a model peptide. We also use the method to probe the dynamics of hard spheres.
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Water density fluctuations are an important statistical mechanical observable that is related to many-body correlations, as well as hydrophobic hydration and interactions. Local water density fluctuations at a solid-water surface have also been proposed as a measure of its hydrophobicity. These fluctuations can be quantified by calculating the probability, $P_v(N)$, of observing $N$ waters in a probe volume of interest $v$. When $v$ is large, calculating $P_v(N)$ using molecular dynamics simulations is challenging, as the probability of observing very few waters is exponentially small, and the standard procedure for overcoming this problem (umbrella sampling in $N$) leads to undesirable impulsive forces. Patel et al. [J. Phys. Chem. B, 114, 1632 (2010)] have recently developed an indirect umbrella sampling (INDUS) method, that samples a coarse-grained particle number to obtain $P_v(N)$ in cuboidal volumes. Here, we present and demonstrate an extension of that approach to other basic shapes, like spheres and cylinders, as well as to collections of such volumes. We further describe the implementation of INDUS in the NPT ensemble and calculate $P_v(N)$ distributions over a broad range of pressures. Our method may be of particular interest in characterizing the hydrophobicity of interfaces of proteins, nanotubes and related systems.
This paper has been withdrawn by the author due to the incorrect application of the divergence theorem to Eqs 7, 8 and 9.
As liquids approach the glass transition temperature, dynamical heterogeneity emerges as a crucial universal feature of their behavior. Dynamic facilitation, where local motion triggers further motion nearby, plays a major role in this phenomenon. Here we show that long-range, elastically-mediated facilitation appears below the mode-coupling temperature, adding to the short-range component present at all temperatures. Our results suggest deep connections between the supercooled liquid and glass states, and pave the way for a deeper understanding of dynamical heterogeneity in glassy systems.
A finite-temperature density functional approach to describe the properties of parahydrogen in the liquid-vapor coexistence region is presented. The first proposed functional is zero-range, where the density-gradient term is adjusted so as to reproduce the surface tension of the liquid-vapor interface at low temperature. The second functional is finite-range and, while it is fitted to reproduce bulk pH2 properties only, it is shown to yield surface properties in good agreement with experiments. These functionals are used to study the surface thickness of the liquid-vapor interface, the wetting transition of parahydrogen on a planar Rb model surface, and homogeneous cavitation in bulk liquid pH2.
Liquid-liquid phase transition (LLPT) in supercooled water has been a long-standing controversial issue. We show simulation results of real stable first-order phase transitions between high and low density liquid (HDL and LDL)-like structures in confined supercooled water in both positive and negative pressures. These topological phase transitions originate from H-bond network ordering in molecular rotational mode after molecular exchanges are frozen. It is explained by the order parameter-dependent free energy change upon mixing liquid-like and ice-like moieties of H-bond orientations which is governed by their two- to many-body interactions. This unexplored purely H-bond orientation-driven topological phase gives mid-density and stable intermediate mixed-phase with high and low density structures. The phase diagram of supercooled water demonstrate the second and third critical points of water.
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