Spatially Resolved Distribution Function and the Medium-Range Order in Metallic Liquid and Glass

The structural description of disordered systems has been a longstanding challenge in physical science. We propose an atomic cluster alignment method to reveal the development of three-dimensional topological ordering in a metallic liquid as it undercools to form a glass. By analyzing molecular dynamic (MD) simulation trajectories of a Cu64.5Zr35.5 alloy, we show that medium-range order (MRO) develops in the liquid as it approaches the glass transition. Specifically, around Cu sites, we observe “Bergman triacontahedron” packing (icosahedron, dodecahedron and icosahedron) that extends out to the fourth shell, forming an interpenetrating backbone network in the glass. The discovery of Bergman-type MRO from our order-mining technique provides unique insights into the topological ordering near the glass transition and the relationship between metallic glasses and quasicrystals

Clathrate structure-type recognition: Application to hydrate nucleation and crystallisation

For clathrate-hydrate polymorphic structure-type (sI versus sII), geometric recognition criteria have been developed and validated. These are applied to the study of the rich interplay and development of both sI and sII motifs in a variety of hydrate-nucleation events for methane and H2S hydrate studied by direct and enhanced-sampling molecular dynamics (MD) simulations. In the case of nucleation of methane hydrate from enhanced-sampling simulation, we notice that already at the transition state, similar to 80% of the enclathrated CH4 molecules are contained in a well-structured (sII) clathrate-like crystallite. For direct MD simulation of nucleation of H2S hydrate, some sI/ sII polymorphic diversity was encountered, and it was found that a realistic dissipation of the nucleation energy (in view of non-equilibrium relaxation to either microcanonical (NVE) or isothermal-isobaric (NPT) distributions) is important to determine the relative propensity to form sI versus sII motifs. (C) 2015 AIP Publishing LLC

A new theoretical approach to biological self-assembly

Upon biological self-assembly, the number of accessible translational configurations of water in the system increases considerably, leading to a large gain in water entropy. It is important to calculate the solvation entropy of a biomolecule with a prescribed structure by accounting for the change in water–water correlations caused by solute insertion. Modeling water as a dielectric continuum is not capable of capturing the physical essence of the water entropy effect. As a reliable tool, we propose a hybrid of the angle-dependent integral equation theory combined with a multipolar water model and a morphometric approach. Using our methods wherein the water entropy effect is treated as the key factor, we can elucidate a variety of processes such as protein folding, cold, pressure, and heat denaturating of a protein, molecular recognition, ordered association of proteins such as amyloid fibril formation, and functioning of ATP-driven proteins