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Register a new userDistributions of pore sizes and atomic densities in binary glasses revealed by molecular dynamics simulations
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Added by
Nikolai Priezjev V.
Publication date
2017
fields
Physics
and research's language is
English
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We report on the results of a molecular dynamics simulation study of binodal glassy systems, formed in the process of isochoric rapid quenching from a high-temperature fluid phase. The transition to vitreous state occurs due to concurrent spinodal decomposition and solidification of the matter. The study is focused on topographies of the porous solid structures and their dependence on temperature and average density. To quantify the pore-size distributions, we put forth a scaling relation that provides a robust data collapse in systems with high porosity. We also find that the local density of glassy phases is broadly distributed, and, with increasing average glass density, a distinct peak in the local density distribution is displaced toward higher values.
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Molecular dynamics simulations are carried out to investigate mechanical properties and porous structure of binary glasses subjected to steady shear. The model vitreous systems were prepared via thermal quench at constant volume to a temperature well below the glass transition. The quiescent samples are characterized by a relatively narrow pore size distribution whose mean size is larger at lower glass densities. We find that in the linear regime of deformation, the shear modulus is a strong function of porosity, and the individual pores become slightly stretched while their structural topology remains unaffected. By contrast, with further increasing strain, the shear stress saturates to a density-dependent plateau value, which is accompanied by pore coalescence and a gradual development of a broader pore size distribution with a discrete set of peaks at large length scales.
The evolution of porous structure, potential energy and local density in binary glasses under oscillatory shear deformation is investigated using molecular dynamics simulations. The porous glasses were initially prepared via a rapid thermal quench from the liquid state across the glass transition and allowed to phase separate and solidify at constant volume, thus producing an extended porous network in an amorphous solid. We find that under periodic shear, the potential energy decreases over consecutive cycles due to gradual rearrangement of the glassy material, and the minimum of the potential energy after thousands of shear cycles is lower at larger strain amplitudes. Moreover, with increasing cycle number, the pore size distributions become more skewed toward larger length scales where a distinct peak is developed and the peak intensity is enhanced at larger strain amplitudes. The numerical analysis of the local density distribution functions demonstrates that cyclic loading leads to formation of higher density solid domains and homogenization of the glass phase with reduced density.
As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones interactions for the carbon dioxide molecules. In previous work, it has been shown that this model reproduces the real phase diagram reasonable well, and also the initial stages of spinodal decomposition in the bulk following a sudden expansion of the system could be studied. Using the parallelized simulation package ESPResSo on a multiprocessor supercomputer, phase separation of thin fluid films confined between parallel walls that are repulsive for both types of molecules are simulated in a rather large system (1356 x 1356 x 67.8 A^3, corresponding to about 3.2 million atoms). Following the sudden system expansion, a complicated interplay between phase separation in the directions perpendicular and parallel to the walls is found: in the early stages the hexadecane molecules accumulate mostly in the center of the slit pore, but as the coarsening of the structure in the parallel direction proceeds, the inhomogeneity in the perpendicular direction gets much reduced. Studying then the structure factors and correlation functions at fixed distances from the wall, the densities are essentially not conserved at these distances, and hence the behavior differs strongly from spinodal decomposition in the bulk. Some of the characteristic lengths show a nonmonotonic variation with time, and simple coarsening described by power-law growth is only observed if the domain sizes are much larger than the film thickness.
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse grained MARTINI models and structure based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein-protein and protein-lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.
We study propagation dynamics of a particle phase in a single-file pore connected to a reservoir of particles (bulk liquid phase). We show that the total mass $M(t)$ of particles entering the pore up to time $t$ grows as $M(t) = 2 m(J,rho_F) sqrt{D_0 t}$, where $D_0$ is the bare diffusion coefficient and the prefactor $m(J,rho_F)$ is a non-trivial function of the reservoir density $rho_F$ and the amplitude $J$ of attractive particle-particle interactions. Behavior of the dynamic density profiles is also discussed.
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