Glassy states in lattice models with many coexisting crystalline phases

We study the emergence of glassy states after a sudden cooling in lattice models with short range interactions and without any a priori quenched disorder. The glassy state emerges whenever the equilibrium model possesses a sufficient number of coexisting crystalline phases at low temperatures, provided the thermodynamic limit be taken before the infinite time limit. This result is obtained through simulations of the time relaxation of the standard Potts model and some exclusion models equipped with a local stochastic dynamics on a square lattice.Comment: 12 pages, 4 figure

Morphology Development in Model Polyethylene via Two-Dimensional Correlation Analysis

Two-dimensional (2D) correlation analysis is applied to synchrotron X-ray scattering data to characterize morphological regimes during nonisothermal crystallization of a model ethylene copolymer (hydrogenated polybutadiene, HPBD). The 2D correlation patterns highlight relationships among multiple characteristics of structure evolution, particularly the extent to which separate features change simultaneously versus sequentially. By visualizing these relationships during cooling, evidence is obtained for two separate physical processes occurring in what is known as “irreversible crystallization” in random ethylene copolymers. Initial growth of primarily lamellae into unconstrained melt (“primary-irreversible crystallization”) is distinguished from subsequent secondary lamellae formation in the constrained, noncrystalline regions between the primary lamellae (“secondary-irreversible crystallization”). At successively lower temperatures (“reversible crystallization”), growth of the crystalline reflections is found to occur simultaneously with the change in shape of the amorphous halo, which is inconsistent with the formation of an additional phase. Rather, the synchronous character supports the view that growth of frustrated crystals distorts the adjacent noncrystalline material. Furthermore, heterocorrelation analysis of small-angle and wideangle X-ray scattering data from the reversible crystallization regime reveals that the size of new crystals is consistent with fringedmicellar structures (~9 nm). Thus, 2D correlation analysis provides new insights into morphology development in polymeric systems

Realistic atomistic structure of amorphous silicon from machine-learning-driven molecular dynamics

Amorphous silicon (a-Si) is a widely studied noncrystalline material, and yet the subtle details of its atomistic structure are still unclear. Here, we show that accurate structural models of a-Si can be obtained using a machine-learning-based interatomic potential. Our best a-Si network is obtained by simulated cooling from the melt at a rate of 1011 K/s (that is, on the 10 ns time scale), contains less than 2% defects, and agrees with experiments regarding excess energies, diffraction data, and 29Si NMR chemical shifts. We show that this level of quality is impossible to achieve with faster quench simulations. We then generate a 4096-atom system that correctly reproduces the magnitude of the first sharp diffraction peak (FSDP) in the structure factor, achieving the closest agreement with experiments to date. Our study demonstrates the broader impact of machine-learning potentials for elucidating structures and properties of technologically important amorphous materials

Shear-transformation-zone theory of plastic deformation near the glass transition

The shear-transformation-zone (STZ) theory of plastic deformation in glass-forming materials is reformulated in light of recent progress in understanding the roles played the effective disorder temperature and entropy flow in nonequilibrium situations. A distinction between fast and slow internal state variables reduces the theory to just two coupled equations of motion, one describing the plastic response to applied stresses, and the other the dynamics of the effective temperature. The analysis leading to these equations contains, as a byproduct, a fundamental reinterpretation of the dynamic yield stress in amorphous materials. In order to put all these concepts together in a realistic context, the paper concludes with a reexamination of the experimentally observed rheological behavior of a bulk metallic glass. That reexamination serves as a test of the STZ dynamics, confirming that system parameters obtained from steady-state properties such as the viscosity can be used to predict transient behaviors.Comment: 15 pages, four figure

The LBFGS Quasi-Newtonian Method for Molecular Modeling Prion AGAAAAGA Amyloid Fibrils

Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein); theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method - an improved LBFGS Quasi-Newtonian mathematical optimization method - to produce 3D structures of Prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field