Bond Angle Distributions Research Articles

Structure and properties of sodium aluminosilicate glasses from molecular dynamics simulations

Addition of alumina to sodium silicate glasses considerably improves the mechanical properties and chemical durability and changes other properties such as ionic conductivity and melt viscosity. As a result, aluminosilicate glasses find wide industrial and technological applications including the recent Corning(®) Gorilla(®) Glass. In this paper, the structures of sodium aluminosilicate glasses with a wide range of Al∕Na ratios (from 1.5 to 0.6) have been studied using classical molecular dynamics simulations in a system containing around 3000 atoms, with the aim to understand the structural role of aluminum as a function of chemical composition in these glasses. The short- and medium-range structures such as aluminum coordination, bond angle distribution around cations, Q(n) distribution (n bridging oxygen per network forming tetrahedron), and ring size distribution have been systematically studied. In addition, the mechanical properties including bulk, shear, and Young's moduli have been calculated and compared with experimental data. It is found that aluminum ions are mainly four-fold coordinated in peralkaline compositions (Al∕Na < 1) and form an integral part of the rigid silicon-oxygen glass network. In peraluminous compositions (Al∕Na > 1), small amounts of five-fold coordinated aluminum ions are present while the concentration of six-fold coordinated aluminum is negligible. Oxygen triclusters are also found to be present in peraluminous compositions, and their concentration increases with increasing Al∕Na ratio. The calculated bulk, shear, and Young's moduli were found to increase with increasing Al∕Na ratio, in good agreement with experimental data.

The structure and mechanical properties in amorphous alumina under pressure

Molecular dynamics simulations of amorphous alumina with various densities ranged from 2.84 to 3.81gcm−3 were carried out to investigate their local atomic configuration and mechanical properties. The local atomic structure was analyzed through the pair radial distribution functions, bond angle distributions and simplex statistics. The simulation reveals that a mathematic expression can be derived from a relationship between bond angle distribution and structural units AlOx (and linkages OAly). The density can be estimated through the fraction of structural units AlOx. Void volume and void radii decrease as the density increases. Based on the analysis of simplex statistics, the perfect tetrahedron AlO4 (PTE) was determined. These PTEs may connect to each other via common oxygen to create a large poly-PTE. The largest poly-PTE consists of 19.2% Al in the sample with the lowest density and 3.8% Al in one with the highest density. From deformation of samples, elastic moduli and Poisson ratio were determined. The Young’s modulus and yield stress increase with the increasing density. The strain hardening becomes more pronounced as the density increases.

Modeling vitreous silica bilayers

We computer model a free-standing vitreous silica bilayer which has recently been synthesized and characterized experimentally in landmark work. Here we model the bilayer using a computer assembly procedure that starts from a single layer of amorphous graphene, generated using a bond switching algorithm from an initially crystalline graphene structure. Next each bond is decorated with an oxygen atom and the carbon atoms are relabeled as silicon. This monolayer can be now thought of as a two dimensional network of corner sharing triangles. Next each triangle is made into a tetrahedron, by raising the silicon atom above each triangle and adding an additional singly coordinated oxygen atom at the apex. The final step is to mirror reflect this layer to form a second layer and then attach the two layers together to form the bilayer. We show that this vitreous silica bilayer has the additional macroscopic degrees of freedom to easily form a network of identical corner sharing tetrahedra if there is a symmetry plane through the center of the bilayer going through the layer of oxygen ions that join the upper and lower layers. This has the consequence that the upper rings lie exactly above the lower rings, which are tilted in general. The assumption of a network of perfect corner sharing tetrahedra leads to a range of possible densities that we have previously characterized in three dimensional zeolites as a flexibility window. Finally, using a realistic potential, we have relaxed the bilayer to determine the density, and other structural characteristics such as the Si-Si pair distribution functions and the Si-O-Si bond angle distribution, which are compared to the experimental results obtained by direct imaging.

Study of the effect of sizes on the structural properties of SiO2 glass by molecular dynamics simulations

To validate the present model and different simulation results of SiO2 considering 169,956 atoms, the total correlation function of solid SiO2 obtained by the present simulation is compared with that of the experimental results obtained by Poulsen et al. [14] and agrees well with the experimental results. To understand the effect of model size on the physical and chemical properties of solid SiO2, SiO2 is formed using four different sizes of model considering the total number of Si and O atoms 666, 5808, 169,956 and 339,915 in the ratio 1:2 using the parameters of SiSi, SiO, and OO in Tersoff potential obtained by Munetoh et al. [40] by the molecular dynamics simulations. The effect of model sizes on the partial radial distribution functions of SiSi, SiO, and OO with the total radial distribution function of solid SiO2 as a function of radial distance is studied. Besides, the effect of model sizes on the bond angle distribution of SiOSi and OSiO with angle, and bond density of SiSi, SiO, and OO in solid SiO2 as a function of radial distance is studied. All of the physical and chemical properties in liquid and solid states of SiO2 are studied during the simulation of SiO2 considering 169,956 atoms and if the model size is increased beyond this size, no size effect is observed on the physical and chemical properties of SiO2. The obtained physical and chemical properties like partial radial distribution functions of SiSi, SiO, and OO and total radial distribution function of liquid and solid SiO2, angle distribution of OSiO and SiOSi in the liquid and solid phases during the simulation considering 169,956 atoms are compared with those of Munetoh et al. [40] and others, and are highlighted as the major limitations of the results of Munetoh et al. [40] and others, and are shown as the superiority of the present simulation results. Details of the bond density of SiSi, SiO, and OO at the liquid and solid phases with bond distance are described. Details of the phase transformation of SiO2 glass are described with the help of graphical representations. The effects of pressure and temperature on the physical and chemical properties of SiO2 (α-quartz) are described with the graphical results. Due to high pressure α-quartz is converted into coesite which is discussed.

Homopolymer adsorption on periodically structured surfaces in systems with incommensurable lengths

Surface-induced selective adsorption of homopolymers on a generic level is numerically analyzed for freely jointed chains (with a fixed bond length) whose monomers are attracted by the sites of regular periodic patterns. In particular, the behavior of the specific heat, the gyration tensor, and the bond order tensor are investigated as functions of the temperature. The properties of the transition are related to the interplay of the characteristic lengths. The adsorption proceeds in two steps for certain incommensurabilities of the bond length and the lattice constant. The corresponding adsorption mechanisms are elucidated by looking at the evolution of the inter bond angle distribution upon adsorption. Moreover, the origin of two steps in contrast to adsorption in one step is traced back to entropic restrictions caused by a strongly reduced phase space of the polymer for certain values of the incommensurability.

Molecular Dynamics Simulation of Structural Changes of Ag&lt;sub&gt;965&lt;/sub&gt; Clusters during Freezing

The structural transitions of Ag965 clusters during two different quenching processes (Q1:1.0×1014 K/s, Q2: 1.0×1012 K/s) were studied using molecular dynamics simulations. This work gives the structure properties including the variations with temperature of pair-correlation function, bond-angle distribution function, bond pairs and bond orientational order parameters in both rapid quenching processes. Our results indicated that the liquid Ag965 was frozen into amorphous structure at 100 K under the quenching condition Q1. While the liquid Ag965 transformed to hexagonal close-packed (hcp) phase at the temperature 100 K under the quenching condition Q2.These instructions give you basic guidelines for preparing papers for conference proceedings.

Glass-forming ability of Al-Co alloy under rapid annealing

By using molecular dynamics method, transition of Al-Co alloy from liquid to amorphous structure has been investigated theoretically. The structure parameters, pair distribution functions (PDF), bond-angle distribution functions, and Voronoi polyhedra analysis are adopted as indicators of the evolution of clusters in Al-Co alloy during the rapid cooling processes. We found that below transition temperature, the second peak of PDF curves splits into two pronounced subpeaks, while at all temperature the PDF curves gradually converge to unity at large distance. This indicates that the amorphous alloy exhibits local ordering structure and has no long-range ordering. Besides, the bond-angle distribution function predicts that the degrees in the vicinity of 63.4 and 113.4 are dominated in the system during the processes of rapid annealing, which represent that the icosahedral structures are dominant. Together with the cluster structures observed in simulation, Voronoi polyhedra analysis shows that the most popular polyhedron is full icosahedron with the Voronoi index 〈0, 0, 12, 0〉, which is always predominant in bulk metallic glass (MG) formers with excellent glass forming ability. Our studies indicated that doping of cobalt atoms in the Al-based alloy should have a better capacity of forming MG.

Preparation and characterization of amorphous carbon (a-C) membranes by molecular dynamics simulation

Amorphous carbon (a-C) membranes with 1,728 particles were prepared from diamond at four different densities (1.8, 2.0, 2.28, and 2.4 g/cm3) using molecular dynamics simulation. Stillinger and Weber potential for carbon was introduced with kinetic energy abided by classical Newton equation. Time mesh was chosen 0.01 or 1 fs. The melt-quenching technology method was adopted with the corresponding cooling rate 5 and 0.05 K/fs, respectively. Different membranes were obtained from higher initial temperature (7,500, 7,000, or 6,500 K at different densities and cooling rates) to room temperature. We compared the radial distribution function, bond angle distribution, and pore size distribution with experimental data. The results agreed well and one membrane at lower density with larger pores was chosen to calculate the gas permeation further. Gas molecules (He, Ne, H2, CO2, N2, CH4, and SF6) permeation through the a-C membrane at low density (1.8 g/cm3) when time mesh equal to 1 fs were calculated at 300, 400, 473, 500, and 600 K. The results of every gas species almost illustrated Knudsen diffusion well. And the number of permeated particles depended on the molecular weight.

HRMC_2.0: Hybrid Reverse Monte Carlo method with silicon, carbon and germanium potentials

The Hybrid Reverse Monte Carlo (HRMC) code models the atomic structure of materials via the use of a combination of constraints including experimental diffraction data and an empirical energy potential. In this version update, germanium potential parameters are introduced and constraints based on the coordination, average coordination and the total bond angle distribution are implemented. Other additional changes include a constraint on three member ring formation, a constraint on porosity and an extension to handle systems with up to three different elements. Program SummaryProgram title: HRMC version 2.0Catalogue identifier: AEAO_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAO_v2_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 94759No. of bytes in distributed program, including test data, etc.: 751023Distribution format: tar.gzProgramming language: Fortran 90.Computer: Any computer capable of running executables produced by the Fortran 90 compiler. For example, the code runs in Windows 7, once compiled with the GNU Fortan 95 compiler.Operating system: Unix, Windows.RAM: Depends on the type of empirical potential used, number of atoms and which constraints are employed. Typically below 2 GB for a system with a few thousand atoms.Classification: 7.7.Does the new version supersede the previous version?: YesCatalogue identifier of previous version: AEAO_v1_1Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 542Nature of problem:Atomic modeling using a combination of empirical potentials, fits to experimental data and other chemically or physically motivated constraints.Solution method:Single move Metropolis Monte Carlo method used to minimize total energy and discrepancy between simulation and experimental data.Reasons for new version:Extension of capabilities from old version.Summary of revisions:Inclusion of Stillinger–Weber parameters for germanium, inclusion of a bond angle distribution constraint, inclusion of more general coordination, average coordination and porosity/volume constraints. Variable step sizes are now supported. Extension to systems containing up to three elements. New quench schemes to control constraint weighting throughout the simulation have been included. Constraints to forbid three member ring formation have been developed. There are changes to the input/output structure.Running time:1000 s for a test run on a Intel Xeon 2.93 GHz—Nehalem series processor.

The evolution of structural and electronic properties during the glass transition process of Al–Ni–Nd alloy

Ab initio molecular dynamic simulations are performed to understand the evolution of structural and electronic properties during the glass transition process of the Al–Ni–Nd alloy based on the density functional theory. The local structural evolution is evaluated by the Honeycutt–Andersen (HA) bond-type index and bond-angle distribution methods. The bond-angle distribution indicates that the close packing of three neighbour atoms and the pentagon configurations become the primary short range order (SRO) as temperature decreases and the HA bond-type result shows that the formation of the crystal structures is suppressed by the increasing pentagonal bi-pyramids ordering during the rapid solidification processes. Our result provides strong evidence for the existence of Al–Ni covalent bonds, where chemical SRO together with the polyhedral local structures play an important role during the glass transition and increase the glass forming ability of the Al–Ni–Nd alloy. We also found that the electrons with an sp character of the Al atoms are more likely to transfer to the d states of the Ni atoms during the glass transition process.

AB INITIO MOLECULAR DYNAMICS SIMULATIONS ON LOCAL STRUCTURE AND ELECTRONIC PROPERTIES IN LIQUID MgxBi1-x ALLOYS

The microscopic structure and dynamics of liquid Mg x Bi 1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg 3 Bi 2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

AB INITIOMOLECULAR DYNAMICS SIMULATIONS ON LOCAL STRUCTURE AND ELECTRONIC PROPERTIES IN LIQUIDSbFROM 913 K TO 1193 K

Ab initio molecular dynamics simulations on liquid Sb have been carried out at five different temperatures from 913 K to 1193 K. We have investigated the temperature dependence of structure properties including structural factor S(Q), pair correlation function g(r), bond-angle distribution function g3(θ), cluster properties and bond order parameter Q4and Q6. A shoulder was reproduced in the high wave number side of the first peak in the S(Q) implying that the residual structure units of crystalline Sb remain in liquid Sb . There is a noticeable bend at around 1023 K in the temperature dependence of the first-peak height of S(Q), the cluster properties and bond order parameter Q4, respectively, indicating that an abnormal structural change may occur at 973–1023 K.

Selective homopolymer adsorption on structured surfaces as a model for pattern recognition

Homopolymer adsorption onto chemically structured periodic surfaces and its potential for pattern recognition is investigated using Monte Carlo simulations. To analyze the surface-induced selective adsorption on a fundamental geometric level polymer chains are represented by freely jointed chains with a fixed bond length whose monomers are attracted by the sites of regular lattice patterns. The structural properties of the adsorbed low-temperature state are comprehensively discussed for different lattices by looking at the radius of gyration and the inter bond angle distributions. These observables show a non-trivial dependence on the commensurability of characteristic lengths given by the lattice constant and by the bond length. Reasons for this behavior are given by exploiting geometric and entropic arguments. The findings are examined in the context of pattern recognition by polymer adsorption. Furthermore, the adsorption transition is discussed briefly. For certain incommensurable situations the adsorption occurs in two steps due to entropic restrictions.

The structural correlation and mechanical properties in amorphous silicon nitride under densification

Molecular dynamics simulations of amorphous silicon nitride (a-Si3N4) with various densities ranging from 2.43 to 3.40gcm−3 were carried out to investigate their structural correlation and mechanical properties. The local structure was analyzed through the pair radial distribution functions, bond angle distributions and simplex statistics. The simulation reveals that although the fractions of structural units SiNx and NSiy strongly change with the density, the partial bond angle distributions of these structural units are identical for all constructed models. This result has enabled us to establish a relationship between the bond angle distributions and the fractions of structural units. Based on the analysis of simplex statistics, we found that all samples contain both the perfect and distorted tetrahedrons (SiN4). These perfect tetrahedrons (PTEs) may connect to each other via common nitrogen to create a large cluster- or poly-PTEs. The largest poly-PTE consists of 45.6% Si in the sample with a density of 3.02gcm−3 and 1.3% Si with the lowest density. We also found that even though at the high density the sample contains a remarkable number of voids in which the radius is larger than 1.1Å. From uniaxial deformation of samples, the Young's modulus, yield and flow stress were determined. The strain hardening and softening become more pronounced as density increases.

Modeling Mechanotransduction Signaling through Actin Filament Network Deformation Linked to Biochemical Response

It is becoming more and more evident that the mechanical forces previously taken for granted actually play a pivotal role in influencing biological phenomenon from cancer metastases to vasculogenesis. Recent literature provides strong evidence for a causative link between the mechanical stretching of the cytoskeleton and the release of mechanotransductive signaling molecules. Understanding the links between mechanical input, the corresponding morphological changes in the actin cytoskeleton, and the resulting biochemical response is not well understood yet is a significant challenge in the field of mechanotransduction. Here, we present a model that integrates actin filament network remodeling under stretch with a novel biophysical model of molecular release to further elucidate the interplay between actin network morphology and resultant biochemical signaling.As stretch is applied to a model of the actin filament network, the distribution of bond angles in the network transitions from a more peaked to a flatter distribution. High variability is observed from site-to-site within the network upon an applied stretch, with a nearly uniform distribution of difference between stretched and unstretched angles (“delta angles”) at high levels of stretching. We used our approach to explore various thresholding models of how actin filament network deformations might influence rates of release of bound signaling molecules. These models allow us to project how a biochemical response might appear from a given applied mechanical stimulus. We validate these simulations using experimental data and use our model to then test different predictive capabilities of how mechanotransduction may function. Our model for the mechanotransductive release of signaling factors represents a potentially versatile mechanistic platform for examining biophysical interactions that link mechanical stimulus at the cellular level to response at the protein level.

Lone-pair distribution and plumbite network formation in high lead silicate glass, 80PbO·20SiO2

For the first time a detailed structural model has been determined which shows how the lone-pairs of electrons are arranged relative to each other in a glass network containing lone-pair cations. High energy X-ray and neutron diffraction patterns of a very high lead content silicate glass (80PbO·20SiO2) have been used to build three-dimensional models using empirical potential structure refinement. Coordination number and bond angle distributions reveal structural similarity to crystalline Pb11Si3O17 and α- and β-PbO, and therefore strong evidence for a plumbite glass network built from pyramidal [PbO(m)] polyhedra (m ~ 3-4), with stereochemically active lone-pairs, although with greater disorder in the first coordination shell of lead compared to the first coordination shell of silicon. The oxygen atoms are coordinated predominantly to four cations. Explicit introduction of lone-pair entities into some models leads to modification of the local Pb environment, whilst still allowing for reproduction of the measured diffraction patterns, thus demonstrating the non-uniqueness of the solutions. Nonetheless, the models share many features with crystalline Pb11Si3O17, including the O-Pb-O bond angle distribution, which is more highly structured than reported for lower Pb content glasses using reverse Monte Carlo techniques. The lone-pair separation of 2.85 Å in the model glasses compares favourably with that estimated in α-PbO as 2.88 Å, and these lone-pairs organise to create voids in the glass, just as they create channels in Pb11Si3O17 and interlayer spaces in the PbO polymorphs.

Structural and Electronic Properties of Cu64Zr36 BMG by ab initio Molecular Dynamics

ABSTRACTMuch attention has been given to bulk metallic glasses (BMG) in recent years, particularly those based on binary alloys due to the simplicity of their atomic composition. Although efforts to understand the atomistic features that give rise to their exceptional properties have been made, the electronic and vibrational properties have been disregarded. We undertook the task of simulating the Cu64Zr36 glassy metal using a supercell with 108 atoms and a different simulational approach: the undermelt-quench approach [1]. The structure was characterized by means of the radial (pair) distribution function and the bond-angle distribution and the electronic density of states was calculated. We find that our results agree well with experimental data.

On the c-Si|a-SiO2 Interface in Hyperthermal Si Oxidation at Room Temperature

The exact structure and properties of the Si|SiO2 interface are very important in microelectronics and photovoltaic devices such as metal-oxide-semiconductor field-effect transistors (MOSFETs) and solar cells. Whereas Si|SiO2 structures are traditionally produced by thermal oxidation, hyperthermal oxidation shows a number of promising advantages. However, the Si|SiO2 interface induced in hyperthermal Si oxidation has not been properly investigated yet. Therefore, in this work, the interface morphology and interfacial stresses during hyperthermal oxidation at room temperature are studied using reactive molecular dynamics simulations based on the ReaxFF potential. Interface thickness and roughness, as well as the bond length and bond angle distributions in the interface are discussed and compared with other models developed for the interfaces induced by traditional thermal oxidation. The formation of a compressive stress is observed. This compressive stress, which at the interface amounts about 2 GPa, significantly slows down the inward silica growth. This value is close to the experimental value in the Si|SiO2 interface obtained in traditional thermal oxidation.

First principle molecular dynamic simulation of the rapid solidification process of Ca50Mg20Cu30 alloy

The rapid solidification processes of Ca50Mg20Cu30 liquid alloy have been simulated by first principle molecular dynamics simulation based on the density functional theory. The local structural evolution of the alloy is analysed using Honeycutt Andersen (HA) bond-type index and bond-angle distribution methods. The electronic properties of this amorphous solid are also studied. The simulated coordination numbers are very close to the theoretical values according to the efficient cluster packing model (ECP) model. The interaction between Ca-Cu atomic pairs is strongest in this alloy. The HA bond-type result shows that a large quantity of pentagonal bipyramids are formed in undercooled alloy liquid and become most common polyhedral local structures of the amorphous solid, which suppress the crystallization and increase the glass forming ability of Ca-Mg-Cu alloy. The bond-angle distribution indicates that the close packing of the three neighbor atoms and the pentagon configurations become the primary short range order (SRO) as temperature decreases. The electronic density demonstrates that the covalent bond of Ca-Mg, Ca-Cu, Mg-Cu, and Cu-Cu pairs is existed in this alloy. This chemical SRO also benefits the glass transition.

Ab initio modelling of boron related defects in amorphous silicon

AbstractWe have modeled boron related point defects in amorphous silicon, using an ab initio method, the Density functional theory‐pseudopotential code Aimpro. The boron atoms were embedded in 64 atom amorphous silicon cubic supercells. The calculations were performed using boron defects in 15 different supercells. These supercells were developed using a modified Wooten‐Winer‐Weaire bond switching mechanism. In average, the properties of the 15 supercells agree with the observed radial and bond angle distributions, as well the electronic and vibrational density of states and Raman spectra. In amorphous silicon it has been very hard to find real self‐interstitials, since for almost all the tested configurations, the amorphous lattice relaxes overall. We found that substitutional boron prefers to be 4‐fold coordinated. We find also an intrinsic hole‐trap in the non‐doped amorphous lattice, which may explain the low efficiency of boron doping. The local vibrational modes are, in average, higher than the correspondent crystalline values (© 2012 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)