Coordination Number Distribution Research Articles

Interparticle interactions and dynamics in BmimBF4 and LiBF4 solutions in propylene carbonate: MD simulation

Ionic liquids have gained immense popularity in recent decades due to a combination of unique properties. Despite the widespread use of ionic liquids mixtures with aprotic dipolar solvents in electrochemistry, it remains relevant to predict their macroscopic, primarily transport, properties based on the microscopic picture of the entire set of interparticle interactions in such systems. The method of molecular dynamics simulation (MDS) is one of the most powerful tools for solving problems of this kind. However, one of the unsolved problems of the classical MDS of ion-molecular systems is the correct accounting of polarization effects. Recently it was proposed to use a variation of the effective ion charges in solutions to solve this task. This paper presents the results of the MDS structural and dynamic properties of 1-butyl-3-methylimidazolium (BmimBF4) and lithium (LiBF4) tetrafluoroborates solutions in propylene carbonate (PC) at 298.15 K in NPT ensemble using GROMACS and MDNAES software packages. The possibility of reproducing the experimental dynamic properties (diffusion coefficients of cations and solvent, viscosity, and electrical conductivity) of binary systems based on mixtures of ionic liquids with PC in a wide concentration range was shown. Polarization effects were taken into account by reducing the partial charges of the ion atoms. The structure of the solvation shell of cations was studied within the framework of radial distribution functions, distribution of coordination numbers and the presence of hydrogen bonds between the organic cation and solvent molecules. The results point to stronger and more structured solvation shell of the Li+ cation compared to Bmim+, which is consistent with the conclusions about the mobility of these cations. The reorientation times of propylene carbonate molecules and their lifetimes in the framework of the first solvation shells of the cations are several times higher for the lithium cation.

Shape-dependent structural and magnetic properties of Fe nanoparticles studied through simulation methods.

Studying the shape-dependent structural and magnetic properties of nanoparticles is one of the most necessary scientific challenges in order to match these nano-objects for adequate applications. In this research paper, the shape effect of iron nanoparticles (FeNPs) on structural and magnetic properties was investigated on the basis of a combination of Molecular Statics (MS) and Monte Carlo (MC) simulations. To this end, three kinds of FeNP shapes (such as spherical, planar and rod) in an equal volume have been considered. The coordination number distribution of FeNPs obtained from the data extracted by MS simulations was exploited for performing MC simulations on the familiar Ising model. The numerical findings obtained showed that the structural stability, the Curie temperature as well as the shape of the hysteresis loop are correlated with the FeNP shape.

Direct shear properties of railway ballast mixed with tire derived aggregates: Experimental and numerical investigations

This paper presents results from laboratory direct shear tests and discrete element method (DEM) simulations of railway ballast mixed with different contents of tire derived aggregate (TDA). The stress-strain behavior of the ballast-TDA mix was obtained. The results from laboratory tests and DEM simulations were compared. The laboratory and DEM tests both showed that the TDA significantly decreased the peak shear stress and the dilation effect of the ballast-TDA mix. According to the Mohr-Coulomb failure criterion, the TDA decreased the cohesion strength and the internal friction angle of the ballast-TDA mix. The DEM simulations provided insights into the microscopic behavior of ballast-TDA mixture through the coordination number (CN) and contact force distribution. The DEM simulation showed that the TDA increased the CN among the particles. As the content of TDA increased, the CN of TDA increased while the CN of ballast particles decreased. The TDA tended to decrease the occurrence of large contact forces (>250 N), and thus lowered ballast breakage in the ballast-TDA mix.

Atomistic simulation study of favored compositions of Ni-Nb-Al metallic glasses

This study investigates the formation process of Ni-Nb-Al metallic glasses. To this end, a long-range n -body potential was constructed for the Ni-Nb-Al ternary metal system, and applied to atomistic simulations. The simulations not only showed the physical origins of the amorphous phase formation, but also quantitatively predicted a hexagonal compositional region that energetically favors the glass formation. The energy difference between the solid solution and metallic glass, which generates the amorphization driving force (ADF), was suggested to indicate the glass-formation ability (GFA) of each alloy. Based on the computed ADFs, the Ni55Nb25Al20 alloy exhibited the highest GFA among the Ni-Nb-Al members, implying that the glass formed by this amorphous alloy is more thermodynamically stable than other alloys in the system. In a Voronoi tessellation analysis, the knee point of the coordination-number distribution curve corresponded to the glass-formation region of the Ni-Nb-Al system.

Hidden order in amorphous structures: Extraction of nearest neighbor networks of amorphous Nd-Fe alloys with Gabriel graph analyses.

Using the scheme of Delaunay and Gabriel graphs, we analyzed the amorphous structures of computationally created Nd-Fe alloys for several composition ratios based on melt quench simulations with finite temperature first-principles molecular dynamics. By the comparison of the radial distribution functions of the whole system and those derived from the Delaunay and Gabriel graphs, it was shown that the Gabriel graphs represent the first nearest neighbor networks well in the examined amorphous systems. From the Gabriel graph analyses, we examined the coordination structures of amorphous Nd-Fe alloys statistically. We found that the ranges of distributions of coordination numbers are wider at the lower Nd composition ratios. The angular distributions among three adjacent atoms were also analyzed, and it was found that the steeper the angular distributions become the higher the Nd composition ratios are. These features mean that the orders in the amorphous system become stronger as the Nd ratio increases, which corresponds to the appearance of crystalline grain boundary phases at high Nd composition ratios [T. T. Sasaki et al., Acta Mater. 115, 269-277 (2016)].

Rheology of Cohesive Granular Particles under Constant Pressure

The rheology of cohesive granular materials, under a constant pressure condition, is studied using molecular dynamics simulations. Depending on the shear rate, pressure, and interparticle cohesiveness, the system exhibits four distinctive phases: uniform shear, oscillation, shear-banding, and clustering. The friction coefficient is found to increase with the inertial number, irrespective of the cohesiveness. The friction coefficient becomes larger for strong cohesion. This trend is explained by the anisotropies of the coordination number and angular distribution of the interparticle forces. In particular, we demonstrate that the second-nearest neighbors play a role in the rheology of cohesive systems.

Simple probability distributions on a Fock-space lattice

We consider some aspects of a standard model employed in studies of many-body localization: interacting spinless fermions with quenched disorder, for non-zero filling fraction, here on d-dimensional hypercubic lattices. The model may be recast as an equivalent tight-binding model on a ‘Fock-space (FS) lattice’ with an extensive local connectivity. In the thermodynamic limit exact results are obtained for the distributions of local FS coordination numbers, FS site-energies, and the density of many-body states. All such distributions are well captured by exact diagonalisation on the modest system sizes amenable to numerics. Care is however required in choosing the appropriate variance for the eigenvalue distribution, which has implications for reliable identification of mobility edges.

Study of Nanoscratching Process of GaAs Using Molecular Dynamics

In this paper, molecular dynamics method was employed to investigate the nanoscratching process of gallium arsenide (GaAs) in order to gain insights into the material deformation and removal mechanisms in chemical mechanical polishing of GaAs. By analyzing the distribution of hydrostatic pressure and coordination number of GaAs atoms, it was found that phase transformation and amorphization were the dominant deformation mechanisms of GaAs in the scratching process. Furthermore, anisotropic effect in nanoscratching of GaAs was observed. The diverse deformation behaviors of GaAs with different crystal orientations were due to differences in the atomic structure of GaAs. The scratching resistance of GaAs(001) surface was the biggest, while the friction coefficient of GaAs(111) surface was the smallest. These findings shed light on the mechanical wear mechanism in chemical mechanical polishing of GaAs.

The random distribution of the coordination numbers in the mixed spin-1/2 and spin-2 Blume-Capel model

The effects of random distribution of coordination numbers are investigated for the mixed spin-1/2 and spin-2 Blume-Capel model on the Bethe lattice in terms of exact recursion relations. The usual coordination numbers, i.e. q=3,4 and 6, corresponding to the honeycomb, square and simple cubic lattices, respectively, are considered. Two different q values are taken as couples and are varied randomly in terms of a standard-random approach on the shells of the Bethe lattice with some probabilities. It is found that the model gives either first- or second-order phase transitions for appropriate values of probability (p) and single ion anisotropy (d). One or two tricritical points are also observed depending on the given values of p and d, respectively.

Structural analysis of WO3-TeO2 glasses by neutron, high energy X-ray diffraction, reverse Monte Carlo simulations and XANES

The structure of WO3-TeO2 glasses containing 15, 20 and 25 mol% WO3 are studied by neutron diffraction (ND), high energy X-ray diffraction (XRD) and X-ray Absorption Near Edge spectroscopy (XANES). The short-range structural properties of glasses i.e. TeO and WO speciation, coordination number distributions, bond-lengths, and the OTeO, OWO and OOO bond angle distributions in the glass network are determined by the Reverse Monte Carlo (RMC) simulations of the ND and XRD data. RMC technique successfully determined all partial pair correlation functions and the coordination number distributions revealed that glass network consists predominantly of TeO4 and WO4 units with small amounts of triangular, penta and hexa co-ordinated units. The average WO and TeO bond lengths are in the ranges: 1.69–1.75 ± 0.01 Å and 1.99–2.00 ± 0.01 Å respectively. Both WO and TeO correlation peaks are asymmetrical, that indicate a distribution of their bond lengths in the respective structural units. The O-Te-O bond angle distribution has a peak at 107 ± 2°. Similarly the O-W-O bond angle distribution has a peak at 108 ± 5°. On increasing the WO3 concentration from 15 to 25 mol%, the average TeO coordination number decreases from 3.80 to 3.61 ± 0.02 due to the structural transformation: TeO4 → TeO3, similarly the WO coordination also decreases and is in the range: 3.79–3.67 ± 0.02. XANES studies found that the oxidation state of Te and W ions in the glasses are 4+ and 6+ respectively.

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure.

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03Å corresponding to a liquid ammonia density of 0.69g/mL at 235.16K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH3 interaction is weak electrostatically.

Effect of phase and size on surface sites in cobalt nanoparticles

Molecular dynamics was applied to simulate cobalt nanoparticles to understand the effects of particles size and crystal phases on the distribution of surfaces sites relevant for Fischer-Tropsch catalysis. The results indicate a minimal change (<5%) in the coordination number distribution of surface atoms for particles larger than 4 nm even at 500 K, implying that temperature is not sufficient to drive surface reconstruction. We found that the distribution of B5 sites differ significantly between hcp and fcc particles, suggesting different CO adsorption properties for the two phases. HCP particles offer different types of B5 sites which are sterically less hindered for CO adsorption and maybe the reason for differences in catalytic behaviors of hcp vs. fcc nanoparticles. Finally, the smaller nanoparticles have higher radial contraction on the surface, which could impact the deactivation mechanism of these particles by inhibiting the sub-surface diffusion of adsorbate species.

Crystallization of supercooled liquid and amorphous silicene

Crystallization under isothermal condition of supercooled liquid and amorphous silicene (a-silicene) models has been studied via molecular dynamics (MD) simulation with Stillinger-Weber (SW) interaction potential. Supercooled liquid and a-silicene models containing 104 atoms are obtained via the rapid solidification process from the melt. At each given temperature below and above Tg, models are annealed from 5 ns up to 8 ns in order to investigate aging effect on two-dimensional structural arrangement of disordered Si-atoms. Time dependence of thermodynamic and structural quantities is analyzed including potential energy, radial distribution function (RDF), coordination number, buckling degree, ring and bond-angle distribution. We find that 2D-crystallization of supercooled liquid and a-silicene exhibits a first-order behavior. Time-temperature-transformation (TTT) diagram exhibits a commonly nose-shape by analyzing a wide temperature range from supercooled liquid to amorphous state. High critical cooling rates of a-silicene are found indicating low glass-formation ability of the system. Thermodynamic properties of crystallization of silicenes attained after-aging are studied in details and we clarify a novel scenario of crystallization. A homogenous tendency of natural quenched-in nucleation atoms aggregate into larger clusters in 2D Si supercooled liquid sheet. Consequently, a polycrystalline layer of silicene is developed with decent low-numbered chain defects as grain boundary. In contrast, crystallization of a-silicene shows a partial crystallization behavior: Crystal clusters are found to exhibit a heterogeneous growth in models obtained below Tg. Crystal formed from a-silicene is a quasi-equilibrium state with a large number of defects still existed in models after a long relaxing time.

Effect of annealing on structural changes and oxygen diffusion in amorphous HfO2 using classical molecular dynamics

Non-volatile memory is a promising alternative to present memory technologies. Oxygen vacancy diffusion has been widely accepted as one of the reasons for the resistive switching mechanism of transition-metal-oxide based resistive random access memory. In this study, molecular dynamics simulation is applied to investigate the diffusion coefficient and activation energy of oxygen in amorphous hafnia. Two sets of empirical potential, Charge-Optimized Many-Body (COMB) and Morse-BKS (MBKS), were considered to investigate the structural and diffusion properties at different temperatures. COMB predicts the activation energy of 0.53 eV for the temperature range of 1000–2000 K, while MBKS predicts 2.2 eV at high temperature (1600–2000 K) and 0.36 eV at low temperature (1000–1600 K). Structural changes and appearance of nano-crystalline phases with increasing temperature might affect the activation energy of oxygen diffusion predicted by MBKS, which is evident from the change in coordination number distribution and radial distribution function. None of the potentials make predictions that are fully consistent with density functional theory simulations of both the structure and diffusion properties of HfO2. This suggests the necessity of developing a better multi-body potential that considers charge exchange.

Monte Carlo simulations of bulk and nano amorphous silica (a-SiO2) melts

Monte Carlo simulations were carried on bulk and nano amorphous silica (SiO2) melts under different thermodynamic conditions and nano-sizes. The potential developed by Ersan, Tahir, Norman and William (ETNW) was used to model the interatomic interactions of SiO2 melts in both cases (bulk and nano systems). The bulk system was developed using periodic boundary conditions. The nano SiO2 melts were prepared by cutting out a sphere from the bulk amorphous SiO2 melt structure to the required size, and then simulated under free boundary conditions. The high-pressure, high-temperature and nano-size effects on the structure and properties of the melts were investigated and studied via radial distribution functions, radial density profiles, potential energy, density, ring size analysis, coordination number distributions, bond distances and angles. In addition, to understand the difference in properties of bulk and nano silica melts, a comparative study was done at the same thermodynamic conditions. Details of the modelling, simulation results and the study are presented in this paper.

Molecular dynamics simulation of melting of 2D glassy monatomic system

The melting of two-dimensional (2D) glassy monatomic systems is studied using the molecular dynamics simulation with Lennard–Jones–Gauss interaction potential. The temperature dependence of various structural and dynamical properties of the systems during heating is analyzed and discussed via the radial distribution functions, the coordination number distributions, the ring statistics, the mobility of atoms and their clustering. Atomic mechanism of melting is also analyzed via tendency to increase mobility and breaking clusters of atoms upon heating. We found that melting of a 2D glass does not follow any theory of the melting of 2D crystals proposed in the past. The melting exhibits a homogeneous nature, i.e. liquid-like atoms occur homogeneously throughout the system and melting proceeds further leading to the formation of an entire liquid phase. In addition, we found a defined transition temperature region in which structural and dynamical properties of systems strongly change with increasing temperature.

A super-stretchable boron nanoribbon network.

We have studied the mechanical properties of a two-dimensional (2D) boron nanoribbon network (BNRN) subjected to a uniaxial or a biaxial tensile strain using first principles calculations. The results show that the 2D BNRN is super-stretchable. The critical tensile strains of the BNRN in the χ-h1 phase along the a- and b-directions are 0.51 and 0.41, respectively, and that for the biaxial strain reaches an ultrahigh value of 0.84. By analyzing the B-B interatomic distance, coordination number and charge distribution, it is found that with increasing biaxial tensile strain, the χ-h1 BNRN undergoes two structural phase transitions, which are characterized by breaking of the B-B bonds and the partial transformation of the nanoribbon-like structures into chain-like structures. The strain-induced phase transitions significantly reduce the strain energy. We also discuss the elastic constants, Young's modulus, shear modulus, and Poisson's ratios. The super-stretchable and flexible mechanical properties of the BNRNs, together with their superior transport properties, make BNRNs useful in a wide range of applications in nanoscale electronic devices.

The Water–Amorphous Calcium Carbonate Interface and Its Interactions with Amino Acids

Amorphous calcium carbonate is often the first phase to precipitate from solution during the mineralization of calcium carbonate, before the formation of one of the crystalline polymorphs. In vivo, this phase is believed to be essential for the manufacture of minerals displaying nonequilibrium morphologies. The precipitation of this, usually transient, phase and its subsequent transformation into one of the crystalline polymorphs can be controlled by organic molecules. Here, we present a series of molecular dynamics simulations that explore the amorphous calcium carbonate–water interface, the attachment of amino acids onto both hydrous and anhydrous amorphous calcium carbonate, and their effect on the surface. The results show that surface ions have a different coordination number distribution from bulk ions and can diffuse up to two orders of magnitude faster than their bulk counterparts, suggesting that crystallization is much more likely to occur in this region. All the amino acids investigated bind to the amorphous calcium carbonate surfaces. However, acidic amino acids have a clear preference for the surface of amorphous CaCO3·H2O. The favored mode of interaction of the amino acids is through amine and/or guanidine moieties. The important ramifications of the results for our understanding of protein–mineral interactions are discussed.

Discrete element modeling of pebble bed packing structures for HCCB TBM

In solid tritium breeder blanket, the tritium breeder and neutron multiplier are used in formed of pebbles. To reveal the inner packing structures of the pebble bed, in this paper, the discrete element method (DEM) was applied to simulate the pebble bed packing structures by pouring pebbles from the top of container. The current numerical results obviously show that with the increase of aspect ratios the packing factor can be significantly increased in both cylinder pebble bed and cubic pebble bed. Namely, the larger aspect ratios in cylinder and cubic pebble bed, the smaller the proportion of the wall affected region, the greater the average packing factor of the cylinder and cubic pebble bed. Furthermore, the pebble packing structures in a U-shaped container were also simulated and analyzed. In the bend pebble bed, the average packing factor of 0.6278 was obtained. Close to the convex and concave container wall, the wall effects of pebble distribution and packing factor were observed. With the increase of the distance to the container wall, the layered arrangements disappear gradually and the oscillating characteristics of local packing factor are also damped little by little. The oscillations of local packing factors are limited in about 5 diameters. A transition region is formed between the layered packing in the near wall region and the uniformly random packing in the inner bulk region. In addition, the contact force distribution and coordination number distribution were also detailed analyzed.

DEM dynamic simulation of tetrahedral particle packing under 3D mechanical vibration

The transition from random loose packing (RLP) to random close packing (RCP) of mono-sized regular tetrahedral particles under 3D mechanical vibration was modeled by using discrete element method. The effects of vibration conditions and container size on the packing densification were systematically studied, and the macro and micro properties such as packing density, coordination number (CN), particle contact type, radial distribution function (RDF), particle orientation correlation, and forces between particles were characterized and analyzed. The randomness of the obtained dense packings and corresponding densification mechanisms were also investigated. The results show that RCP of the tetrahedral particles can be realized by properly controlling the vibration conditions. And the obtained maximum random packing density can reach about 0.7402 by extrapolating the packing densities in different sized containers. The average CN for RLP and RCP are 7 and 6.3, and the CN distribution for RCP is higher and narrower than that for RLP. From RLP to RCP, the frequency of face to face (F-F) contact between two particles increases, while that of vertex to face (V-F) contact and edge to face (E-F) contact decreases, and edge to edge (E-E) contact does not change much. RDF characterization shows four obvious peaks on the curves of RLP and RCP, where the height of the first peak (F-F contact) increases while that of other peaks decreases from RLP to RCP. The densification mechanism can be ascribed to the formation of wagon wheel local dense structures through rearrangement by ‘pushing filling’ and ‘jumping filling’.