Translation In Cells Research Articles

Theoretical investigation of the phase stability and elastic properties of TiZrHfNb-based high entropy alloys

First principles calculations are performed to study the effects of alloying elements (X = Al, Si, Sc, V, Cr, Mn, Cu, Zn, Y, Mo, Ta, W and Re) on the phase stability and elastic properties of TiZrHfNb refractory high entropy alloys. Both equimolar and non-equimolar alloys are considered. It is shown that the calculated lattice parameters, phase stability and elastic moduli of equimolar TiZrHfNbX are consistent with the available experimental and theoretical results. The substitutions of alloying elements at Ti, Zr, and Hf sites with various contents show similar effects on the phase stability and elastic properties of the TiZrHfNb-based alloys. The substitutions on Nb site are found to generally decrease the stability of body centered cubic phase. Close connections between the charge densities at the Wigner-Seitz cell boundary and the bulk moduli of TiZrHfNb-based alloys are found. The present results provide a quantitative model for exploring the phase stability and elastic properties of TiZrHfNb-based alloys from the electronic structure viewpoint.

Ionization equation of state for the dusty plasma including the effect of ion–atom collisions

The ionization equation of state (IEOS) for a cloud of dust particles in the low-pressure gas discharge under microgravity conditions is proposed. IEOS relates pairs of the parameters specific for the charged components of dusty plasma. It is based on the modified collision enhance collection model adapted for the Wigner–Seitz cell model of the dust cloud. This model takes into account the effect of ion–atom collisions on the ion current to the dust particles and assumes that the screening length for the ion–particle interaction is on the same order of magnitude as the radius of the Wigner–Seitz cell. The included effect leads to a noticeable decrease of the particle charge as compared to the previously developed IEOS based on the orbital motion limited model. Assuming that the Havnes parameter of the dusty plasma is moderate, one can reproduce the dust particle number density measured in experiments and, in particular, its dependence on the gas pressure. Although IEOS includes no fitting parameters, it can ensure a satisfactory precision in a wide range of dusty plasma parameters. Based on the developed IEOS, the threshold relation between the dusty plasma parameters for onset of the lane formation in binary dusty plasmas is deduced.

Large thermal anisotropy in monoclinic niobium trisulfide: a thermal expansion tensor study

We present a method based on the Grüneisen formalism to calculate the thermal expansion coefficient (TEC) tensor that is applicable to any crystal system, where the number of phonon calculations associated with different deformations scales linearly with the number of lattice parameters. Compared to simple high-symmetry systems such as cubic or hexagonal systems, a proper consideration of low-symmetry systems such as monoclinic or triclinic crystals demands a clear distinction between the TEC tensor and the lattice-parameter TECs along the crystallographic direction. The latter is more complicated and it involves integrating the equations of motion for the primitive lattice vectors, with input from the TEC tensor. A first-principles study of the TEC is carried out for the first time on a monoclinic crystal, where we unveil high TEC anisotropies in a recently reported monoclinic phase of niobium trisulfide (NbS3-IV) crystal with a relatively large primitive cell (32 atoms per cell) using density-functional theory. We find the occurrence of a negative TEC tensor component is largely due to the mechanical property rather than the anharmonic effect, contrary to common belief. Our theoretical treatment of the monoclinic system with a single off-diagonal tensor element could be routinely generalized to any crystal system, including the lowest-symmetry triclinic system with three off-diagonal tensor elements.

Atomistic simulation of diffusion of the self-interstitial atom in HCP Zr

The paper is devoted to atomistic simulation of the self-interstitial migration in HCP Zr. The simulation has been carried out on the basis of three different interatomic potentials taken from the literature. The location of self-interstitial atoms (SIA), that is defined as a crystal lattice site, whose corresponding Wigner–Seitz cell contains two atoms, was traced. Combined method based on molecular dynamics (MD) and kinetic Monte Carlo (KMC) method was proposed for an atomistic simulation of the SIA migration in HCP zirconium. Calculations of SIA diffusion coefficient were performed for temperatures range from 300 to 1000 K by two methods: ‘pure’ MD simulation and a proposed MD-KMC method. Both methods provided close results. At that, proposed combined MD-KMC method required significantly shorter computational time. All three potentials provided SIA with anisotropic diffusion. At a temperature of 800–1000 K, the estimates of the diffusion coefficient values obtained at different potentials were close. At temperatures below 800 K, significant qualitative and quantitative differences were observed between the results obtained at different potentials. For one of the used potentials, the anomalous dependence of the SIA diffusion coefficient in the basal plane on the temperature was observed.

The Study of Symmetry Energy in Pasta of Neutron Star From Compressible Liquid Drop Model Approximation

The properties of pasta which is located at the bottom of inner crust from neutron star has been studied by using compressibl e liquid drop model. Compressible liquid drop model is a modified liquid drop model as a density function. Liquid drop model based on assumption that the magnitude of nucleus bonding energy is contribution of surface, Coulomb, volume, symmetry, and proton -neutron pair effect. Pasta of neutron star behaves like liquid crystals (mesomhorpic phase). The top layer of pasta filled by free neutron gas, while in the lowest layer of the pasta is filled by proton-neutron gas. The properties of pasta are observed at temperatures close to zero Kelvin with the assumption that neutron star is on ground state and non accretion. The study of pasta emphasizes on symmetry energy’s influence. Symmetry energy reduces the magnitude of bonding energy of nucleon in the nucleus and it causes nucleon to be more easily released from nucleus. After that, symmetry energy influence the properties of pasta, such as the shape of nucleus that is non spherical (some like plates, rods, and bubbles), the fluctuative values of Wigner-Seitz cell, and uneven distribution of protons and neutrons in the pasta region of neutron star.

Structural, Magnetic, Magnetocaloric and Mössbauer Spectrometry Study of $${\hbox {Gd}}_2{\hbox {Fe}}_{17-x}{\hbox {Cu}}_x$$ Gd 2 Fe 17 - x Cu x ( $$x=$$ x = 0, 0.5, 1 and 1.5) Compounds

The structure, magnetic and magnetocaloric properties of arc-melted $${\hbox {Gd}}_2{\hbox {Fe}}_{17-x}{\hbox {Cu}}_x$$ ( $$x =$$ 0, 0.5, 1 and 1.5) solid solution have been studied. The Rietveld refinement shows that these compounds crystallize in the rhombohedral $${\hbox {Th}}_2{\hbox {Zn}}_{17}$$ -type structure with the $$R{\bar{3}}m$$ space group, and the substitution of iron by copper leads to a decrease in the unit cell volume. The Curie temperature ( $$T_{\mathrm{C}}$$ ) of the prepared samples depends on the copper content. The reduction of the ferromagnetic phase transition temperature from 475 K (for $$x = 0$$ ) to 460 K (for $$x = 1.5$$ ) is due to the substitution of the magnetic element (Fe) by non-magnetic atoms (Cu). The magnetocaloric effect was determined in the vicinity of the Curie temperature $$T_{\mathrm{C}}$$ . By increasing the Cu content, an increase in the values of magnetic entropy ( $$\Delta S_{\mathrm{M}}$$ ) in a low applied field is observed. The preferred inequivalent crystallographic site of Cu atoms was determined by Mossbauer spectrometry analysis based on the isomer shift parameter correlation with the Wigner–Seitz cell volumes.

Charge Melting of Liposome Colloidal Crystals

Recently we measured the charge dependence of electrostatic interparticle repulsions in liposome colloidal crystals (Cohen, Wei & Ou-Yang, ms. in preparation). The liposomes were made from binary mixtures of charged and neutral phospholipids at various ratios. The shear modulus (rigidity) of each liposome suspension in deionized water was measured by laser-tweezer methods. As a function of increasing liposome charge, suspension rigidity first increased, peaked at ∼20% charged-lipid content, then decreased, becoming watery near 100% charged lipids. By analogy to colloidal-crystal “shear melting,” we call this phenomenon “charge melting.” The effect was calculated quantitatively by use of the Wigner-Seitz (WS) model, which requires solving the electrostatics problem of a radially symmetric charged sphere and its counterions in an electroneutral spherical WS shell whose radius R is determined by the liposome concentration. Electroneutrality means the entire H+ screening cloud surrounding each liposome is compressed into its WS cell. The compression creates an osmotic pressure related to the electrostatic potential ψ(R) at the WS-cell surface. The osmotic pressure is a measure of the interparticle interaction strength, which is what stiffens the sample. “Melting” as a function of particle charge Z arises because electroneutrality requires (a) as Z increases, so does the number of counterions, which increases osmotic pressure and ψ(R). This effect is linear in Z. (b) More counterions also cause more screening of Z, which decreases ψ(R) and osmotic pressure. This effect is exponential in Z, so it ultimately dominates. We solve the WS electrostatics problem analytically in the Debye-Hückel approximation and numerically with the full Poisson-Boltzmann equation. The problem must be solved self-consistently for a closed system with no reservoir, a counterion-only electrolyte, surface H+ binding with charge regulation, and zero electric fields at the WS-cell surface and liposome center.

The AFLOW Library of Crystallographic Prototypes: Part 2

Materials discovery via high-throughput methods relies on the availability of structural prototypes, which are generally decorated with varying combinations of elements to produce potential new materials. To facilitate the automatic generation of these materials, we developed The AFLOW Library of Crystallographic Prototypes — a collection of crystal prototypes that can be rapidly decorated using the AFLOW software. Part 2 of this work introduces an additional 302 crystal structure prototypes, including at least one from each of the 138 space groups not included in Part 1. Combined with Part 1, the entire library consists of 590 unique crystallographic prototypes covering all 230 space groups. We also present discussions of enantiomorphic space groups, Wigner-Seitz cells, the two-dimensional plane groups, and the various different space group notations used throughout crystallography. All structures — from both Part 1 and Part 2 — are listed in the web version of the library available at http://www.aflow.org/CrystalDatabase.

Nuclear Statistical Equilibrium equation of state for core collapse

Extensive calculations of properties of supernova matter are presented, using the extended Nuclear Statistical Equilibrium model of Ref. [1] based on a statistical distribution of Wigner–Seitz cells modeled using realistic nuclear mass and level density tables, complemented with a non-relativistic Skyrme functional for unbound particles and beyond drip-line nuclei. Both thermodynamic quantities and matter composition are examined as a function of baryonic density, temperature, and proton fraction, within a large domain adapted for applications in supernova simulations. The results are also provided in the form of a table, with grid mesh and format compatible with the CompOSE platform [2] for direct use in supernova simulations. Detailed comparisons are also presented with other existing databases, all based on relativistic mean-field functionals, and the differences between the different models are outlined. We show that the strongest impact on the predictions is due to the different hypotheses used to define the cluster functional and its modifications due to the presence of a nuclear medium.

Transcriptional Responses to ppGpp and DksA.

The stringent response to nutrient deprivation is a stress response found throughout the bacterial domain of life. Although first described in proteobacteria for matching ribosome synthesis to the cell's translation status and for preventing formation of defective ribosomal particles, the response is actually much broader, regulating many hundreds of genes-some positively, some negatively. Utilization of the signaling molecules ppGpp and pppGpp for this purpose is ubiquitous in bacterial evolution, although the mechanisms employed vary. In proteobacteria, the signaling molecules typically bind to two sites on RNA polymerase, one at the interface of the β' and ω subunits and one at the interface of the β' secondary channel and the transcription factor DksA. The β' secondary channel is targeted by other transcription regulators as well. Although studies on the transcriptional outputs of the stringent response date back at least 50 years, the mechanisms responsible are only now coming into focus.

B-Splines and NURBS Based Finite Element Methods for Strained Electronic Structure Calculations

This paper presents B-splines and nonuniform rational B-splines (NURBS)-based finite element method for self-consistent solution of the Schrödinger wave equation (SWE). The new equilibrium position of the atoms is determined as a function of evolving stretching of the underlying primitive lattice vectors and it gets reflected via the evolving effective potential that is employed in the SWE. The nonlinear SWE is solved in a self-consistent fashion (SCF) wherein a Poisson problem that models the Hartree and local potentials is solved as a function of the electron charge density. The complex-valued generalized eigenvalue problem arising from SWE yields evolving band gaps that result in changing electronic properties of the semiconductor materials. The method is applied to indium, silicon, and germanium that are commonly used semiconductor materials. It is then applied to the material system comprised of silicon layer on silicon–germanium buffer to show the range of application of the method.

Distribution of nuclei in equilibrium stellar matter from the free-energy density in a Wigner-Seitz cell

The aim of the present study is to calculate the nuclear distribution associated at finite temperature to any given equation of state of stellar matter based on the Wigner-Seitz approximation, for direct applications in core-collapse simulations. The Gibbs free energy of the different configurations is explicitly calculated, with special care devoted to the calculation of rearrangement terms, ensuring thermodynamic consistency. The formalism is illustrated with two different applications. First, we work out the nuclear statistical equilibrium cluster distribution for the Lattimer and Swesty equation of state, widely employed in supernova simulations. Secondly, we explore the effect of including shell structure, and consider realistic nuclear mass tables from the Brussels-Montreal Hartree-Fock-Bogoliubov model (specifically, HFB-24). We show that the whole collapse trajectory is dominated by magic nuclei, with extremely spread and even bimodal distributions of the cluster probability around magic numbers, demonstrating the importance of cluster distributions with realistic mass models in core-collapse simulations. Simple analytical expressions are given, allowing further applications of the method to any relativistic or nonrelativistic subsaturation equation of state.

Influence of strong magnetic fields on inner crust of neutron star

It is generally believed that a neutron star mainly consists of four parts,that is to say, outer crust, inner crust, outer core, and inner core.From neutron drip density to crust-core transition density,the inner crust of neutron star is a nonuniform system wherenuclei coexist with nucleon and electron gases surrounding them.As density increases, the nuclear pasta phases with different shapes,such as droplet, rod, slab, tube, and bubble may appear in the inner crust.Astronomical observations indicate that strong magnetic fields, which may be as high as 10$^{18}$ G, may exist in some neutron stars.So, the crust structure of neutron star may be influenced significantly by the strong magnetic fields.Consequently, a number of astrophysical observations, such as the neutron star oscillations and glitches in the spin rate of pulsars may be affected by the properties of inner crust.In this paper, we adopt the relativistic mean-field theory to describe the nuclear interaction, andanomalous magnetic moments of proton and neutron are considered as well.In order to study the effects of strong magnetic fields onthe properties of nonuniform nuclear matter in inner crust and crust-core transition of neutron stars,we adopt the Wigner-Seitz approximation to describe the nonuniform matter in inner crust,where only one nucleus exists in a Wigner-Seitz cell.Meanwhile, the charge neutrality and $\beta$ equilibrium conditions are satisfied.We adopt the self-consistent Thomas-Fermi approximation toobtain the distributions of nucleons and electrons in a Wigner-Seitz cellunder strong magnetic fields, and then we calculate the binding energy per nucleon and the properties of Wigner-Seitz cell.It turns out that the properties of inner crust structure and the crust-core transition wouldnot change much with strong magnetic fields $B~\le~10^{17}$ G comparing with $B=0$.The nucleon distribution, binding energy per nucleon,radius of Wigner-Seitz cell, onset density of various nonspherical pasta phases,and crust-core density with $B=10^{17}$ G are very similar to the corresponding results with $B=0$.However, the strong magnetic fields $B\geq10^{18}$ G play an important role in determiningthe pasta phase structure.As a result, the radius of spherical Wigner-Seitz cell, the binding energy per nucleon of various kinds of pasta phases, and the onset densities of nonspherical nuclei and crust-core transition decrease with increasing $B$, while the area of high density in Wigner-Seitz cell increases.For fixed strength of magnetic fields, as the average baryon density in Wigner-Seitz cell increases,the radius of Wigner-Seitz cell decreases, but the area of high density in the center of the cell increases.The nucleon density at the boundary of Wigner-Seitz cell increases with increasing average baryon density for fixed strength magnetic fields, while the nucleon density at the center area of the cell decreases, which leads to the nucleon distribution in the cell becomes more dispersive.

Nuclear structure calculations for neutron star crusts

The goal of this paper is to investigate properties of clusterized nuclear matter which is believed to be present in crusts of neutron stars at subnuclear densities. It is assumed that the whole system can be represented by the set of Wigner-Seitz cells, each containing a nucleus and an electron background under the condition of electroneutrality. The nuclear structure calculations are performed within the relativistic mean-field model with the NL3 parametrization. The first set of calculations is performed assuming the constant electron background. The evolution of neutron and proton density distributions was systematically studied along isotopic chains until very neutron-rich system beyond the neutron dripline. Then we have replaced the uniform electron background with the realistic electron distributions, obtained within the Thomas-Fermi approximation in a self-consistent way with the proton distributions. Finally, we have investigated the evolution of the $\beta$-stability valley as well as neutron and proton driplines with the electron density.

Macroions non-linear screening in complex plasma

The base for consideration is the well-known phase diagram of dusty plasma for an equilibrium charged system with the Yukawa potential in Γ−κ plane, where Γ is a Coulomb non-ideality parameter, κ is a screening parameter, from [Hamaguchi S et al 1997 Phys. Rev. E 92 4671]. Two-component highly asymmetric electroneutral systems of classical macroions with the charge Z and point-like opposite charged microions are considered in the case of big non-uniformity around macroions. Linear screening approximation is not valid for a considerable part of characteristic parameters of substantial dusty plasma. The Poisson–Boltzmann equation is solved numerically in electroneutral Wigner–Seitz cell to consider non-linear screening of a macroion by microions. Distributions of microions and non-linear potentials are calculated. This allows to make charge renormalization and to consider not a real charge Z but an effective one Z*. Also, it is shown that the initial phase changes as non-linear screening is taken into account.

Non‐linear screening and phase states of a complex plasma

The applicability limit of the well‐known phase diagram of complex plasmas in the κ–Γ plane (κ is the structural parameter, Γ is the coupling parameter) is under discussion. The present work is devoted to the analysis of the range of applicability of a basic assumption in the initial phase diagram, that is, linearized (Debye) screening of macro‐ions by micro‐ions, which leads to the Yukawa form of effective interactions between macro‐ions. Parameters of non‐linear screening for macro‐ions were calculated within the direct Poisson–Boltzmann approximation in an averaged Wigner–Seitz cell. Two effects were revealed as a result of such calculations: (a) decomposition of all micro‐ions into two subclasses, free and bound ones, and (b) significant reduction of the effective charge Z* of initial bare macro‐ion Z under non‐linear screening by the small high‐density envelope of bound micro‐ions. This effect leads to a re‐normalization of initial Γ and κ into Γ* and κ* (Γ* < Γ, κ* < κ). It is assumed that the phase states of a complex plasma under non‐linear screening are still the same as in the initial phase diagram, but in κ*–Γ* plane instead of the κ–Γ one. The corresponding calculated shifts of the phase states are discussed and illustrated.

Temperature dependence of migration features of self-interstitials in zirconium**Project supported by the National Natural Science Foundation of China (Grant No. 91126001) and the National Magnetic Confinement Fusion Program of China (Grant No. 2013GB109002).

Molecular dynamics simulations are conducted to study self-interstitial migration in zirconium. By defining crystal lattice points where more than one atom is present in corresponding Wigner–Seitz cells, as the locations of self-interstitial atoms (LSIAs), three types of events are identified as LSIA migrations: the jump remaining in one direction (ILJ), the jump from one to another direction in the same basal plane (OLJ), and the jump from one basal plane to an adjacent basal plane (OPJ). The occurrence frequencies of the three types are calculated. ILJ is found to be a dominant event in a temperature range from 300 K to 1200 K, but the occurrence frequencies of OLJ and OPJ increase with temperature increasing. The total occurrence frequency of all jump types has a good linear dependence on temperature. Moreover, the migration trajectories of LSIAs in the hcp basal-plane is not what is observed if only conventional one- or two-dimensional migrations exists; rather, they exhibit the feature that we call fraction-dimensional. Using Monte Carlo simulations, the potential kinetic effects of fraction-dimensional migration, which is measured by the average number of lattice sites visited per jump event (denoted by nSPE), are analysed. The significant differences between the nSPE value of the fraction-dimensional migration and those of conventional one- and two-dimensional migrations suggest that the conventional diffusion coefficient cannot give an accurate description of the underlying kinetics of SIAs in Zr. This conclusion could be generally meaningful for the cases where the low-dimensional migration of defects are observed.

Dependence of the binding energy of the metal crystal lattice on the average number of conduction electrons

We establish the dependence of the electron binding energy in a separate isolated Wigner–Seitz cell of the metal crystal lattice on the average number of electrons located in this cell. The calculation is made using the modified Hellmann–Feynman theorem, which allows relating the eigenvalue of the steady-state Hamiltonian to the variation in its parameters that do not affect the degree of freedom of a system. As one of these parameters, we choose the average number of electrons in the cell. According to the calculated data, removal of 10–30% of electrons in monovalent metals leads to the crystal lattice fracture. The results obtained using the Hellmann–Feynman theorem are directly compared with the data of the jellium model.

Anderson-Bogoliubov phonons in the inner crust of neutron stars: Dipole excitation in a spherical Wigner-Seitz cell

Background: The Anderson-Bogoliubov (AB) phonon, called also the superfluid phonon, has attracted attentions since it may influence the thermal conductivity and other properties of inner crust of neutron stars. However, there are limited number of microscopic studies of the AB phonon where the presence of clusters is explicitly taken into account.\\ Purpose: We intend to clarify how the presence of clusters affects the AB phonon in order to obtain microscopic information relevant to the coupling between the AB phonon and the lattice phonon. \\ Methods: The Hartree-Fock-Bogoliubov model and the quasiparticle random-phase approximation formulated in a spherical Wigner-Seitz cell are adopted to describe neutron superfluidity and associated collective excitations. We perform systematic numerical calculations for dipole excitation by varying the neutron chemical potential and the number of protons in a cell. \\ Results:The model predicts systematic emergence of the dipole AB phonon mode, which however exhibits strong suppression of phonon amplitude inside the cluster. We find also that the phonon amplitude around the cluster surface varies as the neutron density. At higher neutron densities the AB phonon mode exhibits behaviour similar to the pygmy dipole resonance in neutron-rich nuclei.\\ Conclusions: The dipole AB phonon mode does not penetrate into the clusters. This suggests that the coupling between the AB phonon and the lattice phonon may be weak.

A fast hybrid methodology based on machine learning, quantum methods, and experimental measurements for evaluating material properties

We present a hybrid approach based on both machine learning and targeted ab-initio calculations to determine adhesion energies between dissimilar materials. The goals of this approach are to complement experimental and/or all ab-initio computational efforts, to identify promising materials rapidly and identify in a quantitative manner the relative contributions of the different material attributes affecting adhesion. Applications of the methodology to predict bulk modulus, yield strength, adhesion and wetting properties of copper (Cu) with other materials including metals, nitrides and oxides is discussed in this paper. In the machine learning component of this methodology, the parameters that were chosen can be roughly divided into four types: atomic and crystalline parameters (which are related to specific elements such as electronegativities, electron densities in Wigner-Seitz cells); bulk material properties (e.g. melting point), mechanical properties (e.g. modulus) and those representing atomic characteristics in ab-initio formalisms (e.g. pseudopotentials). The atomic parameters are defined over one dataset to determine property correlation with published experimental data. We then develop a semi-empirical model across multiple datasets to predict adhesion in material interfaces outside the original datasets. Since adhesion is between two materials, we appropriately use parameters which indicate differences between the elements that comprise the materials. These semi-empirical predictions agree reasonably with the trend in chemical work of adhesion predicted using ab-initio techniques and are used for fast materials screening. For the screened candidates, the ab-initio modeling component provides fundamental understanding of the chemical interactions at the interface, and explains the wetting thermodynamics of thin Cu layers on various substrates. Comparison against ultra-high vacuum (UHV) experiments for well-characterized Cu/Ta and Cu/α-Al2O3 interfaces is also discussed. The new hybrid methodology can be applied to effectively and rapidly screen material options for further investigation, and provide a tractable list for experiments to accelerate optimization and integration of new materials in microelectronics. Our unique hybrid methodology lays a framework for using a combination of experimental and computational simulations to estimate properties for faster screening of materials.