Different Types Of Atoms Research Articles

Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis.

Due to the genetic similarity between SARS-CoV-2 and SARS-CoV, the present work endeavored to derive a balanced Quantitative Structure−Activity Relationship (QSAR) model, molecular docking, and molecular dynamics (MD) simulation studies to identify novel molecules having inhibitory potential against the main protease (Mpro) of SARS-CoV-2. The QSAR analysis developed on multivariate GA–MLR (Genetic Algorithm–Multilinear Regression) model with acceptable statistical performance (R2 = 0.898, Q2loo = 0.859, etc.). QSAR analysis attributed the good correlation with different types of atoms like non-ring Carbons and Nitrogens, amide Nitrogen, sp2-hybridized Carbons, etc. Thus, the QSAR model has a good balance of qualitative and quantitative requirements (balanced QSAR model) and satisfies the Organisation for Economic Co-operation and Development (OECD) guidelines. After that, a QSAR-based virtual screening of 26,467 food compounds and 360 heterocyclic variants of molecule 1 (benzotriazole–indole hybrid molecule) helped to identify promising hits. Furthermore, the molecular docking and molecular dynamics (MD) simulations of Mpro with molecule 1 recognized the structural motifs with significant stability. Molecular docking and QSAR provided consensus and complementary results. The validated analyses are capable of optimizing a drug/lead candidate for better inhibitory activity against the main protease of SARS-CoV-2.

Relation of the Probability of Recoil Atom Ionization to Experimental Data on Ionization by Photons and Electrons

The process of atomic nucleus recoil under the elastic scattering of a neutral particle, a hypothetical dark matter particle (WIMP) in particular, is considered. In the case of a low-energy recoil of the nucleus, the relations between the probability of ionization of the recoil atom and the cross section of ionization of such an atom by a photon, as well as by an electron, are obtained. These expressions contain only one parameter, the values of which are calculated for different types of atoms, taking into account experimental data on ionization by photons and electrons. The probabilities of ionization of noble-gas recoil atoms are compared with the results of other theoretical studies, and it is emphasized that the proposed calculating model is quite reliable and its accuracy is determined by the error of the experimental cross sections that are used.

Study on the competitive growth mechanism of SiC polytypes using Kinetic Monte Carlo method

The competitive growth process of the 4H and 6H polytypes of SiC is studied by a competitive Kinetic Monte Carlo model(KMC), which takes the atoms of silicon and carbon as the elementary kinetic particle to fully account for the interaction energy between atoms. In the competitive KMC model, the crystal lattices of two polytypes are represented by a structured mesh which fixed the site positions at the perfect crystal lattice positions. Kinetic events with competitive growth, such as deposition, diffusion are considered in physical criterion in the model. Moreover, the model not only considers the interaction energy between the same kind of atoms (Si-Si), but also considers the interaction energy between different types of atoms (Si-C). Based on the KMC model, the effects of growth conditions on the competitive growth of 4H- and 6H- SiC were studied. The competitive KMC simulation results show that the higher temperature and the larger proportion of Si source in the mixture will promote the preferential growth of 6H polytype during competitive growth. Meanwhile, with the increase of temperature and Si/C ratio, the phenomenon of atom aggregation growth on crystal surface becomes more and more obvious.

Adsorption enhancement of a fatty acid on iron surface with Σ3(1 1 1) grain boundary

Nanocrystallization processes applied to metallic surfaces can enhance their tribological properties under boundary lubrication. To reveal the mechanism, the adsorbability of acetic acid as a fatty lubricant molecule on a nanostructured iron surface was investigated using first-principles calculations. The nanostructured surface was modeled as a surface slab including a grain boundary (GB) per unit cell. Comparing the adsorbability of the Fe (110) surface with symmetrical tilt Σ3 (111) grain boundaries to that of an Fe (110) surface without GBs, we found that the molecule tends to be adsorbed more strongly (0.76 eV in average) on sites close to the grain boundary than on the clean surface. A local energy analysis revealed that the adsorption was enhanced even at a relatively distant position (approximately 5 Å from the adsorbed molecule) and that the energy contributions of atoms of different types were qualitatively different for the adsorption on the surface with GBs.

Prediction of protein-carbohydrate complex binding affinity using structural features.

Protein-carbohydrate interactions play a major role in several cellular and biological processes. Elucidating the factors influencing the binding affinity of protein-carbohydrate complexes and predicting their free energy of binding provide deep insights for understanding the recognition mechanism. In this work, we have collected the experimental binding affinity data for a set of 389 protein-carbohydrate complexes and derived several structure-based features such as contact potentials, interaction energy, number of binding residues and contacts between different types of atoms. Our analysis on the relationship between binding affinity and structural features revealed that the important factors depend on the type of the complex based on number of carbohydrate and protein chains. Specifically, binding site residues, accessible surface area, interactions between various atoms and energy contributions are important to understand the binding affinity. Further, we have developed multiple regression equations for predicting the binding affinity of protein-carbohydrate complexes belonging to six categories of protein-carbohydrate complexes. Our method showed an average correlation and mean absolute error of 0.731 and 1.149kcal/mol, respectively, between experimental and predicted binding affinities on a jackknife test. We have developed a web server PCA-Pred, Protein-Carbohydrate Affinity Predictor, for predicting the binding affinity of protein-carbohydrate complexes. The web server is freely accessible at https://web.iitm.ac.in/bioinfo2/pcapred/. The web server is implemented using HTML and Python and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera.

Aerosol droplet-size distribution and airborne nicotine portioning in particle and gas phases emitted by electronic cigarettes

The reliable characterization of particle size distribution and nicotine delivery emitted by electronic cigarettes (ECs) is a critical issue in their design. Indeed, a better understanding of how nicotine is delivered as an aerosol with an appropriate aerodynamic size is a necessary step toward obtaining a well-designed nicotine transfer from the respiratory tract to the bloodstream to better satisfy craving and improve smoking cessation rates. To study these two factors, recent models of EC devices and a dedicated vaping machine were used to generate aerosols under various experimental conditions, including varying the EC power level using two different types of atomizers. The aerodynamic particle sizing of the resulting aerosol was performed using a cascade impactor. The nicotine concentration in the refill liquid and the aerosol droplet was quantified by liquid chromatography coupled with a photodiode array. The vaporization process and the physical and chemical properties of the EC aerosol were very similar at 15 watts (W) and 25 W using the low-power atomizer but quite distinct at 50 W using the high-power atomizer, as follows: (1) the mass median aerodynamic diameters ranged from 1.06 to 1.19 µm (µm) for low power and from 2.33 to 2.46 µm for high power; (2) the nicotine concentrations of aerosol droplets were approximately 11 mg per milliliter (mg/mL) for low power and 17 mg/mL for high power; and (3) the aerosol droplet particle phase of the total nicotine mass emitted by EC was 60% for low power and 95% for high power. The results indicate that varying the correlated factors (1) the power level and (2) the design of atomizer (including the type of coil and the value of resistance used) affects the particle-size distribution and the airborne nicotine portioning between the particle phase and the gas phase in equilibrium with the airborne droplets.

Influence of composition nonstoichiometry and ordering effects on the properties of ferroelectric ceramics based on lead magnoniobate

The effects of violation of the stoichiometry of lead magnoniobate in the preparation of compositions (1-x)PbMg1/3Nb2/3O3 – xPbMg1/2Nb1/2O2,75 with a step of 0.1 and 0≤x≤1 have been studied by X-ray diffraction methods. Differences in the unit cell parameters of the ferroelectric ceramic samples of the composition under study were found. It was shown that the effect of ordering of different types of atoms in the cells, leading to the formation of a superstructure and a doubling of the lattice period, was not observed in any of the samples. . Measurements of the dielectric constant of the synthesized samples and the tangent of the dielectric loss angle showed a violation of the Curie-Weiss law, which indicates the diffusion of the phase transition.

KI’nın Tavuk ve Kemirgen Epidermal Dokusunun Bilgisayarlı Tomografi Uygulamalarında Kontrast Ajanı Olarak Optimize Edilmesi

X-ray computed tomography (CT) vastly used in many different applications in different fields such as materials science, medical science, entomology, anatomy, marine sciences. Since the X-ray is highly penetrable, 3D image of almost any material can be achieved by CT. The high quality image of the materials, which compose in different types of atoms, can easily be achieved. However, obtain the high quality images of the materials which has similar types of atoms or relatively soft structure becomes a problem. Scientists investigating the soft tissues such as flesh, muscle, cartilage or animals in soft structure suffer from this problem. At this point, staining procedures, treating materials with contrast agents help the researcher to enhance the image quality. In this work, optimisation of KI based staining to obtain enhanced image quality in CT imaging of murine and chicken dermal tissues were studied. Results indicate that overstaining or staining the tissues in less concentration significantly affects the quality of the obtained CT images.

Structural and mechanical properties of Sb and SbX (X=H, F, Cl and Br) monolayers

The influences of four different types of atoms (H, F, Cl and Br) on the elastic and plastic properties of antimonene nanosheet are investigated in this paper using the density functional theory. For this purpose, the SIESTA software is used. It is concluded that Young's modulus of the antimonene nanosheet under the uniaxial strain and bulk modulus under the biaxial strain significantly decreases by the adsorption. Moreover, it is shown that due to the negligible difference in the Young's moduli of these structures they have isotropic behavior. Furthermore, the influence of the adsorption on the plastic properties of the antimonene nanosheet is studied by extending the loading until the indication of the plastic behavior. It is shown that the yield strain of the antimonene nanosheet under the uniaxial strain decreases by the adsorption. However, interestingly, it is observed that the adsorption of named atoms increase the plastic strain under the biaxial loading.

Molecular Dynamics Simulation of Structural and Transport Properties of Solid Solutions of Double Perovskites Based on PrBaCo2O5.5

The oxygen diffusion has been simulated by the molecular dynamics method in the solid solutions of PrBaCo2O5.5-based double perovskites: PrBa0.5Sr0.5Co2O5.5 with random substitution of half of Ba atoms by Sr atoms, PrBa0.5Sr0.5CoFeO5.5 with random substitution Ba → Sr and Co → Fe, PrBa0.5Sr0.5CoCuO5.5 with random substitution Ba → Sr and Co → Cu, and PrBa0.5Sr0.5CuFeO5.5 with random substitution Ba → Sr and random substitution of Co atoms by Fe and Cu atoms. It is shown that, varying the oxygen nonstoichiometry and/or chemical composition of solid solutions based on PrBa0.5Sr0.5Co2O5.5, one can significantly change the coefficient of thermal expansion of the materials. It is established for the first time that the maximum difference between the mobilities of oxygen atoms of different types observed in PrBa0.5Sr0.5Co2O5.5 significantly decreases at partial substitutions of cobalt by iron and copper. In the PrBa0.5Sr0.5CuFeO5.5 solid solution, the oxygen atom mobility in the (Cu,Fe)–O layers becomes somewhat higher than that in the Pr–O layers.

Adsorption characteristics composition of Ge and Si on 4H-SiC(0 0 0 1) surface

• For two different types of atoms, the most stable adsorption site is top site. • Compared with the adsorption of Si, Ge are more active on the adsorption surface. • Si Ge and Si Si bonds are formed between the adsorbed atom and the surface. • DOS indicates the presence of strong interactions of adsorbed atom and surface atoms. Silicon (Si) and germanium (Ge) are two important materials for hetero-epitaxy of 4H-silicon carbide (4H-SiC), so the First-principles calculation is employed to compare the difference of the adsorptions of Ge and Si atoms on the surface of 4H-SiC(0 0 0 1) by calculating the adsorption energy, geometric optimization, charge populations and density of state. For the two different types, four common adsorption models (top, hcp, fcc, bridge) are studied. The calculation results of adsorption energy show that, for two different types of atoms, compared with other sites, the most stable adsorption site is top site. At the same time, another important feature is that Si atom is more stable on Si surface, while Ge atom is easier to diffuse on Si surface. The results of the diffusion barrier indicates that, compared with the adsorption of Si atoms, Ge atoms are more active on the adsorption surface, which is consistent with the adsorption energy. Charge populations results shows that there is obvious charge transfer between the adsorbed atom and the surface atom, which implies that Si-Ge bonds and Si-Si bonds are formed between the adsorbed atom and the surface atom. The behaviors of the DOS of Si are qualitatively similar to that of Ge adsorption. It can be seen from the dos results that there are great resonance peaks, which indicates the presence of strong interactions of adsorbed atom and surface atoms, but extent of depreciation is different.

Ab initio molecular dynamics study of TiZrNbHfTa and VZrMoHfW liquid alloys

The structural and dynamical properties of liquid alloys are directly related to their solidification process, and consequently to the properties of as-cast solid alloys. Ab initio molecular dynamics is a powerful tool that can be used to study both of these factors. Thus, in this work, TiZrNbHfTa and VZrMoHfW liquid equiatomic alloys, exclusively consisting of transition metal (TM) elements, are studied using ab initio molecular dynamics via the CP2K software package; partial-pair correlation functions (PPCFs) are calculated, and their parameters are discussed. The calculated densities of these alloys are shown to be close to the ideal mixture densities. The analysis of the PPCFs is performed to predict the single-phase high-entropy alloy (HEA) formation. The obtained results agree with the semi-empirical phase formation rules. The diffusivities of the elements are calculated using the Green–Kubo relation and the mean square displacement (MSD) plot. The diffusivity is shown to decrease as the atomic mass and radius increase. The scattering process of different types of atoms in TiZrNbHfTa and VZrMoHfW are also discussed.

Anisotropic Fracture Dynamics Due to Local Lattice Distortions.

A brittle material under loading fails by the nucleation and propagation of a sharp crack. In monatomic crystals, such as silicon, the lattice geometries front to the crack-tip changes the way of propagation even with the same cleavage surface. In general, however, crystals have multiple kinds of atoms and how the deformation of each atom affects the failure is still elusive. Here, we show that local atomic distortions from the different types of atoms causes a propagation anisotropy in suspended WS2 monolayers by combining annular dark-field scanning transmission electron microscopy and empirical molecular dynamics that are validated by first-principles calculations. Conventional conditions for brittle failure such as surface energy, elasticity, and crack geometry cannot account for this anisotropy. Further simulations predict the enhancement of the strengths and fracture toughness of the materials by designing void shapes and edge structures.

Size effect on magnetic properties of Zn0.95−xMgxNi0.05O nanoparticles by Monte Carlo simulation

Diluted magnetic semiconductors (DMSs) have been providing a wide research area with various conflicting results of magnetic properties which are generally originated from structural characteristics due to fabrication process. We focused on the size dependent magnetic behavior of Zn0.95−xMgxNi0.05O nanoparticles as a promising novae material introducing room temperature ferromagnetism (FM) at low doping concentrations of Mg+2 and Ni+2 ions. Markov Chain Monte Carlo method based on Metropolis algorithm is used to simulate the system, constructed on experimental parameters such as particle size (D), lattice constants (a and c), uniaxial anisotropy constant (K), applied field (H) herewith doping concentrations of Ni (5%) and Mg (1%). However, we described the system with the Heisenberg Hamiltonian to represent the exotic nature of the DMS type materials since determining the Jij constants by tracing the type of the exchange relation between different types of atoms as reported in former studies. In the light of hysteresis measurements, nanoparticles generated between 5 < D < 15 nm showed strong FM among others. An exciting result is that D = 5 nm, 10 nm and 15 nm curves are so close to be overlapped. Saturation magnetization (Ms) and coercive field (Hc) had peaks of; D = 15 nm remnant magnetization (Mr) increased with increasing D up to 50 nm. Furthermore, D < 5 nm and D> 15 nm sized particles started to lose FM behavior. In addition, magnetic features of Zn0.95−xMgxNi0.05O nanoparticles can be controlled via picking a fabrication method to tune the particle size.

Intrinsic ratchets: A Hamiltonian approach

An asymmetric Brownian particle subjected to an external time-dependent force may acquire a net drift velocity, and thus operate as a motor or ratchet, even if the external force is represented by an unbiased time-periodic function or by a zero-centered noise. For an adequate description of such ratchets, a conventional Langevin equation linear in the particle's velocity is insufficient, and one needs to take into account the first nonlinear correction to the dissipation force which emerges beyond the weak coupling limit. We derived microscopically the relevant nonlinear Langevin equation by extending the standard projection operation technique beyond the weak coupling limit. The particle is modeled as a rigid cluster of atoms and its asymmetry may be geometrical, compositional (when a cluster is composed of atoms of different types), or due to a combination of both factors. The drift velocity is quadratic in the external force's amplitude and increases with decreasing the force's frequency (for a periodic force) and inverse correlation time (for a fluctuating force). The maximum value of the drift velocity is independent on the particle's mass and achieved in the adiabatic limit, i.e. for an infinitely slow change of the external field.

Elastic constants and homogenized moduli of manganese carbonate structure based on molecular dynamics and Reuss-Voigt-Hill methods

With the development of computer technology, the crystal structure of atomic-scale dynamics simulation is a hot research in recent years. The manganese carbonate crystal structure is chosen as the research object, as the elasticity of manganese carbonate crystal structure has been studied based on the plane wave ultra-soft first-principles density functional theory framework pseudopotential method. Based on molecular dynamics, interatomic potential function was introduced to describe the interactions between atoms of manganese carbonate crystals and then elasticity contants of manganese carbonate crystals, bulk modulus, shear modulus, Young’s modulus were simulated. Influencing of the pressure on elastic properties has been studied, the results indicate that: 1) the structure of manganese carbonate crystal shows anisotropy due to the different types of atoms of Coulomb force and van der Waals forces; 2) elastic moduli are also obtained, of which the bulk modulus B is 107.682GPa, shear modulus G is 52.09GPa; 3) the values are very consistent to the results of Chen (B 108GPa and G 49.8GPa), thus the established model and the selected potential functions are verified to be reliable.

Nanometer-scale gradient atomic packing structure surrounding soft spots in metallic glasses

The hidden order of atomic packing in amorphous structures and how this may provide the origin of plastic events have long been a goal in the understanding of plastic deformation in metallic glasses. To pursue this issue, we employ here molecular dynamic simulations to create three-dimensional models for a few metallic glasses where, based on the geometrical frustration of the coordination polyhedra, we classify the atoms in the amorphous structure into six distinct species, where “gradient atomic packing structure” exists. The local structure in the amorphous state can display a gradual transition from loose stacking to dense stacking of atoms, followed by a gradient evolution of atomic performance. As such, the amorphous alloy specifically comprises three discernible regions: solid-like, transition, and liquid-like regions, each one possessing different types of atoms. We also demonstrate that the liquid-like atoms correlate most strongly with fertile sites for shear transformation, the transition atoms take second place, whereas the solid-like atoms contribute the least because of their lowest correlation level with the liquid-like atoms. Unlike the “geometrically unfavored motifs” model which fails to consider the role of medium-range order, our model gives a definite structure for the so-called “soft spots”, that is, a combination of liquid-like atoms and their neighbors, in favor of quantifying and comparing their number between different metallic glasses, which can provide a rational explanation for the unique mechanical behavior of metallic glasses.

Sensors break out of the lab

Sensors break out of the lab

Chemistry Modelling Skills: Students’ Understanding on Transferring Simple Molecule to Model Drawing

The purpose of this paper is to investigate students’ understanding on the third hierarchy of the chemistry modelling skills; transferring simple molecule to model drawing. A total of 112 form four Malaysian school students were participated in this study. The Chemistry Modelling Skills Test (CMST) was used as an instrument for data collection. The collected data was analyzed qualitatively. The findings showed that, the majority of the students exhibited a non-scientific understanding and a significant number exhibited a scientific understanding regarding the transfer of a simple molecule to model drawing. Only a minority of the students exhibited no understanding. This study also had identified six learning difficulties faced by students which were first, determining the angle between the atoms. Second, distinguish different types of atoms. Third, indicate the bond that exists between the atoms. Fourth, determine the number of atoms in subscripts. Fifth, differentiate between atoms and ions. Sixth, understanding the bonding rules in chemical bond. Based on the students’ difficulties, the used of learning approach that emphasized on visualization of structure of molecules are suggested.

Fault Detection of a Wheelset Bearing Based on Appropriately Sparse Impulse Extraction

Convolution sparse representation (CSR) is a novel compressive sensing technique proposed in 2016 and provides an excellent framework for extracting the impulses induced by bearing faults and the unevenness of wheel tread. However, its sparsity performance on extracting impulses is sensitive to the improper penalty parameter. So, a novel fault detection method, appropriately sparse impulse extraction, is proposed based on the combination of CSR, estimating the number of atom types (ENA), and crest factor. The type of atoms embedded in vibration signals is estimated by ENA. Aiming at the different types of atoms, the impulses with different sparse characteristic are spanned by CSR with different penalty parameters. The appropriately sparse impulses are selected for fault detection based on the maximal crest factor. The simulation validation, experiment verification, and practical application are conducted to validate the effectiveness of the proposed appropriately sparse impulses extraction. These results show that the proposed appropriately sparse impulse extraction not only can obtain fault-characteristic frequency and its harmonics for fault judgment but also describes the dynamic behaviour between elementary defects and their matching surfaces. In addition, the proposed appropriately sparse impulse extraction can isolate the impulses with different types of atoms and is very suitable for detecting the wheelset bearing faults.