Analysis Of Atomic Structure Research Articles

Dataset for carbon dioxide adsorption on lizardite

This paper presents data on the adsorption of CO2 on the (001) and (00 ) surface lizardite. The data were obtained from calculations using the density functional theory (DFT) method implemented in the CASTEP software package. The calculations were performed using the plane wave basis set and the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional. A semi-empirical Grimme D2 correction was used to correctly account for dispersion interactions, which play an important role in physical adsorption processes. The data include optimized geometry and electronic properties of equilibrium states of adsorbed CO2 on (001) and (00 ) lizardite surfaces. They contain the most energetically favorable adsorption sites and estimates of the interaction strength between the adsorbate and adsorbent. The analysis of the electronic structure includes calculations of charge distribution, density of states (DOS), and visualizations of electron density difference isosurfaces. These data provide detailed insights into the redistribution of electron density during adsorption and the nature of the bonds formed. All data, including optimized crystal structures, electronic properties, and calculation results, are available in formats that can be read by commonly available text editors and specialized atomic structure visualization and analysis software. The presented dataset can serve as a foundation for further studies on the interactions of various molecules with the lizardite surface.

TEM Investigation on High Dose Al Implanted 4H-SiC Epitaxial Layer

Within this work, the effect of high dose Al ion implantation on 4H-SiC epitaxial layer is displayed. Through TEM investigation it is demonstrated that the implanted surface is suitable as seed for subsequent epitaxial regrowth generating a crystal free of extended defects. In order to assess the defects within the projected range of the ion implanted area, High Angle Annular Dark Field STEM (HAADF-STEM) analyses were performed demonstrating the atomic arrangement of the lattice in correspondence of the dislocation loop and the deviation of the crystallographic planes of 4H-SiC, driven by stress relaxation, that determine the staircase configuration of the implant pattern. Further emphasis is given to the detailed analysis of the precipitates atomic structure, whose preferential localization is ascertained. Using Energy-Dispersive X-ray spectroscopy (EDS) analysis, the precipitate is finally established as Al crystal with an FCC structure.

Comparative structural study on axonemal and cytoplasmic dyneins.

Axonemal dyneins are the driving force of motile cilia, while cytoplasmic dyneins play an essential role in minus-end oriented intracellular transport. Their molecular structure is indispensable for an understanding of the molecular mechanism of ciliary beating and cargo transport. After some initial structural analysis of cytoplasmic dyneins, which are easier to manipulate with genetic engineering, using X-ray crystallography and single-particle cryo-electron microscopy, a number of atomic and pseudo-atomic structural analyses of axonemal dyneins have been published. Currently, several structures of dyneins in the post-power stroke conformation as well as a few structures in the pre-power stroke conformation are available. It will be worth systematically comparing conformations of dynein motor proteins from different sources and at different states, to understand their role in biological function. In this review, we will overview published high- and intermediate-resolution structures of cytoplasmic and axonemal dyneins, compare the high-resolution structures of their core motor domains and overall tail conformations at various nucleotide states, and discuss their force generation mechanism.

Dynamic STEM-EELS for single-atom and defect measurement during electron beam transformations.

This study introduces the integration of dynamic computer vision-enabled imaging with electron energy loss spectroscopy (EELS) in scanning transmission electron microscopy (STEM). This approach involves real-time discovery and analysis of atomic structures as they form, allowing us to observe the evolution of material properties at the atomic level, capturing transient states traditional techniques often miss. Rapid object detection and action system enhances the efficiency and accuracy of STEM-EELS by autonomously identifying and targeting only areas of interest. This machine learning (ML)-based approach differs from classical ML in that it must be executed on the fly, not using static data. We apply this technology to V-doped MoS2, uncovering insights into defect formation and evolution under electron beam exposure. This approach opens uncharted avenues for exploring and characterizing materials in dynamic states, offering a pathway to increase our understanding of dynamic phenomena in materials under thermal, chemical, and beam stimuli.

ScaleLat: A chemical structure matching algorithm for mapping atomic structure of multi-phase system and high entropy alloys

ScaleLat (Scale Lattice) is a computer program written in C for performing the atomic structure analysis of multi-phase system or high entropy alloys (HEAs). The program implements an atomic cluster cell extraction algorithm to obtain all symmetry independent characteristic atomic cluster cells for the complex atomic configurations which are usually obtained from molecular dynamics or kinetic Monte-Carlo simulations at nanoscale or mesoscopic scale. ScaleLat implements an efficient and unique chemical structure matching algorithm to match all extracted atomic clusters from a large supercell (>104 atoms) to a representative small one (∼ 103 or less), providing the possibility to directly use the highly accurate quantum mechanical methods to study the electronic, magnetic, and mechanical properties of multi-component alloys for complex microstructures. We demonstrate the capability of ScaleLat code by conducting both the atomic structure matching analysis for Fe-12.8 at.% Cr binary alloy and equiatomic CrFeCoNiCu high entropy alloy, successfully obtaining the representative supercells containing 102∼103 atoms for two systems. The reliability of the proposed chemical structure matching scheme is tested and confirmed by calculating the electronic structures of both examples using trial supercells with various sizes. Overall, ScaleLat program provides a universal platform to efficiently map all essential chemical structures of large complex atomic structures to a relatively easy-handling small supercell for quantum mechanical calculations of various user interested properties. Program SummaryProgram Title: ScaleLatCPC Library link to program files: https://doi.org/10.17632/cv6wsxy938.1Developer's repository link: https://github.com/NanLi-xjtu/ScaleLat.gitLicensing provisions: MITProgramming language: CNature of Problem: Very large supercells containing more than 104 atoms must be used to describe the atomic structure of multi-phase materials or high entropy alloys, and their electronic and mechanical properties are almost not possible to be investigated using quantum mechanical calculations within conventional computational hardware. Decreasing the total number of atoms in a smaller representative supercell which preserves all essential chemical structures of the original large supercell is the key to tackling the problem.Solution to the Problem: An atomic cluster cell extraction algorithm is realized to thoroughly obtain all symmetry independent characteristic chemical structures of multi-phase system or high entropy alloys. Utilizing the direct atom swapping method, the efficient chemical structure matching procedure is developed to map all extracted characteristic atomic cluster cells of benchmark structure to the small supercell by minimizing their differences in both the types and relative fractions of atomic cluster cell sets.

Atomically Resolved Phase Coexistence in VO2 Thin Films.

Concurrent structural and electronic transformations in VO2 thin films are of 2-fold importance: enabling fine-tuning of the emergent electrical properties in functional devices, yet creating an intricate interfacial domain structure of transitional phases. Despite the importance of understanding the structure of VO2 thin films, a detailed real-space atomic structure analysis in which the oxygen atomic columns are also resolved is lacking. Moreover, intermediate atomic structures have remained elusive due to the lack of robust atomically resolved quantitative analysis. Here, we directly resolve both V and O atomic columns and discover the presence of intermediate monoclinic (M2) phase nanolayers (less than 2 nm thick) in epitaxially grown VO2 films on a TiO2 (001) substrate, where the dominant part of VO2 undergoes a transition from the tetragonal (rutile) phase to the monoclinic M1 phase. Strain analysis suggests that the presence of the M2 phase is related to local strain gradients near the TiO2/VO2 interface. We unfold the crucial role of imaging the spatial configurations of the oxygen anions (in addition to V cations) by utilizing atomic-resolution electron microscopy. Our approach can be used to unravel the structural transitions in a wide range of correlated oxides, offering substantial implications for, e.g., optoelectronics and ferroelectrics.

25 Years of Quasiperiodic Crystallography in Physical Space using the Average Unit Cell Approach

AbstractSince the discovery of quasicrystals 40 years ago, many new paradigms and methods have been introduced to crystallography. 25 years ago, a statistical method of structure and diffraction analysis of aperiodic materials was proposed and, over these years, developed to describe model and real systems. This short review paper briefly invokes the basic concepts of the method: a reference lattice and an average unit cell, but also gives an overview of its application to atomic structure and diffraction analysis of various systems. Results are briefly discussed for mathematical sequences (Fibonacci and Thue‐Morse), model quasilattices in 2D and 3D (Penrose and Ammann tiling), refinements of real decagonal and icosahedral quasicrystals, analysis of structure disorder in quasicrystals, description of modulated systems, including macromolecular biological systems, and beyond usual application in crystallography.

Simulation and analysis of the local atomic structure for melting behavior in metals

Melting is a phase transition from topological order to disorder, leading a solid to transform into a liquid state. However, the microstructural principles governing the melting behavior of metals, particularly during the melting process, remain unclear. This study adopts molecular dynamics simulations to investigate the atomic structure during the melting process of metals, taking Cu as an example. The effects of crystal orientations, surfaces, and surface energies on the anisotropy of the melting point are discussed. Furthermore, the similarities and differences are described between pre–melting, surface melting, and bulk melting in Cu. The investigation addresses superheating issues arising from the inhomogeneous nucleation of crystal defects and the homogeneous nucleation of perfect crystals. Finally, a detailed exploration of the transition in the local atomic structure and the dynamic behavior of Cu atoms is conducted, utilizing the mean square displacement, diffusion coefficient, radial distribution function, and polyhedral template matching.

Dirac equation and its contribution to atomic fine structure

This article aims to establish the comprehensiveness of the Dirac equation as an effective modification of quantum mechanics for the analysis of electrons and atomic fine structure. The Dirac equation is applied to investigate two scenarios involving electron interactions with different potentials. In the case where =0, the Dirac equation aligns naturally with electron theories and yields an electron gyromagnetic factor of g_s=2. With additional radiative corrections, it is possible to bring this value into closer proximity to experimental results. On the other hand, when considering spin-orbit coupling within a central field of V=(-e^2)r, the spin-orbit Hamiltonian derived from the Dirac equation is shown to match calculations based on Larmor and Thomas interactions. These cases collectively demonstrate the superior utility of Diracs theory when dealing with spin-1/2 particles like electrons, underscoring Diracs historical success in addressing the complexities of the time. His achievements in elucidating atomic fine structure and spin-orbit coupling hold pivotal significance for advancing technologies rooted in these theories. However, it is important to note that the Dirac equation primarily remains valid in weak external field situations, as observed in electron orbital motion, while challenges persist in unifying it with general relativity in stronger external field contexts.

Online carbohydrate 3D structure validation with the Privateer web app.

Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to date and available to be used online (https://privateer.york.ac.uk) without installation. This self-updating tool, which runs locally on the user's machine, will allow structural biologists to simply and quickly analyse carbohydrate ligands and protein glycosylation from a web browser whilst retaining all confidential information on their devices.

Atomic mixing mechanisms in nanocrystalline Cu/Ni composites under continuous shear deformation and thermal annealing

Molecular dynamics (MD) simulations are used to reveal the mechanisms of defect substructure evolution and atomic mixing in nanocrystalline Cu/Ni composites under severe shear deformation and subsequent thermal annealing. A continuous shear scheme of MD simulation utilizing an on-the-fly periodic boundary adjustment approach enables it to reach any large shear strain. The comprehensive evaluation on the evolution of dislocation structures at various strain states indicates partial dislocation-mediated plastic deformation and triple junction slide via partial dislocation nucleation and emission from triple junctions and grain boundaries. The analysis of atomic structures in unique mixing regions suggests that triple junction sliding can result in a long-range region of atomic mixing facilitated by net dislocation flux, which is the key mechanism of atomic mixing in nanocrystalline Cu/Ni composite under severe shear, while dislocation emissions at interfaces result in short-range mixing. It is also found that thermal annealing causes the evolution of non-equilibrium defect substructures which assists atomic mixing.

Crystalline Orientation‐Tunable Growth of Hexagonal and Tetragonal 2H─PtSe2 Single‐Crystal Flakes

AbstractDue to the narrow bandgap, environment stability, and Pt vacancy‐induced magnetism, PtSe2 has been considered a promising candidate for future broadband photodetection and electronics. However, the growth of single‐crystal PtSe2 is still a challenge. Herein, the synthesis of hexagonal and tetragonal 2H─PtSe2 single‐crystal flakes by precisely tailoring the growth temperature is reported. Through atomic structure analysis, hexagonal and tetragonal flakes are proven c‐axis and a‐axis orientations of 2H─PtSe2, indicating the preferred nucleation orientations are along the basal plane and vertically basal plane, respectively. The crystalline orientation‐dependent properties are studied including high‐pressure and polarized in situ‐Raman, electrical transport. The out‐of‐basal plane vibration (A1g) is sensitive to pressure showing 2.744 and 3.282 cm−1 GPa−1 corresponding to c‐2H─PtSe2 and a‐2H─PtSe2, respectively. The conductivity of c‐2H─PtSe2 is 57 times higher than that of a‐2H─PtSe2. Furthermore, by studying magnetic transport at low temperatures, both c‐2H─PtSe2 and a‐2H─PtSe2 exhibit butterfly‐shaped magnetoresistance hysteresis suggesting their ferromagnetic property. The c‐2H─PtSe2 has a higher |MR| ratio and higher coercive field compared with a‐2H─PtSe2, indicating that across multilayer carrier regulation for c‐2H─PtSe2 is more difficult than intra‐layer carrier regulation for a‐2H─PtSe2. This study opens the way to grow different crystalline orientations of 2D materials and will bring more abundant properties.

Oxygen Vacancy Ordering and Molten Salt Corrosion Behavior of ZnO-Doped CeYSZ for Solid Oxide Membranes.

Although 4Ce4YSZ has high corrosion resistance, it faces challenges concerning its sinterability and ionic conductivity. Therefore, we studied destabilization behavior caused by corrosion and oxygen vacancy ordering according to ZnO doping. Powders of (4Ce4YSZ)1-x(ZnO)x (x = 0.5, 1, 2, 4 mol%) were synthesized using the sol-gel method. With the addition of ZnO, the cubic phase increased, and secondary phases were not observed. The (111) peak showed a higher angle shift in ZnO-doped 4Ce4YSZ compared to 4Ce4YSZ, and TEM-SAED revealed a reduction in the spacing of the (011)t plane, suggesting lattice contraction due to the substitution of the smaller Zn2+ (60 Å) for Zr4+ (84 Å) in the lattice. The local atomic structure analysis was conducted using EXAFS to investigate the oxygen vacancy ordering behavior. Zr K-edge Fourier transform data revealed a decrease in the Zr-O1 peak intensity with an increasing amount of ZnO doping, indicating an increase in oxygen vacancies. The Zr-O1 peak position shifted to the right, leading to an increase in the Zr-O1 interatomic distance. In the Y K-edge Fourier transform data, the Y-O1 peak intensity did not decrease, and there was little variation in the Y-O1 interatomic distance. These results suggest that the oxygen vacancies formed due to ZnO doping are located in the neighboring oxygen shell of Zn, rather than in the neighboring oxygen shells of Y and Zr. Impedance measurements were conducted to measure the conductivity, and as the amount of ZnO doping increased, the total conductivity increased, while the activation energy decreased. The increase in oxygen vacancies by ZnO doping contributed to the enhancement of conductivity, and it is considered that these created oxygen vacancies did not interact with Zn2+ and did not form defect associations. Fluoride-based molten salts were introduced to the specimens to assess the corrosion behavior in a molten salt environment. Yttrium depletion layers (YDLs) were formed on the surfaces of all specimens due to the leaching of yttrium. However, Ce remained relatively stable at the interface according to EDS line scans, suggesting a reduction in the phase transformation (cubic, tetragonal to monoclinic) typically associated with yttrium leaching in YSZ.

Mapping domain junctions using 4D-STEM: toward controlled properties of epitaxially grown transition metal dichalcogenide monolayers

Abstract Epitaxial growth has become a promising route to achieve highly crystalline continuous two-dimensional layers. However, high-quality layer production with expected electrical properties is still challenging due to the defects induced by the coalescence between imperfectly aligned domains. In order to control their intrinsic properties at the device scale, the synthesized materials should be described as a patchwork of coalesced domains. Here, we report multi-scale and multi-structural analysis on highly oriented epitaxial WS2 and WSe2 monolayers using scanning transmission electron microscopy (STEM) techniques. Characteristic domain junctions are first identified and classified based on the detailed atomic structure analysis using aberration corrected STEM imaging. Mapping orientation, polar direction and phase at the micrometer scale using four-dimensional STEM enabled to access the density and the distribution of the specific domain junctions. Our results validate a readily applicable process for the study of highly oriented epitaxial transition metal dichalcogenides, providing an overview of synthesized materials from large scale down to atomic scale with multiple structural information.

Structural, electronic and mechanical properties of double core carbon nanothreads

The synthesis of double core carbon nanothreads (NTHs) has been recently achieved through compression of aromatic molecules containing two rings connected by short chains featuring either double or triple bonds (such as stilbene, azobenzene and diphenylacetylene). Their structure are characterized by two conventional 1D NTHs cores, interconnected by covalent bonds arranged in several ways. In this paper, we provide a comprehensive analysis of the possible atomic structures for double core NTHs, evaluate their relative stability, and calculate some electronic and mechanical properties, using Density Functional Theory calculations and Molecular Dynamics simulations. Many isomers are possible for these 1D materials, differing by the intrinsic structure of the cores and the nature of the covalent bonds crosslinking them. For stilbene and diphenylacetylene NTHs, the most stable isomers feature continuous sp3 or sp2 C-C chains connecting the cores, while those that preserve the original unsaturation of the molecule (azo group) are the most stable for azobenzene. The mechanical behavior of these NTHs are similar to that of conventional single core ones, with enhanced 1D strength and stiffness when continuous chains connect the cores. Their electronic behavior range from metallic to insulating depending on the arrangement of the bonds connecting the cores, and the materials with the narrowest band gaps feature electron delocalization along the chain connecting the cores. The variations in properties associated to the presence of bonds connecting the cores bring new opportunities to the design of electronic and optical devices employing this class of strong and flexible materials.

Picometer-precision few-tilt ptychotomography of 2D materials

From ripples to defects, edges and grain boundaries, the 3D atomic structure of 2D materials is critical to their properties. However the damage inflicted by conventional 3D analysis precludes its use with fragile 2D materials, particularly for the analysis of local defects. Here we dramatically increase the potential for precise local 3D atomic structure analysis of 2D materials, with both greatly improved dose efficiency and sensitivity to light elements. We demonstrate light atoms can now be located in complex 2D materials with picometer precision at doses 30 times lower than previously possible. Moreover we demonstrate this using WS2, in which the light atoms are practically invisible to conventional methods at low doses. The key advance is combining the concept of few tilt tomography with highly dose efficient ptychography in scanning transmission electron microscopy. We further demonstrate the method experimentally with the even more challenging and newly discovered 2D CuI, leveraging a new extremely high temporal resolution camera.

Metastable high entropy alloys of TiZrHfTa with glass-like characteristics at low temperatures

Metastability engineering of high entropy alloys can widen the alloy-design window through the access of a potentially huge configuration space. At the same time, it has the great capacity to overcome the strength-ductility trade-off, where often one witnesses an actual performance improvement at low to cryogenic temperatures. An in-depth microscopic understanding of the underlying mechanism is now needed to drive the design effort. Here we investigate in detail the energetic, structural and chemical complexity of Ti–Zr–Hf–Ta system. The large configuration space with local chemical interaction heterogeneity is explored by a combination of structure-searching techniques and accurate energy models constructed by cluster expansion based on density functional theory data. We find that the potential energy landscape evolves towards displaying shallow mega-basins when decreasing the Ta content. This is accompanied by an expansion of the configurational density of states, which evolves to be clearly distinct from that of a homogeneous random solid-state solution. Furthermore, the energy-state variability and local configuration flexibility are identified from high throughput analysis of atomic structures and their energies. Such features remind closely what found in glass-like systems. This work suggests a theoretical connection between glass physics and metastability engineering of HEAs is quite promising.

Atomic resolution interface structure and vertical current injection in highly uniform MoS2 heterojunctions with bulk GaN

The integration of two-dimensional MoS2 with GaN recently attracted significant interest for future electronic/optoelectronic applications. However, the reported studies have been mainly carried out using heteroepitaxial GaN templates on sapphire substrates, whereas the growth of MoS2 on low-dislocation-density bulk GaN can be strategic for the realization of “truly” vertical devices. In this paper, we report the growth of ultrathin MoS2 films, mostly composed by single-layers (1L), onto homoepitaxial n−-GaN on n+ bulk substrates by sulfurization of a pre-deposited MoOx film. Highly uniform and conformal coverage of the GaN surface was demonstrated by atomic force microscopy, while very low tensile strain (∼0.05%) and a significant p+-type doping (∼4.5 × 1012 cm−2) of 1L-MoS2 was evaluated by Raman mapping. Atomic resolution structural and compositional analyses by aberration-corrected electron microscopy revealed a nearly-ideal van der Waals interface between MoS2 and the Ga-terminated GaN crystal, where only the topmost Ga atoms are affected by oxidation. Furthermore, the relevant lattice parameters of the MoS2/GaN heterojunction, such as the van der Waals gap, were measured with high precision. Finally, the vertical current injection across this 2D/3D heterojunction has been investigated by nanoscale current-voltage analyses performed by conductive atomic force microscopy, showing a rectifying behavior with an average turn-on voltage Von = 1.7 V under forward bias, consistent with the expected band alignment at the interface between p+ doped 1L-MoS2 and n-GaN.

Fine electron and phonon transports manipulation by Mn compensation for high thermoelectric performance of Sb2Te3(SnTe)n materials

Fabricating the Sb2Te3(SnTe)n compound has been proved as an effective way to suppress the lattice thermal conductivity and optimize the band structure simultaneously for enhancing the thermoelectric (TE) performance of SnTe. In view of the ultra-low carrier mobility resulted from the strong vacancy-electron scattering in SnTe–Sb2Te3 alloy, an appropriate weakening of vacancy scattering to pursue ideal compromise among carrier mobility (μ), concentration (n), and density-of-state effective mass (m*) is of great significance for more effective performance promotion. Herein, we propose an approach of cation-site compensation to finely manipulate the transport properties in Sb2Te3(SnTe)10 alloy. We, for the first time in the SnTe community, contrastively investigated diverse cation-site fillers, including homogeneous atoms (Sn, Pb) and heterogeneous atoms (Cd, Mn) for maintaining high μ with a large m*, which indicated that Mn compensation exhibits the most appealing effect on synergistically modulating the three electrical transport parameters, μ, n and m*. Our study archives a satisfied electrical transport property in the optimized Sb2Te3(SnMn0.08Te)10 specimen. The atomic structural analysis discovered the coherent Mn-rich nanostructures which will enrich the phonon scattering mechanism while having minimal effect on electron transport. Benefiting from the finely manipulated electron and phonon transports, a peak ZT of ∼1.3 at 773 K and an average ZT of ∼0.78 (300–823 K) are achieved in the Sb2Te3(SnMn0·.08Te)10 alloy. This work provides a feasible strategy to realize the sharply enhanced TE performance in medium-temperature TE system with abundant vacancies.

New Composite Materials Based on Chitosan Films Reinforced with Chitin Nanofibrils for Cosmetic Application

Bioactive biodegradable chitosan films containing chitin nanofibrils have been developed for use as face masks in cosmetology. It was found that thermal modification of chitosan films promotes the transformation of the polymer into insoluble form without the use of alkali or aldehydes. The structure and properties of the films were studied by IT spectroscopy, atomic force microscopy, thermogravimetric analysis, and X-ray structural analysis. Analysis of infrared (IR) spectra showed that the addition of nanofibrils accelerates the process of thermal transformation in the composite films. This is apparent from the observed increase in the intensity ratio of 1030 cm−1\1580 cm−1 peaks in the spectrum of the thermally treated film (as compared to the spectrum of the initial sample and the spectrum of a chitosan film without chitin nanofibrils). The prepared composite films containing chitin nanofibrils possess improved mechanical characteristics: tensile strength 99 MPa and tensile strain 14%. The tetrazolium bromide (MTT) test revealed good viability of human dermal fibroblasts cultivated in the presence of the conditioned medium obtained after incubation of all types of films in the nutrient medium. The used process of thermal modification of chitosan and composite films (which is efficient and environmentally safe) allows one to prepare bioactive materials for applications in medicine and cosmetology.