Atomic Structure Research Articles

Computational Screening of Promising Deep-Ultraviolet Light Emitters.

Deep-ultraviolet (DUV) light sources are technologically highly important, but DUV light-emitting materials are extremely rare; AlN and its alloys are the only materials known so far, significantly limiting the chemical and structural spaces for materials design. Here, we perform a high-throughput computational search for DUV light emitters based on a set of carefully designed screening criteria relating to the sophisticated electronic structure. In this way, we successfully identify 5 promising material candidates that exhibit comparable or higher radiative recombination coefficients than AlN, including BeGeN2, Mg3NF3, KCaBr3, KHS, and RbHS. Further, we unveil the unique features in the atomic and electronic structures of DUV light emitters and elucidate the fundamental genetic reasons why DUV light emitters are extremely rare. Our study not only guides the design and synthesis of efficient DUV light emitters but also establishes the genetic nature of ultrawide-band-gap semiconductors in general.

Topological ordering during flexible to rigid transitions in disordered networks

This contribution focuses on the structural origin of flexible to rigid transitions and the possible underlying intermediate phase which have been reported to occur in a variety of network glasses such as chalcogenides or modified oxides. Here, using molecular dynamics simulations of densified glass-forming liquids, 2SiO 2 -Na 2 O, which are known to display a numerical reversibility window as a signature of an intermediate phase, we focus on structural functions emphasizing topological ordering using the Bhatia–Thornton formalism. Results not only reveal that densified silicates display topological ordering on lengthscales of about 25 Å, but also display obvious threshold behaviors close to the isostatic condition when the network undergoes a flexible to rigid transition. The mechanical constraint count of the atomic network structure reveals that a typical lengthscale characterizing the decay of topological correlations emerges for stressed rigid systems at ≃3.5 Å, whereas small wavevector oscillations are found to be minimal when the isostatic condition is merely satisfied. An additional analysis building on diffusivity and liquid entropy suggests that the locus of flexible to rigid transitions has also connections with water-like anomalies of densified tetrahedral liquids.

Molecular dynamics simulations into rolling scraping of nickel-copper bilayer film

In order to investigate the nanoscale friction mechanism and deformation behavior of nickel-copper bilayer film under rolling scraping, the effects of different factors during friction process such as the translation velocity, rotation velocity, radius of abrasive grain, contact depth, texture direction and crystallographic orientation are analyzed through molecular dynamics methods in terms of contact force, atomic lattice structure, internal substrate dislocation, kinetic energy and temperature. Results show that the contact force increases with the increase of the translation velocity or the decrease of the rotation velocity. Abrasive grains in a purely rolling state cause the most serious damage to the substrate. The contact force increases with the increase of contact depth or the decrease of abrasive grain radius. The crystallographic orientation has a significant effect on rolling scraping process and there is a crystallographic orientation with the minimum contact force. The degrees of substrate dislocation and the numbers of lattice reconstruction atoms under different factors and levels vary widely.

Bragg Spot Finder (BSF): a new machine-learning-aided approach to deal with spot finding for rapidly filtering diffraction pattern images

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages (Dozor and DIALS), demonstrating that this is an appropriate framework to support future extensions and improvements.

Electron impact broadening and atomic data for As IV-V, Mo V and In V spectral lines

Missing Stark broadening parameters for 33 spectral lines of several arsenic, molybdenum and indium ions (7 As IV, 4 As V, 12 Mo V and 10 In V lines) have been calculated using a quantum-mechanical method. All the considered spectral lines for As IV and As V have been detected for the first time in the atmospheres of cool DO white dwarfs HD 149499 B and p=HZ 21, these four As V lines that have been discovered in HD 149499 B are also present in the UV spectrum of hot white dwarf (WD) RE 0503−289. All the considered spectral lines for Mo V have been recently discovered for the first time in the ultraviolet (UV) spectrum of the DO-type white dwarf (WD) RE 0503−289. Also, the ten considered lines for In V have been detected in the ultraviolet (UV) spectrum of the DO-type white dwarf (WD) RE 0503−289, that five among those discovered — recently — for the first time. This recent discovery encourages us to calculate their Stark widths to fill the lack of the data base STARK-B and for use in investigations of observed spectra in such stars. Before the Stark widths evaluation, two calculation steps have been carried out : in the first step, we calculate the atomic structure and then the electron-ion collision as a second step using the sequence of the codes (superstructure, distorted wave, and jajom) of University College London. We provide our results for these lines at different temperature values and at density Ne=1017 cm−3.

Plutonium oxide melt structure and covalency.

Advances in nuclear power reactors include the use of mixed oxide fuel, containing uranium and plutonium oxides. The high-temperature behaviour and structure of PuO2-x above 1,800 K remain largely unexplored, and these conditions must be considered for reactor design and planning for the mitigation of severe accidents. Here, we measure the atomic structure of PuO2-x through the melting transition up to 3,000 ± 50 K using X-ray scattering of aerodynamically levitated and laser-beam-heated samples, with O/Pu ranging from 1.57 to 1.76. Liquid structural models consistent with the X-ray data are developed using machine-learned interatomic potentials and density functional theory. Molten PuO1.76 contains some degree of covalent Pu-O bonding, signalled by the degeneracy of Pu 5f and O 2p orbitals. The liquid is isomorphous with molten CeO1.75, demonstrating the latter as a non-radioactive, non-toxic, structural surrogate when differences in the oxidation potentials of Pu and Ce are accounted for. These characterizations provide essential constraints for modelling pertinent to reactor safety design.

Topographical and morphological changes of the single‐crystal (La0.3Sr0.7)(Al0.65Ta0.35)O3 (001) surface treated with high‐purity deionized water

The topological and morphological changes of the (001) surface of single‐crystal (La0.3Sr0.7)(Al0.65Ta0.35)O3 during treatment with high‐purity deionized water (DI) have been investigated by atomic force microscopy and scanning transmission electron microscopy (STEM). Etching by DI treatment at room temperature proceeded mainly in anisotropic etching mode, resulting in rectangular etch pits with {001} inner surfaces forming in the surface. The dominant etching mode changed from anisotropic to isotropic with increasing DI‐treatment temperature, and the lowest surface roughness occurred for DI treatment at 50°C for 60 min. Direct observation of the atomic structure of the surface by STEM showed that the etched surface was the B‐site‐terminated (001) surface after anisotropic etching at 50°C for 60 min, in which the B‐site‐terminated atomic layer was found to maintain the B‐site ordered structure existing in the crystal. This is because DI treatment, which does not require high‐temperature heat treatment of the substrate, suppresses element diffusion, sublimation, and formation of point defects on and in the vicinity of the surface.

Cluster-based multidimensional scaling embedding tool for data visualization

Abstract We present a new technique for visualizing high-dimensional data called cluster MDS (cl-MDS), which addresses a common difficulty of dimensionality reduction methods: preserving both local and global structures of the original sample in a single 2-dimensional visualization. Its algorithm combines the well-known multidimensional scaling (MDS) tool with the k-medoids data clustering technique, and enables hierarchical embedding, sparsification and estimation of 2-dimensional coordinates for additional points. While cl-MDS is a generally applicable tool, we also include specific recipes for atomic structure applications. We apply this method to non-linear data of increasing complexity where different layers of locality are relevant, showing a clear improvement in their retrieval and visualization quality.

Influence of Zr element on the atomic structure of Al-Cu alloy liquid

The relationship among chemical composition, structure and glass-forming ability in multicomponent alloys is a long-standing puzzle due to the complexity of compositions. In this work, Al77.8Cu22.2 and Al70Cu20Zr10 amorphous alloy liquids were investigated by combining high-energy X-ray diffraction at a synchrotron facility, ab-initio molecular dynamics and reverse Monte Carlo simulations. The analysis of short- and medium-range order structures of two liquid alloys show that the addition of Zr element increases the number of cluster types and makes the distribution of cluster content more uniform, and enhances the structural heterogeneity and correlation of clusters with high five-fold symmetry. These findings reveal the influence of Zr element on the atomic structure of the Al-Cu liquid alloy and deepen the understanding of Al-based metallic glasses formation.

Tailored Local Electronic Environment of Co-N4 Sites in Cobalt Phthalocyanines for Enhanced CO2 Reduction Reaction.

Atomically dispersed Co-N4-based catalysts have been recently emerging as one of the most promising candidates for facilitating CO2 reduction reaction (CO2RR). The local electronic environment of Co-N4 sites in these catalysts is considered to play a critical role in adjusting the catalytic performance, the effort of which however is not yet clearly verified. Herein, a series of cobalt phthalocyanines with different peripheral substituents including unsubstituted phthalocyanine Co(II) (CoPc), 2,9,16,23-tetramethoxyphthalocyaninato Co(II) (CoPc-4OCH3), and 2,9,16,23-tetranitrophthalocyaninato Co(II) (CoPc-4NO2) are supported onto the surface of the multi-walled carbon nanotubes (CNTs), affording CoPc@CNTs, CoPc-4OCH3@CNTs, and CoPc-4NO2@CNTs. X-ray photoelectron spectroscopy and X-ray absorption near-edge structure measurements disclose the influence of the peripheral substituents on the local electronic structure of Co atoms in these three catalysts. Electrochemical tests indicate the higher CO2RR performance of CoPc-4OCH3@CNTs compared to CoPc@CNTs and CoPc-4NO2@CNTs as exemplified by the higher Faraday efficiency of CO, larger part current densities, and better stability displayed by CoPc-4OCH3@CNTs at the applied voltage range from -0.6 to -1.0V versus RHE in both H-cell and flow cell. These results highlight the effect of the electron-donating -OCH3 substituent on the enhanced catalytic activity of CoPc-4OCH3@CNTs, which will help develop Co-N4-based catalysts with promising catalytic performance toward CO2RR.

Structural insights into human exon-defined spliceosome prior to activation.

Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition.

Atomic-scale observation of localized phonons at FeSe/SrTiO3 interface

In single unit-cell FeSe grown on SrTiO3, the superconductivity transition temperature features a significant enhancement. Local phonon modes at the interface associated with electron-phonon coupling may play an important role in the interface-induced enhancement. However, such phonon modes have eluded direct experimental observations. The complicated atomic structure of the interface brings challenges to obtain the accurate structure-phonon relation knowledge. Here, we achieve direct characterizations of atomic structure and phonon modes at the FeSe/SrTiO3 interface with atomically resolved imaging and electron energy loss spectroscopy in an electron microscope. We find several phonon modes highly localized (~1.3 nm) at the unique double layer Ti-O terminated interface, one of which (~ 83 meV) engages in strong interactions with the electrons in FeSe based on ab initio calculations. This finding of the localized interfacial phonon associated with strong electron-phonon coupling provides new insights into understanding the origin of superconductivity enhancement at the FeSe/SrTiO3 interface.

First-principles study of the structures and redox mechanisms of Ni-rich lithium nickel manganese cobalt oxides

To reduce the cobalt (Co) content in lithium-ion batteries, Ni-rich (high-Ni) lithium nickel manganese cobalt oxides (NMC) are pursued as one of the next-generation cathode materials. However, there is still debate on the crystal and electronic structures of the baseline, LiNiO2. Density Functional Theory (DFT) calculations were performed to provide a theoretical understanding of Ni-rich NMC. First, it was found that the commonly used R3¯m structure for LiNiO2 is metallic, contrary to the experimentally reported mix-conducting behavior. Among the four different space groups, R3¯m, C2/m, P21/c, and P2/c, P2/c with charge disproportionation of Ni2+ and Ni4+ is the most energetically stable and semiconducting structure of LiNiO2. Therefore, the atomic structures of representative Ni-rich NMC were built by partially replacing Ni with Co or Mn in the P2/c LiNiO2 to form LixNiyMnzCo1-y-zO2. In the fully lithiated (x = 1.0) high Ni content NMC (y > 0.5), the oxidation state of all Mn ions becomes 4+, while Co ions still maintain 3+, and part of the Ni ions become 2+ to compensate for the charge. Upon delithiation, the local environment shows more variation of the charge states on the transition metal (TM) ions. The average oxidation on each TM follows a sequence of losing electrons that starts from Ni2+ to Ni3+, then oxidizing Ni3+ and Co3+, while Mn4+ remains electrochemically inactive till x = 0. A general relationship for the oxidation state change in each TM as a function of x and y is derived and shows agreement with both modeling and experimental data.

Atomistic insights into chemical vapor deposition process of preparing silicon carbide materials using ReaxFF-MD simulation

SiC is a kind of key advanced coating material used widely. The in-depth understanding of the CVD process of preparing SiC materials at the atomic scale is beneficial for studying the CVD mechanism and then optimizing the materials. Here, a CVD model of preparing SiC materials is established based on ReaxFF-MD considering the whole pyrolysis-adsorption-desorption-growth mechanism. The accuracy of the ReaxFF potential and its parameters is verified by DFT at first. Then an energy-based Monte Carlo (EMC)-MD-CVD model is proposed based on the bonding formation energy originating from DFT. It is used to simulate the CVD process of preparing SiC materials. The CVD of MTS is studied by deposition efficiency and deposited film components at different temperatures, and it can be found it in good agreement with experimental results. Finally, the crystallization of SiC film prepared by the CVD of MTS is studied by energy evolution and atomic structure evolution. The results are helpful to understand the CVD mechanism for preparing coatings and it can be used to optimize the CVD parameters of preparing SiC materials in the future.

Analysis of extreme ultraviolet radiation and hydrodynamics simulation at the core of laser-produced nickel plasmas

The non-uniformity and transient nature of laser-produced plasma are critical factors that affect the analysis of the extreme ultraviolet spectra of highly charged ions and the diagnosis of plasma states. This paper systematically investigates the characteristics of extreme ultraviolet radiation and the hydrodynamic evolution of laser-produced nickel plasmas from two perspectives: high-spatio-temporal-resolution extreme-ultraviolet spectroscopic measurement and radiation hydrodynamics simulation. The consistency between the four-band experimental spectra and their theoretically simulated spectra confirms the accuracy of the atomic structure parameters and plasma state parameters. We also analyze the significant contribution of the 3d-4f double-excited state radiation to the spectral profile and discuss the influence of the self-absorption caused by plasma opacity on the characteristics of extreme ultraviolet radiation. The findings are crucial for accurately understanding the characteristics of extreme ultraviolet radiation, the hydrodynamic evolution, and the application of medium- and high-Z laser-produced plasma as a pulsed short-wavelength light source.

Tuning grain boundary cation segregation with oxygen deficiency and atomic structure in a perovskite compositionally complex oxide thin film

Compositionally complex oxides (CCOs) are an emerging class of materials encompassing high entropy and entropy stabilized oxides. These promising advanced materials leverage tunable chemical bond structure, lattice distortion, and chemical disorder for unprecedented properties. Grain boundary (GB) and point defect segregation to GBs are relatively understudied in CCOs even though they can govern macroscopic material properties. For example, GB segregation can govern local chemical (dis)order and point defect distribution, playing a critical role in electrochemical reaction kinetics, and charge and mass transport in solid electrolytes. However, compared with conventional oxides, GBs in multi-cation CCO systems are expected to exhibit more complex segregation phenomena and, thus, prove more difficult to tune through GB design strategies. Here, GB segregation was studied in a model perovskite CCO LaFe0.7Ni0.1Co0.1Cu0.05Pd0.05O3−x textured thin film by (sub-)atomic-resolution scanning transmission electron microscopy imaging and spectroscopy. It is found that GB segregation is correlated with cation reducibility—predicted by an Ellingham diagram—as Pd and Cu segregate to GBs rich in oxygen vacancies (VO··). Furthermore, Pd and Cu segregation is highly sensitive to the concentration and spatial distribution of VO·· along the GB plane, as well as fluctuations in atomic structure and elastic strain induced by GB local disorder, such as dislocations. This work offers a perspective of controlling segregation concentration of CCO cations to GBs by tuning reducibility of CCO cations and oxygen deficiency, which is expected to guide GB design in CCOs.

Prediction of the essential intermolecular contacts for side-binding of VASP on F-actin.

Vasodilator-stimulated phosphoprotein (VASP) family proteins play a crucial role in mediating the actin network architecture in the cytoskeleton. The Ena/VASP homology 2 (EVH2) domain in each of the four identical arms of the tetrameric VASP consists of a loading poly-Pro region, a G-actin-binding domain (GAB), and an F-actin-binding domain (FAB). Together, the poly-Pro, GAB, and FAB domains allow VASP to bind to sides of actin filaments in a bundle, and recruit profilin-G-actin to processively elongate the filaments. The atomic resolution structure of the ternary complex, consisting of the loading poly-Pro region and GAB domain of VASP with profilin-actin, has been solved over a decade ago; however, a detailed structure of the FAB-F-actin complex has not been resolved to date. Experimental insights, based on homology of the FAB domain with the C region of WASP, have been used to hypothesize that the FAB domain binds to the cleft between subdomains 1 and 3 of F-actin. Here, in order to develop our understanding of the VASP-actin complex, we first augment known structural information about the GAB domain binding to actin with the missing FAB domain-actin structure, which we predict using homology modeling and docking simulations. In earlier work, we used mutagenesis and kinetic modeling to study the role of domain-level binding-unbinding kinetics of Ena/VASP on actin filaments in a bundle, specifically on the side of actin filaments. We further look at the nature of the side-binding of the FAB domain of VASP at the atomistic level using our predicted structure, and tabulate effective mutation sites on the FAB domain that would disrupt the VASP-actin complex. We test the binding affinity of Ena with mutated FAB domain using total internal reflection fluorescence microscopy experiments. The binding affinity of VASP is affected significantly for the mutant, providing additional support for our predicted structure.

Equivariant neural network force fields for magnetic materials

Neural network force fields have significantly advanced ab initio atomistic simulations across diverse fields. However, their application in the realm of magnetic materials is still in its early stage due to challenges posed by the subtle magnetic energy landscape and the difficulty of obtaining training data. Here we introduce a data-efficient neural network architecture to represent density functional theory total energy, atomic forces, and magnetic forces as functions of atomic and magnetic structures. Our approach incorporates the principle of equivariance under the three-dimensional Euclidean group into the neural network model. Through systematic experiments on various systems, including monolayer magnets, curved nanotube magnets, and moiré-twisted bilayer magnets of CrI3, we showcase the method’s high efficiency and accuracy, as well as exceptional generalization ability. The work creates opportunities for exploring magnetic phenomena in large-scale materials systems.

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.

Ultralow Strain-Induced Emergent Polarization Structures in a Flexible Freestanding BaTiO3 Membrane.

The engineering of ferroic orders, which involves the evolution of atomic structure and local ferroic configuration in the development of next-generation electronic devices. Until now, diverse polarization structures and topological domains are obtained in ferroelectric thin films or heterostructures, and the polarization switching and subsequent domain nucleation are found to be more conducive to building energy-efficient and multifunctional polarization structures. In this work, a continuous and periodic strain in a flexible freestanding BaTiO3 membrane to achieve a zigzag morphology is introduced. The polar head/tail boundaries and vortex/anti-vortex domains are constructed by a compressive strain as low as ≈0.5%, which is extremely lower than that used in epitaxial rigid ferroelectrics. Overall, this study c efficient polarization structures, which is of both theoretical value and practical significance for the development of next-generation flexible multifunctional devices.