Atomic Structure Research Articles

Single‐element amorphous metals

AbstractTo unveil the nature of amorphous states, single‐element amorphous metals have been the perfect research subject due to the simplest composition. However, the extreme crystal nucleation and growth rate in single‐element metal make the synthesis of single‐element amorphous metals seemingly impossible in the past. Fortunately, benefited by several delicate synthetic strategies developed recently, the single‐element amorphous metals have been successfully demonstrated. This review aims to provide a systematic overview of the synthesis of single‐element amorphous metals covering the challenges in physics and recent achievements. In addition, current understanding of the atomic and electronic structures of single‐element amorphous metal has also been included. Finally, the challenges that worth further investigation are discussed. By identifying the potential avenues for further exploration, this review aims to contribute valuable insights that will propel the cognition of single‐element amorphous metals.

Wall-crossing effects on quiver BPS algebras

BPS states in supersymmetric theories can admit additional algebro-geometric structures in their spectra, described as quiver Yangian algebras. Equivariant fixed points on the quiver variety are interpreted as vectors populating a representation module, and matrix elements for the generators are then defined as Duistermaat-Heckman integrals in the vicinity of these points. The well-known wall-crossing phenomena are that the fixed point spectrum establishes a dependence on the stability (Fayet-Illiopolous) parameters ζ, jumping abruptly across the walls of marginal stability, which divide the ζ-space into a collection of stability chambers — “phases” of the theory. The standard construction of the quiver Yangian algebra relies heavily on the molten crystal model, valid in a sole cyclic chamber where all the ζ-parameters have the same sign. We propose to lift this restriction and investigate the effects of the wall-crossing phenomena on the quiver Yangian algebra and its representations — starting with the example of affine super-Yangian \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\ ext{Y}}\\left({\\widehat{\\mathfrak{g}\\mathfrak{l}}}_{1\\left|1\\right.}\\right)$$\\end{document}. In addition to the molten crystal construction more general atomic structures appear, in other non-cyclic phases (chambers of the ζ-space). We call them glasses and also divide in a few different classes. For some of the new phases we manage to associate an algebraic structure again as a representation of the same affine Yangian \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\ ext{Y}}\\left({\\widehat{\\mathfrak{g}\\mathfrak{l}}}_{1\\left|1\\right.}\\right)$$\\end{document}. This observation supports an earlier conjecture that the BPS algebraic structures can be considered as new wall-crossing invariants.

Crystallography applications: A comprehensive review

Crystallography is an essential scientific technique profoundly influencing our understanding of atomic and molecular structures in materials, providing insights into the arrangement and interactions of atoms. This review highlights crystallographys extensive applications across chemistry, biology, physics, and materials science, emphasizing its critical role and adaptability. The paper traces crystallographys historical development, outlines its fundamental principles, and celebrates its significant milestones and contributions to science. By revealing the complex structures and functions of compounds, from simple molecules to complex macromolecules, crystallography has catalyzed advancements in drug development, material innovation, and fundamental scientific understanding. The paper asserts crystallographys continued prominence in scientific research, with its application and influence steadily growing. Its pivotal in enhancing our understanding of matter, driving technological and material advancements, and offering solutions to complex scientific questions. Moreover, the review addresses the current challenges and future directions of crystallography, pointing out potential areas for innovation and improvement. As technology advances, crystallographys significance in various scientific disciplines remains indispensable, solidifying its position as a cornerstone of scientific inquiry and discovery. The paper concludes by reinforcing the techniques vital role in pushing the boundaries of science and technology.

Improved Mechanical Performance in FDM Cellular Frame Structures through Partial Incorporation of Faces

The utilization of lattice-type cellular architectures has seen a significant increase, owing to their predictable shape and the ability to fabricate templated porous materials through low-cost 3D-printing methods. Frames based on atomic lattice structures such as face-centered cubic (FCC), body-centered cubic (BCC), or simple cubic (SC) have been utilized. In FDM, the mechanical performance has been impeded by stress concentration at the nodes and melt-solidification interfaces arising from layer-by-layer deposition. Adding plates to the frames has resulted in improvements with a concurrent increase in weight and hot-pocket-induced dimensional impact in the closed cells formed. In this paper, we explore compressive performance from the partial addition of plates to the frames of a SC-BCC lattice. Compression testing of both single unit cells and 4 × 4 × 4 lattices in all three axial directions is conducted to examine stress transfer to the nearest neighbor and assess scale-up stress transfer. Our findings reveal that hybrid lattice structure unit cells exhibit significantly improved modulus in the range of 125% to 393%, specific modulus in the range of 13% to 120%, and energy absorption in the range of 17% to 395% over the open lattice. The scaled-up lattice modulus increased by 8% to 400%, specific modulus by 2% to 107%, and energy absorption by 37% to 553% over the lattice frame. Parameters that emerged as key to improved lightweighting.

Strong-field photoelectron holography in the subcycle limit

Strong-field photoelectron holography is promising for the study of electron dynamics and structure in atoms and molecules, with superior spatiotemporal resolution compared to conventional electron and X-ray diffractometry. However, the application of strong-field photoelectron holography has been hindered by inter-cycle interference from multicycle fields. Here, we address this challenge by employing a near-single-cycle field to suppress the inter-cycle interference. We observed and separated two distinct holographic patterns for the first time. Our measurements allow us not only to identify the Gouy phase effect on electron wavepackets and holographic patterns but also to correctly extract the internuclear separation of the target molecule from the holographic pattern. Our work leads to a leap jump from theory to application in the field of strong-field photoelectron holography-based ultrafast imaging of molecular structures.

Relativistic atomic structure calculations of Li-like ions used for plasma diagnostic studies

Abstract We have carried out atomic structure calculations using systematically enlarged multiconfiguration Dirac- Fock wavefunctions of Li-like ions of the most prominent plasma impurities (Ar, Ti, Fe, Ni, Kr and W) found in presently working tokamaks. Relativistic Breit interaction and quantum electrodynamic (QED) corrections such as vacuum polarization and self-energy corrections are also included in the calculations prior to the evaluation of low lying energy levels, transition probabilities, oscillator strengths and line strengths. Selective radiative data for electric dipole and magnetic quadrupole transitions are also reported. Special emphasis is given in the computations of fundamental quantities such as oscillator strengths as they are widely used in atomic data and analysis structure (ADAS) databases to evaluate quantities such as effective collision strengths. Present com- puted values are compared with existing available results on NIST database and few similar earlier computations and a good agreement has been found. We believe that the detailed atomic data with the relativistic and QED corrections will assist in spectroscopic studies such as accurate line identification and plasma modelling work in tokamak plasma, laser induced breakdown spectroscopy (LIBS), highly charged ions clocks and astrophysical observations.

Optical and electrical properties and applications of two-dimensional carbon-based nanomaterials

As an emerging material, two-dimensional (2D) carbon-based nanomaterials have unique optical and electrical properties due to their unique atomic layer structure. On the one hand, due to their high transmittance, high carrier mobility, controllable Fermi level, and wide spectral light saturation absorption characteristics, they can be applied in new-generation solar cells, organic light-emitting diodes, touch screens, and fiber optic devices. On the other hand, due to their unique nanostructure, they have high specific surface area, low diffusion distance, high conductivity, and ion conductivity. They can serve as substrates and work together with other materials as electrode materials for future fuel cells and lithium-ion batteries and have significant advantages in fields such as sensors. This article mainly summarizes the impact of two-dimensional carbon-based nanomaterials represented by graphene, Mxene, and 2D covalent organic frameworks (COFs) on their optical and electrical properties, and summarizes the latest practical applications and research progress of these nanomaterials in the field of optics and electronics. In addition, a corresponding summary and outlook have been made on the problems that need to be solved in future applications of 2D carbon-based nanomaterials.

Regular relations of the composition, structure and properties of crystals of hydrogen-containing compounds

Research subject. Crystals of hydrogen-containing compounds belonging to the superprotonic family. Aim. To obtain knowledge about regular relations between composition, atomic structure, real structure and physical properties of materials, with the purpose of elucidating processes occurring in condensed state and forming the basis for modification of known or obtaining new compounds. Materials and methods. Experimental data were obtained using a set of complementary physical methods, including structural analysis using X-rays, synchrotron radiation and neutrons, optical microscopy, and atomic force microscopy. Results. Experimental data on the atomic structure, real structure, and physical properties of superprotonic crystals, including systems of hydrogen bonds and their changes, were obtained. Conclusions. The physical properties of superprotonic crystals are significantly affected by hydrogen bonding systems and their changes, primarily by the formation of dynamically disordered hydrogen bonds with energetically equivalent positions of hydrogen atoms. When carrying out diagnostics of crystalline samples, account should be taken of their real structure, including the structure of surface layers and the presence of crystallization water. These factors may affect the measured physical parameters, the boundaries of existence of phases, the formation of a multiphase state under variations in temperature.

JARVIS-Leaderboard: a large scale benchmark of materials design methods

Lack of rigorous reproducibility and validation are significant hurdles for scientific development across many fields. Materials science, in particular, encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC), and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboard/

Chemical bonding and electronic properties along Group 13 metal oxides

ContextThe present work provides a systematic theoretical analysis of the nature of the chemical bond in Al2O3, Ga2O3, and In2O3 group 13 cubic crystal structure metal oxides. The influence of the functional in the resulting band gap is assessed. The topological analysis of the electron density provides unambiguous information about the degree of ionicity along the group which is linearly correlated with the band gap values and with the cost of forming a single oxygen vacancy. Overall, this study offers a comprehensive insight into the electronic structure of metal oxides and their interrelations. This will help researchers to harness information effectively, boosting the development of novel metal oxide catalysts or innovative methodologies for their preparation.MethodsPeriodic density functional theory was used to predict the atomic structure of the materials of interest. Structure optimization was carried out using the PBE functional, using a plane wave basis set and the PAW representation of the atomic cores, using the VASP code. Next, the electronic properties were computed by carrying out single point calculations employing PBE, PBE + U functionals using VASP and also with PBE and the hybrid HSE06 functionals using the FHI-AIMS software. For the hybrid HSE06, the impact of the screening parameter, ω, and mixing parameter, α, on the calculated band gap has also been assessed.

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.

Understanding the Decomposition of Dimethyl Methyl Phosphonate on Metal-Modified TiO2(110) Surfaces Using Ensembles of Product Configurations.

The decomposition of dimethyl methyl phosphonate (DMMP), a simulant for the nerve agent sarin, was investigated on Cu4/TiO2(110) and K/Cu4/TiO2(110) surfaces using a combination of near-ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) and density functional theory calculations (DFT). Mass-selected Cu4 clusters and potassium (K) atoms were deposited onto TiO2(110) as a metal catalyst and alkali promoter to improve the reactivity and recyclability of the TiO2 surface after exposure to DMMP. Surface reaction products resulting from decomposition of DMMP were probed by NAP-XPS measurements of phosphorus (P) 2p and carbon 1s core-level spectra. The Cu4/TiO2(110) surface is found to be very active for DMMP decomposition with highly reduced P-species observed even at room temperature (RT). The codeposition of K atoms and Cu4 clusters further improves the reactivity with no intact DMMP detectable. Temperature-dependent measurements show that the presence of K atoms promotes the removal of residual P-species at temperatures > 600 K. Detailed DFT calculations were performed to determine the surface structures and energetically accessible pathways for DMMP decomposition on Cu4/TiO2(110) and K/Cu4/TiO2(110) surfaces. The calculations show that DMMP and P-containing reaction products preferentially bind to the TiO2 surface, while the molecular fragments, i.e., methoxy and methyl, bind to both the Cu4 clusters and TiO2. The Cu4 clusters make the P-O, O-C, and P-C bond cleavages of DMMP markedly more exothermic. The Cu4 clusters are highly fluxional with atomic structures that depend on the configuration of fragments bound to them. Finally, the manifold of P 2p chemical shifts calculated for a large number of energetically favorable configurations of decomposition products is in good agreement with the observed XPS spectra and provides an alternative way of interpreting incompletely resolved core-level spectra using an ensemble of observed structures.

Scalable Customization of Crystallographic Plane Controllable Lithium Metal Anodes for Ultralong-Lasting Lithium Metal Batteries.

A formidable challenge to achieve the practical applications of rechargeable lithium (Li) metal batteries (RLMBs) is to suppress the uncontrollable growth of Li dendrites. One of the most effective solutions is to fabricate Li metal anodes with specific crystal plane, but still lack of a simple and high-efficient approach. Herein, to overcome this key challenge, we report a facile and controllable way for the scalable customization of polished Li metal anodes with highly preferred (110) and (200) crystallographic orientation (donating as polished Li(110) and polished Li(200), respectively) by regulating the times of accumulative roll bonding at room temperature. In light of the inherent characteristics of polished Li(110) and polished Li(200), the influence of Li atomic structure on the electrochemical performance of RLMBs is deeply elucidated by combining theoretical calculations with relative experimental proofs. In particular, polished Li(110) crystal plane is demonstrated to induce Li+ uniform deposition, promoting the formation of flat and dense Li deposits. Impressively, the polished Li(110)||LiFePO4 full cells exhibit unprecedented cycling stability with 10000 cycles at 10 C almost without capacity degradation, indicating the great potential application prospect of such textured Li metal. More valuably, this work provides an important reference for low-cost, continued, and large-scale production of Li metal anodes with highly preferred crystal orientation through roll-to-roll manufacturability. This article is protected by copyright. All rights reserved.

Atomic structure of a NbTiN/AlN/NbTiN Josephson junction grown by molecular-beam epitaxy

Atomic structure of a NbTiN/AlN/NbTiN Josephson junction grown by molecular-beam epitaxy

Current problems in the field of structure, properties of minerals and methods of their investigation

The main goal of research into the structure and properties of minerals, as well as their crystal chemistry and physics, consists in obtaining fundamental information about the actual atomic and electronic structure of mineral objects and physical regularities of their transformations under the influence of external factors (temperature, pressure, radiation, and environmental chemistry). Such information forms the basis for mineral typification and restoration of mineral crystallization conditions and their evolution in a certain geological situation. This information is widely used in petrogenetic and geochronological constructions. Such studies are also relevant to the development of nature-like technologies for obtaining new promising functional materials. Knowledge of the structure, crystal chemistry, and physics of minerals, typomorphism of their spectroscopic properties, as well as the development of analytical techniques and methods for the synthesis of mineral-like materials are of particular significance. This thematic issue of the Lithosphere journal aims to review of these problems in the context of the materials reported at the XIII All-Russian Scientific Conference “Minerals: Structure, Properties, Research Methods” held in 2023 at the Institute of Geology and Geochemistry of the Ural Branch of the Russian Academy of Sciences in Yekaterinburg.

Atomistic to continuum mechanics description of crystal defects with dislocation density fields: Application to dislocations and grain boundaries

The atomic structure of crystal defects such as dislocations, grain or phase boundaries, control these defects’ properties: their mobility, ability to cross-slip, or solute segregation. These crystal defects can be conveniently studied by atomistic simulations and one then needs to transfer relevant information at the upper scale to model microstructures containing a large number of defects, e.g., a polycrystal. Here, we propose an atomistic to continuum mechanics crossover method that (i) represents the atomic structure of dislocations cores by an appropriate Nye dislocation density tensor field and (ii), captures quantitatively the short and long range mechanical fields of defects. For (i), we propose a modified and improved interpolation method based on the original work by Hartley and Mishin. For (ii), we use a field dislocation mechanics framework that rigorously calculates/evaluates the mechanical fields associated with any Nye dislocation density distribution. The transfer method relies on molecular static calculations using two energetic models — ab-initio for screw dislocation core simulations in tungsten, and EAM potential for low and large angle grain boundaries in copper. Our findings demonstrate the effectiveness of the proposed approach in reconstructing the Burgers vector, and continuous strain and rotation fields. The framework is further applied to analyze the elastic interactions between extrinsic edge dislocations and a low angle grain boundary in copper.

High-Quality Data Enabling Universality of Band Gap Descriptor and Discovery of Photovoltaic Perovskites.

Extensive machine-learning-assisted research has been dedicated to predicting band gaps for perovskites, driven by their immense potential in photovoltaics. Yet, the effectiveness is often hampered by the lack of high-quality band gap data sets, particularly for perovskites involving d orbitals. In this work, we consistently calculate a large data set of band gaps with a high level of accuracy, which is rigorously validated by experimental and state-of-the-art GW band gaps. Leveraging this achievement, our machine-learning-derived descriptor exhibits exceptional universality and robustness, proving effectiveness not only for single and double, halide and oxide perovskites regardless of the underlying atomic structures but also for hybrid organic-inorganic perovskites. With this approach, we comprehensively explore up to 15,659 materials, unveiling 14 unreported lead-free perovskites with suitable band gaps for photovoltaics. Notably, MASnBr3, FA2SnGeBr6, MA2AuAuBr6, FA2AuAuBr6, FA2InBiCl6, FA2InBiBr6, and Ba2InBiO6 stand out with direct band gaps, small effective masses, low exciton binding energies, and high stabilities.

Synthesis, atomic structure and electronic properties of ferroelectric AgBiP2Se6 ultrathin flakes

Layered transition metal thiophosphate ABP2X6(A=Ag or Cu, B=V, Cr, In or Bi, X=S or Se) as a promising 2D ferroelectric material, has attracted great attention nowadays. In this work, ultrathin AgBiP2Se6 sheets down to 6nm were synthesized for the first time. Atomic force microscopy, double spherical aberration scanning TEM and Raman spectra were performed to investigate the morphology, atomic structure and vibration modes of the samples. The first-principles calculations utilizing density-functional theory(DFT) were also used to analyze the electronic properties, band structures and projected density of states (PDOS) for both ferroelectric (FE) and paraelectric(PE) states of AgBiP2Se6 monolayer.

Discharge and ignition mechanism of high-entropy alloy induced by crack propagation under quasi-static compressive load

In order to reveal the discharge and ignition mechanism of high-entropy alloy under quasi-static compression load, the stress, potential and ignition evolution process of high-entropy alloy with prefabricated cracks were tested. The atomic structure and dislocation evolution of high-entropy alloy during crack propagation and compression were determined by molecular dynamics simulation, and the discharge mechanism of crack tip was analyzed at the micro level. Based on the calculation of Gibbs free energy, the products in the ignition reaction process were predicted. The results of mechanical/thermal/electrical characteristics induced by compressive load show that the discharge usually occurs near the ignition moment of specimen fracture, and the maximum potential signal can reach 34.2 V. The formation of crack group, crack propagation, local stress concentration, charge accumulation and release at the crack tip jointly induce the generation of discharge signals. With the propagation of cracks, a large number of stacking faults appear and a diamond-shaped failure zone is formed. The increase of disordered atoms leads to fracture. During the compression process, a large number of dislocations induce the separation of charges, which aggravates the discharge at the crack tip. In the Hf-Zr-Ti-Ta-Nb-Cu high-entropy alloy system, the reaction product Ta2O5 is preferentially generated, while in the Ti–Zr-Hf-Cu system, Ti2O3 is preferentially generated. The tip discharge and chemical bond fracture during crack propagation induce ignition, and the chemical bond recombines with energy release.

The collective photothermal effect of silver nanoparticles probed by a microbolometer

The collective photothermal effect of silver nanoparticles probed by a microbolometer