Effects of Voigt diffraction peak profiles on the pair distribution function

Powder diffraction and pair distribution function (PDF) analysis are well established techniques for investigation of atomic configurations in crystalline materials, and the two are related by a Fourier transformation. In diffraction experiments, structural information, such as crystallite size and microstrain, is contained within the peak profile function of the diffraction peaks. However, the effects of the PXRD (powder X-ray diffraction) peak profile function on the PDF are not fully understood. Here, all the effects from a Voigt diffraction peak profile are solved analytically, and verified experimentally through a high-quality X-ray total scattering measurement on Ni powder. The Lorentzian contribution to the microstrain broadening is found to result in Voigt-shaped PDF peaks. Furthermore, it is demonstrated that an improper description of the Voigt shape during model refinement leads to overestimation of the atomic displacement parameter.

The Thermal Stability of Janus Monolayers SnXY (X, Y = O, S, Se): Ab-Initio Molecular Dynamics and Beyond

In recent years, the Janus monolayers have attracted tremendous attention due to their unique asymmetric structures and intriguing physical properties. However, the thermal stability of such two-dimensional systems is less known. Using the Janus monolayers SnXY (X, Y = O, S, Se) as a prototypical class of examples, we investigate their structure evolutions by performing ab-initio molecular dynamics (AIMD) simulations at a series of temperatures. It is found that the system with higher thermal stability exhibits a smaller difference in the bond length of Sn–X and Sn–Y, which is consistent with the orders obtained by comparing their electron localization functions (ELFs) and atomic displacement parameters (ADPs). In principle, the different thermal stability of these Janus structures is governed by their distinct anharmonicity. On top of these results, we propose a simple rule to quickly predict the maximum temperature up to which the Janus monolayer can stably exist, where the only input is the ADP calculated by the second-order interatomic force constants rather than time-consuming AIMD simulations at various temperatures. Furthermore, our rule can be generalized to predict the thermal stability of other Janus monolayers and similar structures.

Timing Performance Simulation for 3D 4H-SiC Detector

To meet the high radiation challenge for detectors in future high-energy physics, a novel 3D 4H-SiC detector was investigated. Three-dimensional 4H-SiC detectors could potentially operate in a harsh radiation and room-temperature environment because of its high thermal conductivity and high atomic displacement threshold energy. Its 3D structure, which decouples the thickness and the distance between electrodes, further improves the timing performance and the radiation hardness of the detector. We developed a simulation software—RASER (RAdiation SEmiconductoR)—to simulate the time resolution of planar and 3D 4H-SiC detectors with different parameters and structures, and the reliability of the software was verified by comparing the simulated and measured time-resolution results of the same detector. The rough time resolution of the 3D 4H-SiC detector was estimated, and the simulation parameters could be used as guideline to 3D 4H-SiC detector design and optimization.

High-Precision X-ray Total Scattering Measurements Using a High-Accuracy Detector System

The total scattering method, which is based on measurements of both Bragg and diffuse scattering on an equal basis, has been still challenging even by means of synchrotron X-rays. This is because such measurements require a wide coverage in scattering vector Q, high Q resolution, and a wide dynamic range for X-ray detectors. There is a trade-off relationship between the coverage and resolution in Q, whereas the dynamic range is defined by differences in X-ray response between detector channels (X-ray response non-uniformity: XRNU). XRNU is one of the systematic errors for individual channels, while it appears to be a random error for different channels. In the present study, taking advantage of the randomness, the true sensitivity for each channel has been statistically estimated. Results indicate that the dynamic range of microstrip modules (MYTHEN, Dectris, Baden-Daettwil, Switzerland), which have been assembled for a total scattering measurement system (OHGI), has been successfully restored from 104 to 106. Furthermore, the correction algorithm has been optimized to increase time efficiencies. As a result, the correcting time has been reduced from half a day to half an hour, which enables on-demand correction for XRNU according to experimental settings. High-precision X-ray total scattering measurements, which has been achieved by a high-accuracy detector system, have demonstrated valence density studies from powder and PDF studies for atomic displacement parameters.

Atomic-Scale Insights on Large-Misfit Heterointerfaces in LSMO/MgO/c-Al2O3

Understanding the interfaces in heterostructures at an atomic scale is crucial in enabling the possibility to manipulate underlying functional properties in correlated materials. This work presents a detailed study on the atomic structures of heterogeneous interfaces in La0.7Sr0.3MnO3 (LSMO) film grown epitaxially on c-Al2O3 (0001) with a buffer layer of MgO. Using aberration-corrected scanning transmission electron microscopy, we detected nucleation of periodic misfit dislocations at the interfaces of the large misfit systems of LSMO/MgO and MgO/c-Al2O3 following the domain matching epitaxy paradigm. It was experimentally observed that the dislocations terminate with 4/5 lattice planes at the LSMO/MgO interface and with 12/13 lattice planes at the MgO/c-Al2O3 interface. This is consistent with theoretical predictions. Using the atomic-resolution image data analysis approach to generate atomic bond length maps, we investigated the atomic displacement in the LSMO/MgO and MgO/c-Al2O3 systems. Minimal presence of residual strain was shown at the respective interface due to strain relaxation following misfit dislocation formation. Further, based on electron energy-loss spectroscopy analysis, we confirmed an interfacial interdiffusion within two monolayers at both LSMO/MgO and MgO/c-Al2O3 interfaces. In essence, misfit dislocation configurations of the LSMO/MgO/c-Al2O3 system have been thoroughly investigated to understand atomic-scale insights on atomic structure and interfacial chemistry in these large misfit systems.

Orientation Dependent Mechanical Responses and Plastic Deformation Mechanisms of ZnSe Nano Films under Nanoindentation

Although ZnSe has been widely studied due to its attractive electronic and optoelectronic properties, limited data on its plastic deformations are available. Through molecular dynamics simulations, we have investigated the indentations on the (001), (110), and (111) planes of ZnSe nano films. Our results indicate that the elastic modulus, incipient plasticity, elastic recovery ratio, and the structural evolutions during the indenting process of ZnSe nano films show obvious anisotropy. To analyze the correlation of structural evolution and mechanical responses, the atomic displacement vectors, atomic arrangements, and the dislocations of the indented samples are analyzed. Our simulations revealed that the plastic deformations of the indented ZnSe nano films are dominated by the nucleation and propagation of 1/2<110> type dislocations, and the symmetrically distributed prismatic loops emitted during the indenting process are closely related with the mechanical properties. By studying the evolutions of microstructures, the formation process of the dislocations, as well as the formation mechanisms of the emitted prismatic loops under the indented crystalline planes are discussed. The results presented in this work not only provide an answer for the questions about indentation responses of ZnSe nano films, but also offer insight into its plastic deformation mechanisms.

Modification of SiO2, ZnO, Fe2O3 and TiN Films by Electronic Excitation under High Energy Ion Impact

It has been known that the modification of non-metallic solid materials (oxides, nitrides, etc.), e.g., the formation of tracks, sputtering representing atomic displacement near the surface and lattice disordering are induced by electronic excitation under high-energy ion impact. We have investigated lattice disordering by the X-ray diffraction (XRD) of SiO2, ZnO, Fe2O3 and TiN films and have also measured the sputtering yields of TiN for a comparison of lattice disordering with sputtering. We find that both the degradation of the XRD intensity per unit ion fluence and the sputtering yields follow the power-law of the electronic stopping power and that these exponents are larger than unity. The exponents for the XRD degradation and sputtering are found to be comparable. These results imply that similar mechanisms are responsible for the lattice disordering and electronic sputtering. A mechanism of electron–lattice coupling, i.e., the energy transfer from the electronic system into the lattice, is discussed based on a crude estimation of atomic displacement due to Coulomb repulsion during the short neutralization time (~fs) in the ionized region. The bandgap scheme or exciton model is examined.

Protein Structure Prediction Using a Maximum Likelihood Formulation of a Recurrent Geometric Network

Only ~40% of the human proteome has structural coordinates available from experiment (i.e., X-ray crystallography, NMR spectroscopy, or cryo-EM) or homology modeling with quality templates (i.e., 30% sequence identity or greater), leaving most of the proteome structurally unsolved. Deep learning (DL) methods for predicting protein structure can help close knowledge gaps where experimental and homology models are difficult to obtain. Recent advances in these DL methods have shown promising results in expanding structural coverage to the scale of the entire human proteome, providing researchers with more complete protein structural information. Here, we improve upon an existing DL algorithm for protein structure prediction, the Recurrent Geometric Network (RGN). We first expand the training dataset to include experimental uncertainty data in the form of atomic displacement parameters, then derive a maximum likelihood loss function that incorporates this uncertainty data into model training. Compared to the original RGN, our novel maximum likelihood model improves the rate of convergence of initial model training and ultimately results in more accurate structure prediction according to the root mean square deviation (RMSD) of backbone atoms, the Global Distance Test (GDT), the Global Distance Test High Accuracy (GDT-HA), and the Template-Modeling Score (TM-Score). Our model also predicts structures with more favorable backbone torsions, which provide more accurate starting coordinates for downstream physics-based simulations. Based on these results, our maximum likelihood reformulation provides a framework for improving existing or future machine learning algorithms for protein structure prediction. The augmented dataset, data collection scripts, reformulated RGN source code, and a series of trained models are publicly available at https://github.com/SchniedersLab/likelihood-rgn.

Exploring ligand dynamics in protein crystal structures with ensemble refinement

Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein–ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein–ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and R free values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.