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At least 1,603 records · Page 89

Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies

Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via high-density lipoprotein (HDL) and low-density lipoprotein (LDL) maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics, and to develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep Learning Segmentation of Complex Features in Atomic-Resolution Phase-Contrast Transmission Electron Microscopy Images

Phase-contrast transmission electron microscopy (TEM) is a powerful tool for imaging the local atomic structure of materials. TEM has been used heavily in studies of defect structures of two-dimensional materials such as monolayer graphene due to its high dose efficiency. However, phase-contrast imaging can produce complex nonlinear contrast, even for weakly scattering samples. It is, therefore, difficult to develop fully automated analysis routines for phase-contrast TEM studies using conventional image processing tools. For automated analysis of large sample regions of graphene, one of the key problems is segmentation between the structure of interest and unwanted structures such as surface contaminant layers. In this study, we compare the performance of a conventional Bragg filtering method with a deep learning routine based on the U-Net architecture. We show that the deep learning method is more general, simpler to apply in practice, and produces more accurate and robust results than the conventional algorithm. We provide easily adaptable source code for all results in this paper and discuss potential applications for deep learning in fully automated TEM image analysis.

47 OTHER INSTRUMENTATION↗

p-i-n High-Speed Photodiodes for X-RAY and Infrared Imagers Fabricated by In-Situ -Doped APCVD Germanium Homoepitaxy

Design, simulation, fabrication, and measurement have been performed using a new method for obtaining high-speed p-i-n germanium photodiodes for use in backside imaging arrays. These devices are proof-of-principal in situ-doped vertical mesa structures fabricated using single-wafer, atmospheric-pressure chemical vapor deposition (APCVD) homoepitaxy on Czochralski-grown Ge substrates. Excellent impurity profiles resulting from in situ doping, as measured by spreading-resistance profilometry, were 5 × 10 16 , 2 × 10 15 , and 2 × 10 18 (cm -3 ) for the p-type anode, i-region absorber, and n+ cathode, respectively. Scanning electron microscopy analysis revealed very-low defect densities in the epitaxial layers. The diodes, with diameters ranging 100-500 μm, exhibited excellent ideality (n = 1.15) and less than 1-μA dark current, corresponding to up to 80 kV-cm -1 electric field in the smallest devices. Avalanche breakdown bias was consistently at a magnitude of 50 V or lower. External quantum efficiencies in the near-infrared spectrum peaked at 70%. Pulsed illumination experiments, both in the infrared and X-ray regions, showed pulse rise times in the 100-140 ps range, indicating excellent applicability of this method to high-speed X-ray or infrared applications.

36 MATERIALS SCIENCE↗

Recent Progress in the Electroweak Structure of Light Nuclei Using Quantum Monte Carlo Methods

Nuclei will play a prominent role in searches for physics beyond the Standard Model as the active material in experiments. In order to reliably interpret new physics signals, one needs an accurate model of the underlying nuclear dynamics. In this review, we discuss recent progress made with quantum Monte Carlo approaches for calculating the electroweak structure of light nuclei. We place particular emphasis on recent β decay, muon capture, neutrinoless double β decay, and electron scattering results.

Physics↗

A deep learning approach for semantic segmentation of unbalanced data in electron tomography of catalytic materials

In computed TEM tomography, image segmentation represents one of the most basic tasks with implications not only for 3D volume visualization, but more importantly for quantitative 3D analysis. In case of large and complex 3D data sets, segmentation can be an extremely difficult and laborious task, and thus has been one of the biggest hurdles for comprehensive 3D analysis. Heterogeneous catalysts have complex surface and bulk structures, and often sparse distribution of catalytic particles with relatively poor intrinsic contrast, which possess a unique challenge for image segmentation, including the current state-of-the-art deep learning methods. To tackle this problem, we apply a deep learning-based approach for the multi-class semantic segmentation of a γ-Alumina/Pt catalytic material in a class imbalance situation. Specifically, we used the weighted focal loss as a loss function and attached it to the U-Net’s fully convolutional network architecture. We assessed the accuracy of our results using Dice similarity coefficient (DSC), recall, precision, and Hausdorff distance (HD) metrics on the overlap between the ground-truth and predicted segmentations. Our adopted U-Net model with the weighted focal loss function achieved an average DSC score of 0.96 ± 0.003 in the γ-Alumina support material and 0.84 ± 0.03 in the Pt NPs segmentation tasks. We report an average boundary-overlap error of less than 2 nm at the 90th percentile of HD for γ-Alumina and Pt NPs segmentations. The complex surface morphology of γ-Alumina and its relation to the Pt NPs were visualized in 3D by the deep learning-assisted automatic segmentation of a large data set of high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) tomography reconstructions.

36 MATERIALS SCIENCE↗

A new route to obtain fluorescence X-ray absorption spectra of compounds and to remove the self-absorption induced nonlinearity in the spectra

A new route to obtain fluorescence X-ray absorption spectra of compounds and to remove the self-absorption induced nonlinearity in the spectra is described. The fluorescent intensity If is linearly proportional to the absorption coefficient μ. For studies of surface structures around an element (κ) the fluorescence detection is often the mode of choice. However, the measurement may suffer from a self-absorption (SA) effect which nonlinearly distorts the spectra. The effect is severe when κ is concentrated or the measurements are carried out in certain geometries. Here, the correlations among emission events in compounds are examined following resonance X-ray core-electron excitation within κ. Under conditions leading to SA, If emitted from κ apparently has a conjugated relationship with the fluorescent intensities simultaneously emitted from other elements (ξ). Normalizing the former (κ) by the latter (ξ) will largely remove SA effects and reduce this nonlinear problem to a tractable linear problem. This does result in a moderate reduction of the spectral amplitude due to the so-called secondary emission from ξ excited by the emission from κ. Nonetheless, the resulting spectra will allow one to accurately determine bond distances and disorder and, in some respects, can be superior to spectra obtained via the absorption channel. For μξ < μκ and grazing incidence geometry, the amplitude reduction can be small and simple normalization is sufficient to restore the spectral integrity with remarkable accuracy. This has been instrumental in unravelling the surface and subsurface structures around cations in amorphous Ga–In–O and Zn–Sn–O films which are otherwise inaccessible due to severe SA effects. This method has also been applied to several samples with μξ ≃ μκ to examine its applicability. For these samples, the amplitude reduction is 12 ± 4% versus their standards for the data measured with the classical 45°/45° geometry. This experimental method is easy to implement. Since If from κ and ξ are measured by the same detector system, it is also superior to other methods in removing systematic errors such as detector system nonlinearity, electronic noise, and some beam instabilities, and in removing spectral imperfections due to, for example, SA effects, diffraction effects and sample inhomogeneity. The distortions resulting from the latter can be severe in the spectra measured in transmission mode.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Performing In Situ Closed-Cell Gas Reactions in the Transmission Electron Microscope

Gas reactions studied by in situ electron microscopy can be used to capture the real-time morphological and microchemical transformations of materials at length scales down to the atomic level. In situ closed-cell gas reaction (CCGR) studies performed using (scanning) transmission electron microscopy (STEM) can separate and identify localized dynamic reactions, which are extremely challenging to capture using other characterization techniques. For these experiments, we used a CCGR holder that utilizes microelectromechanical systems (MEMS)-based heating microchips (hereafter referred to as "E-chips"). The experimental protocol described here details the method for performing in situ gas reactions in dry and wet gases in an aberration-corrected STEM. This method finds relevance in many different materials systems, such as catalysis and high-temperature oxidation of structural materials at atmospheric pressure and in the presence of various gases with or without water vapor. Here, several sample preparation methods are described for various material form factors. During the reaction, mass spectra obtained with a residual gas analyzer (RGA) system with and without water vapor further validates gas exposure conditions during reactions. Integrating an RGA with an in situ CCGR-STEM system can, therefore, provide critical insight to correlate gas composition with the dynamic surface evolution of materials during reactions. In situ/operando studies using this approach allow for detailed investigation of the fundamental reaction mechanisms and kinetics that occur at specific environmental conditions (time, temperature, gas, pressure), in real-time, and at high spatial resolution.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Determining the twist angle of stacked MoS 2 layers using machine learning-assisted low-frequency interlayer Raman fingerprints

The investigation of twisted stacked few-layer MoS 2 has revealed novel electronic, optical, and vibrational properties over an extended period. For the successful integration of twisted stacked few-layer MoS 2 into a wide range of applications, it is crucial to employ a noninvasive, versatile technique for characterizing the layered architecture of these complex structures. Here, in this work, we introduce a machine learning-assisted low-frequency Raman spectroscopy method to characterize the twist angle of few-layer stacked MoS 2 samples. A feedforward neural network (FNN) is utilized to analyze the low-frequency breathing mode as a function of the twist angle. Moreover, using finite difference method (FDM) and density functional theory (DFT) calculations, we show that the low-frequency Raman spectra of MoS 2 are mainly influenced by the effect of the nearest and second nearest layers. A new improved linear chain model (TA-LCM) with taking the twist angle into the consideration is developed to understand the interlayer breathing modes of stacked few-layer MoS 2 . This approach can be extended to other 2D materials systems and provides an intelligent way to investigate naturally stacked and twisted interlayer interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analysis of X-ray images and spectra (aXis2000): A toolkit for the analysis of X-ray spectromicroscopy data

Spectromicroscopy refers to analytical methods that combine imaging and spectroscopy to provide detailed, spatially resolved analytical information about a sample, such as the type and quantitative spatial distributions of chemical components, geometric or magnetic alignment information, crystal structure, etc. The analysis of X-ray images and spectra (aXis2000) software described in this work provides a set of routines within a single, integrated, graphical-oriented package to read, display, manipulate and analyze spectromicroscopy data, with particular focus on soft X-ray spectromicroscopy methods such as scanning transmission X-ray microscopy (STXM), X-ray photoemission electron microscopy (XPEEM), scanning photoelectron X-ray microscopy (SPEM) and transmission X-ray microscopy (TXM). Here, this free software is described and compared to other software that can provide similar or complementary capabilities. Examples of spectromicroscopic analyses using advanced features of aXis2000 are provided.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Importance of Engineered and Learned Molecular Representations in Predicting Organic Reactivity, Selectivity, and Chemical Properties

Machine-readable chemical structure representations are foundational in all attempts to harness machine learning for the prediction of reactivities, selectivities, and chemical properties directly from molecular structure. The featurization of discrete chemical structures into a continuous vector space is a critical phase undertaken before model selection, and the development of new ways to quantitatively encode molecules is an active area of research. Here, we highlight the application and suitability of different representations, from expert-guided “engineered” descriptors to automatically “learned” features, in different prediction tasks relevant to organic and organometallic chemistry, where differing amounts of training data are available. These tasks include statistical models of stereo- and enantioselectivity, thermochemistry, and kinetics developed using experimental and quantum chemical data. The use of expert-guided molecular descriptors provides an opportunity to incorporate chemical knowledge, domain expertise, and physical constraints into statistical modeling. In applications to stereoselective organic and organometallic catalysis, where data sets may be relatively small and 3D-geometries and conformations play an important role, mechanistically informed features can be used successfully to obtain predictive statistical models that are also chemically interpretable. We provide an overview of several recent applications of this approach to obtain quantitative models for reactivity and selectivity, where topological descriptors, quantum mechanical calculations of electronic and steric properties, along with conformational ensembles, all feature as essential ingredients of the molecular representations used. Alternatively, more flexible, general-purpose molecular representations such as attributed molecular graphs can be used with machine learning approaches to learn the complex relationship between a structure and prediction target. This approach has the potential to out-perform more traditional representation methods such as “hand-crafted” molecular descriptors, particularly as data set sizes grow. One area where this is particularly relevant is in the use of large sets of quantum mechanical data to train quantitative structure–property relationships. A general approach toward curating useful data sets and training highly accurate graph neural network models is discussed in the context of organic bond dissociation enthalpies, where this strategy outperforms regression using precomputed descriptors. Finally, we describe how graph neural network predictions can be incorporated into mechanistically informed statistical models of chemical reactivity and selectivity. Once trained, this approach avoids the expensive computational overhead associated with quantum mechanical calculations, while maintaining chemical interpretability. We illustrate examples for which fast predictions of bond dissociation enthalpy and of the identities of radicals formed through cleavage of a molecule’s weakest bond are used in simple physical models of site-selectivity and reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A 2A receptor (A 2A AR) at 2.0 Å resolution is determined and compared with previous A 2A AR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reviewing computational studies of defect formation and behaviors in carbon fiber structural units

Solid-state carbon materials, such as graphite and graphene, are at the forefront of materials research because of their unique electronic, vibrational, and mechanical properties, leading to a broad range of potential and realized applications. One key application is their role as basic structural units of carbon fiber (CF), a lightweight alternative to steel. In CF, a delicate relationship exists between ultimate material strength and the atomic-scale density of defects contained at the inter- and intra-subunit levels. Computational studies provide insight into the stability of various types of defects that can form in these systems and connect with experimental observables such as bandgap and spectroscopic measurements. Therefore, the literature contains many computational studies that focus on changes induced by defects, including vacancies and Dienes transformations (Stone-Wales and Thrower defects). However, wide-ranging methods and cell sizes have been used, and property-specific information is often lacking. Furthermore, this review summarizes key literature findings, paying particular attention to changes in the electronic, vibrational, and mechanical properties induced by defects in graphitic materials relevant to CF.

36 MATERIALS SCIENCE↗

Tunable Semiconducting Behavior and Linear-Nonlinear Optical Properties of Ag–Sn Dual-Doped Nanocrystalline CdO Thin Films for Optoelectronics

Semiconductor-based thin films have a great impact on determining the anticipated optoelectronic device construction and the advancement of cutting-edge applications. Herein, Ag and Sn dual-doped nanocrystalline transparent conducting CdO thin films were prepared on glass substrates using a cost-effective spray coating method, and their structural, morphological, optical, and semiconducting behaviors were investigated. The successful incorporation of Ag and Sn resulted in the polycrystalline nature of the deposited films without the additional peaks, as verified by X-ray diffraction (XRD) analysis. The XRD report also revealed the enhanced crystallinity (65%) at the higher doping level (3 wt % Ag and Sn-doped CdO film). All the deposited CdO films exhibited homogeneous, spherical, or round-shaped grains, with agglomeration revealed by scanning electron microscopy analysis. UV–visible spectroscopy was utilized to determine the linear and nonlinear optical properties of the deposited CdO thin films, and a reduction in the band gap from 3.891 to 3.772 eV was observed. A significant enhancement in the first- and third-order nonlinear susceptibility and nonlinear refractive index of the doped CdO films was also observed with increasing doping concentration. Hall effect data were collected at room temperature to investigate the electrical properties of all of the CdO films. The charge carrier concentration of CdO thin films was increased from 142.08 × 10 18 to 169.10 × 10 18 cm –3 , and the highest conductivity was found to be 192 s/cm on doping 3 wt % Ag–Sn. All the CdO thin films exhibited n-type conductivity, while an incredible n-type to p-type charge carrier transition was noticed at a higher doping level (3 wt % Ag–Sn). The findings of the current work are expected to advance the synthesis of semiconductor thin films through cost-effective spray coating methods for optoelectronic device applications.

deposition↗

Visualization of defect induced in-gap states in monolayer MoS 2

Atomic-scale intrinsic defects play a key role in controlling functional electronic properties of two-dimensional (2D) materials. Here, we present a low-temperature scanning–tunneling microscopy and spectroscopy investigation of a common point-defect in monolayer molybdenum disulfide (MoS 2 ). We employ a sample preparation method in which the film surface is never exposed to air so that the native dangling bonds surrounding the defects in the film are preserved. Molybdenum vacancies are identified by their three characteristic in-gap resonances by combining scanning–tunneling measurements with parallel Green’s function-based theoretical modeling. The relative energy shifts between the various in-gap states allow us to identify a relative charge difference between two of the observed vacancies. The role of the substrate on the band structure of the defective MoS 2 monolayer is unveiled. Our study highlights the effects of the substrate on the in-gap states of common defects found in MoS 2 providing a pathway in designing and optimizing 2D materials for electronic applications.

36 MATERIALS SCIENCE↗

Steam‐Induced Coarsening of Single‐Unit‐Cell MFI Zeolite Nanosheets and Its Effect on External Surface Brønsted Acid Catalysis

Abstract Commonly used methods to assess crystallinity, micro‐/mesoporosity, Brønsted acid site density and distribution (in micro‐ vs. mesopores), and catalytic activity suggest nearly invariant structure and function for aluminosilicate zeolite MFI two‐dimensional nanosheets before and after superheated steam treatment. Yet, pronounced reaction rate decrease for benzyl alcohol alkylation with mesitylene, a reaction that cannot take place in the zeolite micropores, is observed. Transmission electron microscopy images reveal pronounced changes in nanosheet thickness, aspect ratio and roughness indicating that nanosheet coarsening and the associated changes in the external (mesoporous) surface structure are responsible for the changes in the external surface catalytic activity. Superheated steam treatment of hierarchical zeolites can be used to alter nanosheet morphology and regulate external surface catalytic activity while preserving micro‐ and mesoporosity, and micropore reaction rates.

Guefrachi, Yasmine↗

Diffusion Monte Carlo approaches for studying nuclear quantum effects in fluxional molecules

Abstract Diffusion quantum Monte Carlo (DMC) provides a powerful approach for obtaining the ground state energy and wave function of molecules, ions, and molecular clusters. The approach is uniquely well suited for studies of fluxional molecules, which undergo large amplitude vibrational motions even in their ground state. In contrast to the electronic structure problem, where the wave function must be antisymmetric with respect to exchange of any pair of electrons, the wave function for the ground vibrational state is nodeless. This greatly simplifies the application of DMC for vibrational problems. Because there is not a single potential function that can be used to describe the intramolecular and intermolecular interactions in all molecular systems, most methods that are used to describe nuclear quantum effects rely on a carefully chosen zero‐order description of the molecular vibrations. In contrast, DMC calculations can be performed in Cartesian coordinates, making the DMC algorithm easily transferable between different chemical systems. In this contribution, the theory that underlies DMC will be discussed along with important considerations for performing DMC calculations. Extensions for evaluating vibrationally excited states and molecular properties are also discussed. Insights that can be obtained from DMC calculations are illustrated in the context of the protonated water clusters. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Theoretical and Physical Chemistry > Spectroscopy

Chemistry↗

Finite temperature properties of uranium mononitride

Uranium mononitride (UN) is a promising nuclear fuel that combines the advantageous properties of readily used UO 2 and uranium alloys, such as high melting temperature and high uranium density, and thermal conductivity, respectively. A better understanding of UN behavior at operating temperatures can be obtained from finite temperature data, such as elastic properties. To get this information, ab initio molecular dynamics (AIMD) simulations were performed at five different temperatures using constant volume (NVT) and constant pressure (NPT) ensembles. Initially, the performance of PBE functional in reproducing experimental crystallographic properties and magnetic ordering is assessed. The finite temperature phonon dispersions are calculated using NVT simulation results, which show a softening of the phonon modes with increasing temperature. The NPT results are used to obtain the thermal expansion of UN and finite temperature electronic properties. The calculated thermal expansion is compared with our measurements using neutron diffraction. Additionally, the temperature dependent elastic properties of UN are evaluated using the strain-stress method in AIMD simulations, indicating that UN becomes softer and more compressible with increasing temperature. Also, the calculated Young’s modulus slope is in very good agreement with the experiment. The finite temperature heat capacity and electronic thermal conductivity are calculated from AIMD simulations, which are in better agreement with the experiment than the heat capacity and thermal conductivity calculated using the structures relaxed at 0K. Finally, the thermal diffusivity from AIMD has opposite temperature dependence compared to experimental results, which we argued comes from the underestimated electronic thermal conductivity.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Effect of 3D-printed surface textures on wear mechanism in 3-body abrasion of soil

This study systematically investigates the enhancement of wear resistance in 3D printed surface textures through both experimental and theoretical approaches. Three distinct surface morphologies (Smooth Surface, Surface with uniformly distributed Pits, and Surface with uniformly distributed Bumps) were fabricated using High-Impact Polystyrene, where the meso-scale textures were precisely controlled through the 3D printing process. Wear behavior was evaluated using a 3-body wear tester in an abrasive particle environment, analyzing the influence of surface textures under various operating conditions. Systematic wear tests revealed that optimally designed surface textures achieved a remarkable 77 % reduction in wear compared to the worst-performing sample. The wear mechanisms were comprehensively characterized through weight loss measurements, Scanning Electron Microscopy (SEM), and Energy Dispersive Spectroscopy (EDS) analyses, elucidating the surface morphology changes and their interaction with wear particles. Notably, the study identified how the geometric characteristics of surface textures influence the movement of wear particles and the distribution of contact stresses. Discrete element method simulations corroborated the experimental findings, providing theoretical validation for the enhanced wear resistance of the optimal structure. The high correlation between simulated wear patterns and experimental results validates the reliability of the proposed design methodology. In conclusion, these results demonstrate that 3D printed surface texturing offers a cost-effective and scalable approach to significantly improve wear resistance in engineering applications, presenting a practical alternative to conventional, high-cost surface engineering methods.

3-body abrasion↗