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Accelerating self-consistent field iterations in Kohn-Sham density functional theory using a low-rank approximation of the dielectric matrix

We present an efficient preconditioning technique for accelerating the fixed-point iteration in real-space Kohn-Sham density functional theory (DFT) calculations. The preconditioner uses a low-rank approximation of the dielectric matrix (LRDM) based on Gâteaux derivatives of the residual of fixed-point iteration along appropriately chosen direction functions. We develop a computationally efficient method to evaluate these Gâteaux derivatives in conjunction with the Chebyshev filtered subspace iteration procedure, an approach widely used in large-scale Kohn-Sham DFT calculations. Further, we propose a variant of LRDM preconditioner based on adaptive accumulation of low-rank approximations from previous self-consistent field iterations, and also extend the LRDM preconditioner to spin-polarized Kohn-Sham DFT calculations. We demonstrate the robustness and efficiency of the LRDM preconditioner against other widely used preconditioners on a range of benchmark systems with sizes ranging from ~100 to 1100 atoms (~500–20,000 electrons). The benchmark systems include various combinations of metal-insulating-semiconducting heterogeneous material systems, nanoparticles with localized d orbitals near the Fermi energy, nanofilm with metal dopants, and magnetic systems. In all benchmark systems, the LRDM preconditioner converges robustly within 20–30 iterations. In contrast, other widely used preconditioners show slow convergence in many cases, as well as divergence of the fixed-point iteration in some cases. Lastly, we demonstrate the computational efficiency afforded by the LRDM method, with up to 3.4-fold reduction in computational cost for the total ground-state calculation compared to other preconditioners.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Defect suppression in wet-treated etched-and-regrown nonpolar m-plane GaN vertical Schottky diodes: A deep-level optical spectroscopy analysis

In this work, steady-state photocapacitance (SSPC) was conducted on nonpolar m-plane GaN n-type Schottky diodes to evaluate the defects induced by inductively coupled plasma (ICP) dry etching in etched-and-regrown unipolar structures. An ~10× increase in the near-midgap Ec – 1.9 eV level compared to an as-grown material was observed. Defect levels associated with regrowth without an etch were also investigated. The defects in the regrown structure (without an etch) are highly spatially localized to the regrowth interface. Subsequently, by depth profiling an etched-and-regrown sample, we show that the intensities of the defect-related SSPC features associated with dry etching depend strongly on the depth away from the regrowth interface, which is also reported previously. A photoelectrochemical etching (PEC) method and a wet AZ400K treatment are also introduced to reduce the etch-induced deep levels. A significant reduction in the density of deep levels is observed in the sample that was treated with PEC etching after dry etching and prior to regrowth. An ~2× reduction in the density of Ec – 1.9 eV level compared to a reference etched-and-regrown structure was observed upon the application of PEC etching treatment prior to the regrowth. The PEC etching method is promising for reducing defects in selective-area doping for vertical power switching structures with complex geometries.

36 MATERIALS SCIENCE↗

Surface Modification of Nickel-Rich Cathode Materials by Ionically Conductive Materials at Room Temperature

Nickel-rich cathode materials (LiNi x Mn y Co 1-x-y O 2 , NMC) are promising to push the limits of lithium-ion batteries to higher energy density. This approach is favored in practical applications including electric vehicles and aviation transportation. However, the instability of the NMC at charged state results in safety concerns and poor cycling stability. Surface coating is a practical and effective strategy to address this. Cubic Li7La3Zr2O12 (LLZO) is an ideal coating material regarding the low electron transfer rate and high Li+ conductivity. Thus, a LLZO coating layer can suppress the parasitic reactions in the electrode/electrolyte interface without deteriorating the lithium migration. However, high-temperature calcination seems to inevitably create the chemical couplings between NMC and LLZO, leading to the interdiffusion and degradation of NMC and LLZO crystal structures. This work presents a simple mechanochemical method to effectively coat LLZO on the NMC particle surface. Furthermore, the coated cathode demonstrates superior electrochemical performance compared with the pristine NMC cathode.

25 ENERGY STORAGE↗

Robust Spectral Anomaly Detection in EELS Spectral Images via 3D Convolutional Variational Autoencoders

Abstract A 3D Convolutional Variational Autoencoder (3D‐CVAE) is introduced for automated anomaly detection in electron energy‐loss spectroscopy spectrum imaging (EELS‐SI) data. This approach leverages the full 3D structure of EELS‐SI data to detect subtle spectral anomalies while preserving both spatial and spectral correlations across the datacube. By employing cross‐entropy loss and training on bulk spectra, the model learns to reconstruct bulk features characteristic of the defect‐free material. In exploring methods for anomaly detection, both the 3D‐CVAE approach and principal component analysis (PCA) are evaluated, testing their performance using FeL‐edge ΔEpeak shifts designed to simulate material defects. These results show that 3D‐CVAE achieves superior anomaly detection and maintains consistent performance across various shift magnitudes. The method demonstrates clear bimodal separation between bulk and anomalous spectra, enabling reliable classification. Further analysis verifies that lower‐dimensional representations are robust to anomalies in the data. While performance advantages over PCA diminish with decreasing anomaly concentration, our method maintains high reconstruction quality even in challenging, noise‐dominated spectral regions. This approach provides a robust framework for unsupervised automated detection of spectral anomalies in EELS‐SI data, particularly valuable for analyzing complex material systems.

Chemistry↗

Microsphere LiMn 0.6 Fe 0.4 PO 4 /C cathode with unique rod-like secondary architecture for high energy lithium ion batteries

LiMn x Fe 1-x PO 4 /C is considered a promising next-generation cathode material with significant commercial potential, inheriting the safety of LiFePO 4 while offering higher energy densities. However, the extremely low conductivity and the Jahn-Teller effect induced by Mn 3+ limit its practical capacity and rate performance. Effective modifications can be achieved through particle nanonization and uniform carbon coating. Here, in this work, we synthesized microspherical LiMn 0.6 Fe 0.4 PO 4 /C cathode materials using a hydrothermal method combined with spray drying carbon coating. The cathode material exhibits a microsphere structure composed of aggregated nanorods with a uniform 3 nm carbon coating, showing good dispersibility, small specific surface area and high tap density. In-situ diffraction analysis showed that expanding the single-phase solid solution region during (de)lithiation can reduce the energy barrier for electron transport, improve the kinetics of the (dis)charge process, and enhance both cycling and rate performance. The initial capacity at 0.1C can reach 155 mAh/g, and the capacity remains at 133.5 mAh/g with a retention rate of 97.1 % after 300 cycles. The synergistic effect of particle nanonization and uniform carbon coating endows the LiMn x Fe 1-x PO 4 /C material with excellent electrochemical performance.

25 ENERGY STORAGE↗

Main and Satellite Features in the Ni 2p XPS of NiO

The origin and assignment of the complex main and satellite XPS features of the cations in ionic compounds has been the subject of extensive theoretical studies using different methods. There is agreement that within a molecular orbital model one needs to take into account different types of configurations. Specifically, those where a core electron is removed but no other configuration changes are made and those where in addition to ionization there are also shake or charge transfer changes to the ionic configuration. However, there are strong disagreements about the assignment of XPS features to these configurations. The present work is directed toward resolving the origin of main and satellite features for the Ni 2p XPS of NiO based on ab initio molecular orbital wavefunctions for a cluster model of NiO. A major problem in earlier ab initio XPS studies of ionic compounds has been the use of a common set of orbitals that was not able to properly describe all the ionic configurations that contribute to the full XPS spectra. This is resolved in the present work by using orbitals that are optimized for averages of the occupations of the different configurations that contribute to the XPS. The approach of using State Averaged orbitals is validated through comparisons between different averages and through use of higher order excitations in the wavefunctions for the ionic states. It represents a major extension of our earlier work on the main and satellite features of the Fe 2p XPS of Fe 2 O 3 and proves the reliability and the generality of the assignments of the character and origin of the different features of the XPS obtained with orbitals optimized for State Averages. These molecular orbital methods permit the characterization of the ionic states in terms of the importance of shake excitations and of the coupling of ionization of 2p 1/2 and 2p 3/2 spin-orbit split sub shells. Further, the work lays the foundation for definitive assignments of the character of main and satellite XPS features and points to their origin in the electronic structure of the material.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design considerations for an ultrahigh-bandwidth Phase Contrast Imaging system applied to fusion grade devices

Abstract The PCI diagnostic is an internal reference interferometer that creates an image of absolutely calibrated electron density fluctuations integrated along the line of sight of the probing light beam. While conventional PCI diagnostics installed on fusion experiments worldwide employ light of wavelength equal to 10.59 μm, the same system using light at 1.55 μm wavelength would extend the spectral response in wave-number and frequency by factors of seven and over one hundred, respectively, thereby potentially providing quantitative measurements of the internal structure of density perturbations induced by either turbulent or radio-frequency waves, simultaneously covering ion to electron gyro-radius scales up to the GHz frequency region. Based on a previously developed 1.55 μm PCI prototype system, constraints to the design for such a diagnostic in fusion grade devices are presented and compared to those faced with the conventional method.

Instruments & Instrumentation↗

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗

Probing Nanocrystal Optical Properties in the Limit of Single Nanocrystals

The Bawendi lab has been at the forefront of the synthesis and characterization of the fundamental photo-physics of quantum confined systems for the past three decades. During this DoE project, our progress has been enabled by both our expertise in single nanocrystal (NC) photoluminescence (PL) spectroscopy as well as our extensive knowledge of the synthetic optimization of various NC semiconductors - all of this forming an efficient feedback loop between characterization and synthesis. Our research in this project has focused on the development and application of novel single emitter optical tools for the characterization of colloidal quantum dots (CQDs) which are semiconducting NCs with size-tunable quantum confined electronic structure. CQDs have had a significant commercial impact as display technologies. They are also commercially available as fluorescent biological markers. CQDs are being investigated as a potential material for photovoltaic or optical sensing applications and as emerging optical quantum materials. We have focused on the fundamental understanding of the optical properties of NCs through the development of novel spectroscopic methods at the single emitter level, including understanding how synthetic and environmental heterogeneities influence NC properties. A major advance in our research has been the development of novel photon resolved correlation spectroscopies that allow us to extract the physics of photo-excited single NCs with unprecedented time and spectral resolution from the photon stream of individual NCs.

36 MATERIALS SCIENCE↗

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 ↗

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