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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Real-space texture and pole-figure analysis using the 3D pair distribution function on a platinum thin film

An approach is described for studying texture in nanostructured materials. The approach implements the real-space texture pair distribution function (PDF), txPDF, laid out by Gong & Billinge {(2018). arXiv:1805.10342 [cond-mat]}. It is demonstrated on a fiber-textured polycrystalline Pt thin film. The approach uses 3D PDF methods to reconstruct the orientation distribution function of the powder crystallites from a set of diffraction patterns, taken at different tilt angles of the substrate with respect to the incident beam, directly from the 3D PDF of the sample. A real-space equivalent of the reciprocal-space pole figure is defined in terms of interatomic vectors in the PDF and computed for various interatomic vectors in the Pt film. Furthermore, it is shown how a valid isotropic PDF may be obtained from a weighted average over the tilt series, including the measurement conditions for the best approximant to the isotropic PDF from a single exposure, which for the case of the fiber-textured film was in a nearly grazing incidence orientation of ∼10°. Finally, an open-source Python software package, FouriGUI , is described that may be used to help in studies of texture from 3D reciprocal-space data, and indeed for Fourier transforming and visualizing 3D PDF data in general.

3D pair distribution functions↗
DOE OSTI2025

Accounting for electron-beam-induced warping of molecular nanocrystals in MicroED structure determination

High-energy electrons induce sample damage and motion at the nanoscale to fundamentally limit the determination of molecular structures by electron diffraction. Using a fast event-based electron counting (EBEC) detector, we characterize beam-induced, dynamic, molecular crystal lattice reorientations (BIRs). These changes are sufficiently large to bring reciprocal lattice points entirely in or out of intersection with the sphere of reflection, occur as early events in the decay of diffracted signal due to radiolytic damage, and coincide with beam-induced migrations of crystal bend contours within the same fluence regime and at the same illuminated location on a crystal. These effects are observed in crystals of biotin, a series of amino acid metal chelates, and a six-residue peptide, suggesting that incident electrons inevitably warp molecular lattices. The precise orientation changes experienced by a given microcrystal are unpredictable but are measurable by indexing individual diffraction patterns during beam-induced decay. Reorientations can often tilt a crystal lattice several degrees away from its initial position before irradiation, and for an especially beam-sensitive Zn(II)-methionine chelate, are associated with dramatic crystal quakes prior to 1 e − Å −2 electron beam fluence accumulates. Since BIR coincides with the early stages of beam-induced damage, it echoes the beam-induced motion observed in single-particle cryoEM. As with motion correction for cryoEM imaging experiments, accounting for BIR-induced errors during data processing could improve the accuracy of MicroED data.

Vlahakis, Niko (ORCID:0000000250920265)↗
DOE OSTI2024

An Active Learning-Based Streaming Pipeline for Reduced Data Training of Structure Finding Models in Neutron Diffractometry

Structure determination workloads in neutron diffractometry are computationally expensive and routinely require several hours to many days to determine the structure of a material from its neutron diffraction patterns. The potential for machine learning models trained on simulated neutron scattering patterns to significantly speed up these tasks have been reported recently. However, the amount of simulated data needed to train these models grows exponentially with the number of structural parameters to be predicted and poses a significant computational challenge. To overcome this challenge, we introduce a novel batch-mode active learning (AL) policy that uses uncertainty sampling to simulate training data drawn from a probability distribution that prefers labelled examples about which the model is least certain. We confirm its efficacy in training the same models with ∼ 75% less training data while improving the accuracy. We then discuss the design of an efficient stream-based training workflow that uses this AL policy and present a performance study on two heterogeneous platforms to demonstrate that, compared with a conventional training workflow, the streaming workflow delivers ∼ 20% shorter training time without any loss of accuracy.

Wang, Tianle [Brookhaven National Laboratory (BNL)↗
DOE OSTI2022

Real-Time Interactive 4D-STEM Phase-Contrast Imaging From Electron Event Representation Data: Less computation with the right representation

The arrival of direct electron detectors (DED) with high frame-rates in the field of scanning transmission electron microscopy has enabled many experimental techniques that require collection of a full diffraction pattern at each scan position, a field which is subsumed under the name four dimensional-scanning transmission electron microscopy (4D-STEM). DED frame rates approaching 100 kHz require data transmission rates and data storage capabilities that exceed commonly available computing infrastructure. Current commercial DEDs allow the user to make compromises in pixel bit depth, detector binning or windowing to reduce the per-frame file size and allow higher frame rates. This change in detector specifications requires decisions to be made before data acquisition that may reduce or lose information that could have been advantageous during data analysis. The 4D Camera, a DED with 87 kHz frame-rate developed at Lawrence Berkeley National Laboratory, reduces the raw data to a linear-index encoded electron event representation (EER). Here we show with experimental data from the 4D Camera that linear-index encoded EER and its direct use in 4D-STEM phase contrast imaging methods enables real-time, interactive phase-contrast from large-area 4D-STEM datasets. Furthermore, we detail the computational complexity advantages of the EER and the necessary computational steps to achieve real-time interactive ptychography and center-of-mass differential phase contrast using commonly available hardware accelerators.

4D-STEM↗
DOE OSTI2023

Projected Multi-Agent Consensus Equilibrium (PMACE) With Application to Ptychography

Multi-Agent Consensus Equilibrium (MACE) formulates an inverse imaging problem as a balance among multiple update agents such as data-fitting terms and denoisers. However, each such agent operates on a separate copy of the full image, leading to redundant memory use and slow convergence when each agent affects only a small subset of the full image. In this article, we extend MACE to Projected Multi-Agent Consensus Equilibrium (PMACE), in which each agent updates only a projected component of the full image, thus greatly reducing memory use for some applications. We describe PMACE in terms of an equilibrium problem and an equivalent fixed-point problem and show that in most cases the PMACE equilibrium is not the solution of an optimization problem. To demonstrate the value of PMACE, we apply it to the problem of ptychography, in which a sample is reconstructed from the diffraction patterns resulting from coherent X-ray illumination at multiple overlapping spots. In our PMACE formulation, each spot corresponds to a separate data-fitting agent, with the final solution found as an equilibrium among all the agents. In conclusion, our results demonstrate that the PMACE reconstruction algorithm generates more accurate reconstructions at a lower computational cost than existing ptychography algorithms when the spots are sparsely sampled.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Simplex‐based model for nanoparticle grain identification in four‐dimensional scanning transmission electron microscopy data

Grain identification in polycrystalline nanoparticles, for example, determining which crystal phases are present at each spatial location, is fundamental to materials characterisation. This is particularly challenging when grains overlap extensively, as commonly occurs in four-dimensional scanning transmission electron microscopy (4D-STEM) datasets. We propose a simplex-based model (SBM) in which each simplex vertex represents the diffraction pattern (DP) of a pure grain, and the simplex edges and interior represent overlapping grains. Our SBM grain identification algorithm operates on the Bragg disk (BD) data matrix distilled from the 4D-STEM data to identify the grain membership at each scan position, together with a BD feature matrix whose columns represent the DPs for each constituent grain, which is important for identifying the crystal structure of each grain. We solve the model using a two-stage algorithm. In Stage 1, we adapt a linear mixing algorithm to estimate an initial BD feature matrix whose columns represent DPs of potentially overlapping grains. Our Stage 2 algorithm incorporates sparsity considerations to transform the initial BD feature matrix so that its columns represent DPs of pure grains. Using simulated datasets with various grain configurations, we demonstrate that SBM recovers both the BD feature matrix and membership maps more accurately than existing methods, even when a grain lacks any pure region and completely overlaps with other grains.

4D-STEM segmentation↗
DOE OSTI2021

Electronic surface reconstruction of TiO 2 nanocrystals revealed by resonant inelastic x-ray scattering

The identification of lattice multiphases in TiO 2 nanocrystals is studied by high resolution transmission electron microscope and electron diffraction patterns. Based on the spectroscopic analysis using soft x-ray absorption and resonant inelastic soft x-ray scattering, it is believed that the oxygen vacancies at the interface exhibit structural distortion of the TiO$^{8-}_6$ cluster around the defect site as for the multiphase lattice. We elucidate that the extra 3d electrons nearby induce the inelastic scattering features with the excitation energy dependence owing to different energy relaxation processes, a characteristic of the electron-phonon coupling or the nature of the electron-hole pair at the intermediate state. The manifold dd excitations driven by the strong interaction between Ti-3d and O-2p electrons are noticeably rich, coexisting on both Ti and O sites. Finally, this sophisticated experiment can advance the perspective of nanocomposite TiO 2 for various interactions of surface Ti 3+ in applications of future devices.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Binary pseudo-random array for calibration of interferometers with transmission spheres and cylinders

Binary pseudo-random array (BPRA) “white noise” artifacts are highly effective for characterizing the instrument transfer function (ITF) of surface topography metrology tools and wavefront measurement instruments. These BPRA artifacts feature all spatial frequencies within the instrument bandpass equally, resulting in a power spectral density with a white-noise-like character. This characteristic allows for direct ITF determination with uniform sensitivity across the entire spatial frequency range. We have developed a novel BPRA calibration standard that combines the diffractive pattern of a reflection computer-generated hologram (CGH) with the white noise generating BPRA pattern. By integrating these technologies using the same lithographic techniques, the resulting calibration sample enables ITF characterization of a Fizeau interferometer with a transmission sphere, or any nulling optic.

Munechika, K↗
DOE OSTI2020

Mechanism and dynamics of fatty acid photodecarboxylase

The deposition contains diffraction patterns after hit-finding of time-resolved serial femtosecond crystallography measurements on fatty acid photodecarboxylase performed at LCLS XFEL (proposal ID: LT59). Five datasets are available. One dataset without pump laser excitation, labeled as "dark" and four time-resolved datasets with pump laser excitation at four different time-points labeled as "20 ps", "900 ps", "300 ns" and "2 μs". Please check the publication for more information about the datasets.

CXI↗
DOE OSTI2021

KSpaceNavigator (KSN)

Intuitive GUI for manipulating microscope stages, allowing to align crystallographic data with stages, allowing to align crystallographic data with stage coordinates and microscope images. Simulates kinematic diffraction patterns and Kikuchi line patterns. Simulated patterns can be displayed as overlay to actually measured data, allowing manual fingerprinting and angular alignment. Crystallographic data is fed to the program in form of CIF (crystallographic information file) files, which are available from many databases and cover virtually all crystal structure ever reported in any journal. Actual goniometer scales can be linearized by lookup tables, program can be used with any microscope goniometer, double tilt and tilt-rotation type. Software requirements: Win32 platform (XP); Compiler/Version: Borland C++ Builder 5; Type of files: Executable modules; Hardware requirement: PC

Duden, Thomas↗
DOE OSTI2020

Single-frame far-field diffractive imaging with randomized illumination

We introduce a single-frame diffractive imaging method called randomized probe imaging (RPI). In RPI, a sample is illuminated by a structured probe field containing speckles smaller than the sample’s typical feature size. Quantitative amplitude and phase images are then reconstructed from the resulting far-field diffraction pattern. The experimental geometry of RPI is straightforward to implement, requires no near-field optics, and is applicable to extended samples. When the resulting data are analyzed with a complimentary algorithm, reliable reconstructions which are robust to missing data are achieved. To realize these benefits, a resolution limit associated with the numerical aperture of the probe-forming optics is imposed. RPI therefore offers an attractive modality for quantitative X-ray phase imaging when temporal resolution and reliability are critical but spatial resolution in the tens of nanometers is sufficient. We discuss the method, introduce a reconstruction algorithm, and present two proof-of-concept experiments: one using visible light, and one using soft X-rays.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

PhaseGAN: a deep-learning phase-retrieval approach for unpaired datasets

Phase retrieval approaches based on deep learning (DL) provide a framework to obtain phase information from an intensity hologram or diffraction pattern in a robust manner and in real-time. However, current DL architectures applied to the phase problem rely on i) paired datasets, i. e., they arc only applicable when a satisfactory solution of the phase problem has been found, and ii) the fact that most of them ignore the physics of the imaging process. Here, we present PhaseGAN, a new DL approach based on Generative Adversarial Networks, which allows the use of unpaired datasets and includes the physics of image formation. The performance of our approach is enhanced by including the image formation physics and a novel Fourier loss function, providing phase reconstructions when conventional phase retrieval algorithms fail, such as ultra-fast experiments. Thus, PhaseGAN offers the opportunity to address the phase problem in real-time when no phase reconstructions but good simulations or data from other experiments are available.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Predicting ptychography probe positions using single-shot phase retrieval neural network

Ptychography is a powerful imaging technique that is used in a variety of fields, including materials science, biology, and nanotechnology. However, the accuracy of the reconstructed ptychography image is highly dependent on the accuracy of the recorded probe positions which often contain errors. These errors are typically corrected jointly with phase retrieval through numerical optimization approaches. When the error accumulates along the scan path or when the error magnitude is large, these approaches may not converge with satisfactory result. We propose a fundamentally new approach for ptychography probe position prediction for data with large position errors, where a neural network is used to make single-shot phase retrieval on individual diffraction patterns, yielding the object image at each scan point. The pairwise offsets among these images are then found using a robust image registration method, and the results are combined to yield the complete scan path by constructing and solving a linear equation. We show that our method can achieve good position prediction accuracy for data with large and accumulating errors on the order of 10 2 pixels, a magnitude that often makes optimization-based algorithms fail to converge. For ptychography instruments without sophisticated position control equipment such as interferometers, our method is of significant practical potential.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Nanoscale structural evolution and phase transformation of geopolymers: In situ SAXS/WAXS investigation under uniaxial tension at elevated temperatures

This investigation delves into the degradation mechanisms of high-density polyethylene geomembranes (PE GMXs) under a spectrum of conditions, replicating real-world scenarios within a rigorously controlled laboratory setting. The treatment protocols applied induced a notable increase in the crystallinity of the treated specimens relative to the untreated controls. Small-angle x-ray scattering (SAXS) analysis identified an initial long period (interlamellar distance) of 16.9 nm for the untreated polymer, which expanded by 19.5% at a strain of 16.7 percent. Conversely, the treated PE GMXs exhibited a more gradual elongation of the long period, with an increase of merely 10.6% at a strain of 23.3 percent. At an elevated temperature of 65°C, both samples exhibited pronounced strain hardening, with the treated PE GMXs demonstrating superior stability even at a strain of 150 percent. Wide-angle x-ray scattering (WAXS) experiments corroborated these observations, revealing that the diffraction patterns of the untreated PE remained stable up to a strain of 16.7%, whereas those of the treated PE remained distinct up to a strain of 46.1 percent. Scanning electron microscopy (SEM) images substantiated the formation of a shish–kebab structure in the treated samples. The study concludes that the geopolymer underwent oxidation and material degradation as a result of the chemical and mechanical treatments, transitioning to a more crystalline state and concomitantly losing its initial elasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Adaptive Machine Learning for Bragg Coherent Diffraction Imaging (BCDI) of 3D Electron Density Maps with Application to La 2-x Ba x CuO 4 (LBCO) High Temperature Superconductor Studies [PowerPoint]

Understanding mesoscale heterogeneity is important for evaluating fatigue and failure of structural materials and for manufacturing processes. Data-driven tools can facilitate in guiding effort investment (measurements and computations) at various stages of the materials development. Our 3D reconstruction approach is to find a set of coefficients which define a bounding surface of the electron density. Data for training the 3D CNN was generated by sampling coefficients from uniform distributions. Test vs. prediction values are shown for the 28 even-valued coefficients for 1000 test structures, with the best and worst performers highlighted. The adaptive part of this work utilized a model independent extremum seeking (ES). The predictions of the CNN were used as the starting point for the ES algorithm. The convergence of the ES algorithm for 3 different structures is illustrated, and the robustness of the adaptive ML approach was demonstrated on experimentally measured 3D crystal from high energy diffraction microscopy. Reconstruction of a non-uniform density volume with different levels of Poisson noise is also shown. Preliminary attempts at reconstructing measured La 2-x Ba x CuO 4 diffraction patterns have so far failed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

MOCVD Growth and Characterization of ZnSnN 2

Since the first few reports of its synthesis in 2011 and 20121-3, interest in ZnSnN 2 for diverse applications, including photovoltaics1,3,4, visible light photocatalysis5, and optoelectronics, has been growing. Novel nitride-based LED device designs promise high gains in efficiency at emission wavelengths into the green, amber and even red.6-8 Their realization requires the precise insertion of an ultrathin layer of ZnGeN 2 or ZnSnN 2 into the active region of an InGaAs-GaAs LED structure. While thin films of ZnSnN 2 have been synthesized by RF sputtering1,9 and by MBE 2,10,11, and thin films of ZnGeN 2 , ZnSiN 2 and their alloys by MOCVD, the synthesis of ZnSnN 2 thin films by MOCVD has not yet been reported. It is a challenging goal, given the narrow temperature window between efficient activation of ammonia and the thermal decomposition of ZnSnN 2 at near-atmospheric pressures. We report here the results of studies of ZnSnN 2 films grown on r- and c-plane sapphire substrates, GaN templates on sapphire, and In 0.15 Ga 0.85 N templates on GaN-on-sapphire, at temperatures from 500 °C to 560 °C, using tetramethyltin (TMSn), diethylzinc (DEZn), germane and ammonia. Chamber pressures were varied between 200 and 500 torr. In addition, the ratios of the cation precursors and the total cation-to-anion precursor ratios were varied. Single crystal growth, as evidenced by 2θ-ω x-ray diffraction scans, was achieved on all of these substrates. Wurtzitic (0002) ZnSnN 2 diffraction were observed at 2θ ~ 32.90 for the samples grown on c-sapphire, GaN (0001) and InGaN (0001) templates, and wurtzitic (11-20) peak at 2θ ~ 54.80 for the films grown on r-sapphire. Higher pressures and higher temperatures promoted better crystallinity and more continuous films, as revealed by scanning electron microscopy (SEM) images and 2θ-ω x-ray diffraction peak widths and intensities. Crystal quality was observed to be highly dependent on growth temperature. For example, in one series a 10 °C change in growth temperature resulting in a factor of 15 increase in diffraction peak intensity. SEM images show that films grown on the GaN templates had better uniformity in nucleation than those grown on sapphire. The presence of satellite peaks around the Bragg peak in the XRD 2θ-ω scan for a film grown on a GaN template, and the absence of satellite peaks for the films grown simultaneously on c- and r-sapphire, also indicate superior quality for the film grown on GaN. HAADF-STEM images of films grown on these templates showed smooth interfaces at the film-substrate boundary and show growth rates as high as 167 nm/h, considerably higher than reported previously for MBE growth.9,10 Electron diffraction patterns show single crystallinity. Rocking curves show FWHM as low as 0.100. RMS surfaces roughnesses, measured by atomic force microscopy, are of the order of 3 nm for 1µm x 1µm areas. Current work is focusing on optimizing growth on InGaN templates. These templates are promising for their relatively lower lattice mismatch with ZnSnN 2 . Their use is a next step toward producing LED device structures.

Jayatunga, Benthara Hewage Dinushi↗