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At least 271 records · Page 15

Modeling and experimental validation of dynamical effects in Bragg coherent x-ray diffractive imaging of finite crystals

Bragg coherent diffractive imaging (BCDI) is a noninvasive microscopy technique that can visualize the shape and internal lattice deviations of crystals with nanoscale spatial resolution and picometer deformation sensitivity. Its strain imaging capability relies on Fourier transform–based iterative phase retrieval algorithms, which are mostly developed under the kinematical approximation. Such approximation prohibits the application of BCDI on larger crystals, which are commonly seen in most emerging functional materials. Understanding the dynamical effect in BCDI, as well as developing a validated method for modeling BCDI at the dynamical diffraction limit, is crucial for applying BCDI to hierarchical systems that contain micron-sized crystals and grains. Thus we report a comparative study on the impact of dynamical diffraction effects by comparing the reconstruction results from two measurements of the same crystal. Forward simulation is implemented to show subtle changes of interference fringes in the diffraction pattern due to the dynamical diffraction, and is compared directly with the experimental data.

36 MATERIALS SCIENCE↗

Invasion and rapid adaptation of guppies ( Poecilia reticulata ) across the Hawaiian Archipelago

How much does natural selection, as opposed to genetic drift, admixture, and gene flow, contribute to the evolution of invasive species following introduction to a new environment? Here we assess how evolution can shape biological invasions by examining population genomic variation in non-native guppies (Poecilia reticulata) introduced to the Hawaiian Islands approximately a century ago. By examining 18 invasive populations from four Hawaiian islands and four populations from the native range in northern South America, we reconstructed the history of introductions and evaluated population structure as well as the extent of ongoing gene flow across watersheds and among islands. Patterns of differentiation indicate that guppies have developed significant population structure, with little natural or human-mediated gene flow having occurred among populations following introduction. Demographic modeling and admixture graph analyses together suggest that guppies were initially introduced to O‘ahu and Maui and then translocated to Hawai‘i and Kaua‘i. We detected evidence for only one introduction event from the native range, implying that any adaptive evolution in introduced populations likely utilized the genetic variation present in the founding population. Environmental association tests accounting for population structure identified loci exhibiting signatures of adaptive variation related to predators and landscape characteristics but not nutrient regimes. When paired with high estimates of effective population sizes and detectable population structure, the presence of environment-associated loci supports the role of natural selection in shaping contemporary evolution of Hawaiian guppy populations. Our findings indicate that local adaptation may engender invasion success, particularly in species with life histories that facilitate rapid evolution. Finally, evidence of low gene flow between populations suggests that removal could be an effective approach to control invasive guppies across the Hawaiian archipelago.

59 BASIC BIOLOGICAL SCIENCES↗

Performance of plane wavefront Fizeau interferometers in power spectral density measurements with tilted plane optics

Binary pseudo-random array (BPRA) test samples are useful devices for calibrating the instrument transfer function (ITF) of Fizeau interferometers, interferometric microscopes, and other optical and non-optical surface and wavefront metrology instruments. The intrinsic white noise character of the power spectral density (PSD) function of the BPRA pattern simplifies the extraction of the ITF from the measured PSD. The ITF determined in a dedicated calibration experiment can be used to reconstruct the surface height profile from the measured data, effectively enhancing the instrument’s spatial resolution. For a high confidence reconstruction procedure, a reliable analytical model of the IFT is desirable. Usually, the model accounts for the contributions to the ITF related the imperfections of the instrument’s optical and detector systems. Here, we experimentally demonstrate that in the case of surface height metrology with Fizeau interferometers, the PSD measurements and, therefore, the efficacy of the ITF calibration of the tool, are strongly affected by the instrument data acquisition and processing procedures, as well as by the shape of the optic under test and its alignment with respect to the interferometer.

Yashchuk, V V↗

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↗

Determining the nanostructure of polymer foams using 3D ptycho-tomography for inertial fusion energy applications

Polymer foams play a critical role in contemporary inertial fusion energy (IFE) target designs by enhancing energy yield and optimizing implosion dynamics. However, the lack of high-resolution characterization of the nanostructure of these foams restricts progress in fusion science. In this work, we demonstrate the first high-resolution three-dimensional (3D) reconstruction of a low-density, Si-doped polymer foam fabricated via two-photon polymerization, using ptychographic x-ray computed tomography (PXCT) at an x-ray free electron laser (XFEL). This imaging method reconstructs two-dimensional (2D) attenuation and phase information at multiple sample angles that are combined into a 3D density map used to extract local mass density and determine structural dimensions. We achieve a 2D spatial resolution of 19 ± 3 nm on a high-contrast Ronchi pattern target and 78.7 ± 3 nm for low-contrast polymer foams, marking a significant advancement for XFEL-based ptychography of low-density materials. Furthermore, our experimental results reveal an average foam strut thickness of 1.17 ± 0.4 μm, consistent with fabrication expectations, and a reconstructed average mass density of 0.35 g/cc, aligning closely with the predicted density of 0.29 g/cc. These findings provide important insights for improving foam design and refining radiation hydrodynamics modeling in future IFE experiments. Our study establishes PXCT at an XFEL as a powerful tool for high-resolution characterization of fusion-relevant materials, paving the way for enhanced target performance in IFE research.

Hancock, Levi [Colorado State Univ., Fort Collins,↗

The vestibular nerve of the chinchilla. III. Peripheral innervation patterns in the utricular macula

1. Nerve fibers supplying the utricular macula of the chinchilla were labeled by extracellular injection of horseradish peroxidase into the vestibular nerve. The peripheral terminations of individual fibers were reconstructed and related to the regions of the end organ they innervated and to the sizes of their parent axons. 2. The macula is divided into medial and lateral parts by the striola, a narrow zone that runs for almost the entire length of the sensory epithelium. The striola can be distinguished from the extrastriolar regions to either side of it by the wider spacing of its hair cells. Calyx endings in the striola have especially thick walls, and, unlike similar endings in the extrastriola, many of them innervate more than one hair cell. The striola occupies 10% of the sensory epithelium; the lateral extrastriola, 50%; and the medial extrastriola, 40%. 3. The utricular nerve penetrates the bony labyrinth anterior to the end organ. Axons reaching the anterior part of the sensory epithelium run directly through the connective tissue stroma. Those supplying more posterior regions first enter a fiber layer located at the bottom of the stroma. Approximately one-third of the axons bifurcate below the epithelium, usually within 5-20 microns of the basement membrane. Bifurcations are more common in fibers destined for the extrastriola than for the striola. 4. Both calyx and bouton endings were labeled. Calyces can be simple or complex. Simple calyces innervate individual hair cells, whereas complex calyces supply 2-4 adjacent hair cells. Complex endings are more heavily concentrated in the striola than in the extrastriola. Simple calyces and boutons are found in all parts of the epithelium. Calyces emerge from the parent axon or one of its thick branches. Boutons, whether en passant or terminal, are located on thin collaterals. 5. Fibers can be classified into calyx, bouton, or dimorphic categories. The first type only has calyx endings; the second, only bouton endings; and the third, both kinds of endings. Calyx units make up 6% of the labeled fibers, bouton units less than 2%, and dimorphic units greater than 92%. The three fiber types differ in the macular zones they supply and in the diameters of their parent axons. Calyx units were restricted to the striola. The few bouton units were found in the extrastriola.(ABSTRACT TRUNCATED AT 400 WORDS).

NASA Discipline Neuroscience↗

Spontaneous Localization at a Potential Saddle Point from Edge State Reconstruction in a Quantum Hall Point Contact

Quantum point contacts (QPCs) are an essential component in mesoscopic devices. Here, in this work, we study the transmission of quantum Hall edge modes through a gate-defined QPC in monolayer graphene. We observe resonant tunneling peaks and a nonlinear conductance pattern characteristic of Coulomb-blockaded localized states. The in-plane electric polarizability reveals the states are localized at a classically unstable electrostatic saddle point. We explain this unexpected finding within a self-consistent Thomas-Fermi model, finding that localization of a zero-dimensional state at the saddle point is favored whenever the applied confinement potential is sufficiently soft compared to the Coulomb energy. Our results provide a direct demonstration of Coulomb-driven reconstruction at the boundary of a quantum Hall system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Multi-Dimensional, Inviscid Flux Reconstruction for Simulation of Hypersonic Heating on Tetrahedral Grids

The quality of simulated hypersonic stagnation region heating on tetrahedral meshes is investigated by using a three-dimensional, upwind reconstruction algorithm for the inviscid flux vector. Two test problems are investigated: hypersonic flow over a three-dimensional cylinder with special attention to the uniformity of the solution in the spanwise direction and hypersonic flow over a three-dimensional sphere. The tetrahedral cells used in the simulation are derived from a structured grid where cell faces are bisected across the diagonal resulting in a consistent pattern of diagonals running in a biased direction across the otherwise symmetric domain. This grid is known to accentuate problems in both shock capturing and stagnation region heating encountered with conventional, quasi-one-dimensional inviscid flux reconstruction algorithms. Therefore the test problem provides a sensitive test for algorithmic effects on heating. This investigation is believed to be unique in its focus on three-dimensional, rotated upwind schemes for the simulation of hypersonic heating on tetrahedral grids. This study attempts to fill the void left by the inability of conventional (quasi-one-dimensional) approaches to accurately simulate heating in a tetrahedral grid system. Results show significant improvement in spanwise uniformity of heating with some penalty of ringing at the captured shock. Issues with accuracy near the peak shear location are identified and require further study.

Gnoffo, Peter A.↗

Rapid Prototyping Integrated With Nondestructive Evaluation and Finite Element Analysis

Most reverse engineering approaches involve imaging or digitizing an object then creating a computerized reconstruction that can be integrated, in three dimensions, into a particular design environment. Rapid prototyping (RP) refers to the practical ability to build high-quality physical prototypes directly from computer aided design (CAD) files. Using rapid prototyping, full-scale models or patterns can be built using a variety of materials in a fraction of the time required by more traditional prototyping techniques (refs. 1 and 2). Many software packages have been developed and are being designed to tackle the reverse engineering and rapid prototyping issues just mentioned. For example, image processing and three-dimensional reconstruction visualization software such as Velocity2 (ref. 3) are being used to carry out the construction process of three-dimensional volume models and the subsequent generation of a stereolithography file that is suitable for CAD applications. Producing three-dimensional models of objects from computed tomography (CT) scans is becoming a valuable nondestructive evaluation methodology (ref. 4). Real components can be rendered and subjected to temperature and stress tests using structural engineering software codes. For this to be achieved, accurate high-resolution images have to be obtained via CT scans and then processed, converted into a traditional file format, and translated into finite element models. Prototyping a three-dimensional volume of a composite structure by reading in a series of two-dimensional images generated via CT and by using and integrating commercial software (e.g. Velocity2, MSC/PATRAN (ref. 5), and Hypermesh (ref. 6)) is being applied successfully at the NASA Glenn Research Center. The building process from structural modeling to the analysis level is outlined in reference 7. Subsequently, a stress analysis of a composite cooling panel under combined thermomechanical loading conditions was performed to validate this process.

Abdul-Aziz, Ali↗

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Abstract Background Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor. Results We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO 2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor. Conclusions The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.

54 ENVIRONMENTAL SCIENCES↗

Adaptive 3D convolutional neural network-based reconstruction method for 3D coherent diffraction imaging

We present a novel adaptive machine-learning based approach for reconstructing three-dimensional (3D) crystals from coherent diffraction imaging. We represent the crystals using spherical harmonics (SH) and generate the corresponding synthetic diffraction patterns. We utilize 3D convolutional neural networks (CNNs) to learn a mapping between 3D diffraction volumes and the SH, which describe the boundary of the physical volumes from which they were generated. We use the 3D CNN-predicted SH coefficients as the initial guesses, which are then fine-tuned using adaptive model-independent feedback for improved accuracy. We also adaptively tune the locations, intensities, and decay rates of collections of radial basis functions in order to reproduce the non-uniform internal structure of 3D objects and demonstrate the method for a synthetic volume that has an internal void and a density ramp.

36 MATERIALS SCIENCE↗

Single-shot x-ray phase-contrast and dark-field imaging based on coded binary phase mask

We introduce a coded-mask-based multi-contrast imaging method for high-resolution phase-contrast and dark-field imaging. The method uses a binary phase mask designed to provide an ultra-high-contrast pattern and reference-free single-shot measurement and an algorithm based on maximum-likelihood optimization and automatic differentiation to perform simultaneous reconstruction of absorption, phase, and dark-field object images. Further, we demonstrate that the method has great potential for real-time quantitative phase imaging and wavefront sensing when combined with deep learning.

Qiao, Zhi (ORCID:0000000286285320)↗

DKDP /potassium dideuterium phosphate/ light valves

The use of potassium dideuterium phosphate (DKDP) light valves for optical data processing is discussed. The operating principles and structure of optically and electron beam addressed DKDPs are compared, and specifications for both devices given. Optically addressed DKDPs are capable of higher resolution and contrast, but both systems represent viable real time spatial light modulators adaptable to optical processing. Examples of real time data processing performed by the DKDPs include: image addition and subtraction; reduction of noise introduced by scattered light in recording media; reconstruction of computer generated and acoustic holograms; reconstruction of synthetic aperture radar data; retrieval of three-dimensional information in X-ray diagnoses; radar signal processing and display; and optical pattern recognition and correlation of images, which has applications for missile guidance systems.

Casasent, D.↗

Imaging supermoiré relaxation in helical trilayer graphene

In twisted van der Waals materials, local atomic relaxation can alter the underlying electronic structure. Characterizing lattice reconstruction and its susceptibility to strain is essential for understanding emergent electronic states, especially in multilayers in which interference between moiré lattices yields larger supermoiré patterns whose energy is highly sensitive to local stacking. Here, in this study, we image spatial modulations in the electronic character of helical trilayer graphene, which indicate relaxation into a superstructure of large domains with uniform moiré periodicity. We show that the supermoiré domain size is increased by strain and can be altered in the same device while preserving the local properties within each domain. Finally, we observe a higher conductance at the domain boundaries, consistent with predictions that they host counterpropagating edge modes. Our work provides a real-space visualization of moiré-periodic domains, reveals two independently tunable length scales and demonstrates strain engineering as a route towards designing correlated topological networks at the supermoiré scale.

36 MATERIALS SCIENCE↗

Soft X-ray reflection ptychography

Scanning transmission X-ray microscopy and ptychography have become mature tools for high-resolution, element-specific imaging of nanoscale structures. However, transmission geometries impose stringent constraints on sample thickness and preparation, thereby limiting investigations of extended or bulk specimens, especially in the soft X-ray region. Here, we demonstrate reflection-geometry soft X-ray ptychography as a robust imaging mode. Instrumental feasibility and spatial resolution are established using a lithographically defined Siemens star and barcode test pattern on a multilayer substrate. We empirically demonstrate a full-pitch spatial resolution of ca. 45 nm from Fourier ring correlation analysis of the reconstructed object. The results highlight the potential of the reflection geometry for nondestructive X-ray studies of materials without the need for transmissive samples.

Guenzing, Damian [Lawrence Berkeley National Labor↗

New Mesoscale Fluvial Landscapes - Seismic Geomorphology and Exploration

Megafans (100-600 km radius) are very large alluvial fans that cover significant areas on most continents, the surprising finding of recent global surveys. The number of such fans and patterns of sedimentation on them provides new mesoscale architectures that can now be applied on continental fluvial depositional systems, and therefore on. Megafan-scale reconstructions underground as yet have not been attempted. Seismic surveys offer new possibilities in identifying the following prospective situations at potentially unsuspected locations: (i) sand concentrations points, (ii) sand-mud continuums at the mesoscale, (iii) paleo-valley forms in these generally unvalleyed landscapes, (iv) stratigraphic traps, and (v) structural traps.

Wilkinson, M. J.↗

Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)

Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

59 BASIC BIOLOGICAL SCIENCES↗

Combined speckle- and propagation-based single shot two-dimensional phase retrieval method

Single-shot two-dimensional (2D) phase retrieval (PR) can recover the phase shift distribution within an object from a single 2D x-ray phase contrast image (XPCI). Two competing XPCI imaging modalities often used for single-shot 2D PR to recover material properties critical for predictive performance capabilities are: speckle-based (SP-XPCI) and propagation-based (PB-XPCI) XPCI imaging. However, PR from SP-XPCI and PB-XPCI images are, respectively, limited to reconstructing accurately slowly and rapidly varying features due to noise and differences in their contrast mechanisms. Herein, we consider a combined speckle- and propagation-based XPCI (SPB-XPCI) image by introducing a mask to generate a reference pattern and imaging in the near-to-holographic regime to induce intensity modulations in the image. We develop a single-shot 2D PR method for SPB-XPCI images of pure phase objects without imposing restrictions such as object support constraints. It is compared against PR methods inspired by those developed for SP-XPCI and PB-XPCI on simulated and experimental images of a thin glass shell before and during shockwave compression. Reconstructed phase maps show improvements in quantitative scores of root-mean-square error and structural similarity index measure using our proposed method.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗