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At least 145 records · Page 8

Imaging and spatially resolved mass spectrometry applications in nephrology

The application of spatially resolved mass spectrometry (MS) and MS imaging approaches for studying biomolecular processes in the kidney is rapidly growing. These powerful methods, which enable label-free and multiplexed detection of many molecular classes across omics domains (including metabolites, drugs, proteins and protein post-translational modifications), are beginning to reveal new molecular insights related to kidney health and disease. Further, the complexity of the kidney often necessitates multiple scales of analysis for interrogating biofluids, whole organs, functional tissue units, single cells and subcellular compartments. Various MS methods can generate omics data across these spatial domains and facilitate both basic science and pathological assessment of the kidney. Optimal processes related to sample preparation and handling for different MS applications are rapidly evolving. Emerging technology and methods, improvement of spatial resolution, broader molecular characterization, multimodal and multiomics approaches and the use of machine learning and artificial intelligence approaches promise to make these applications even more valuable in the field of nephology. Overall, spatially resolved MS and MS imaging methods have the potential to fill much of the omics gap in systems biology analysis of the kidney and provide functional outputs that cannot be obtained using genomics and transcriptomic methods.

60 APPLIED LIFE SCIENCES↗

Chemical screening by time-resolved X-ray scattering to discover allosteric probes

Abstract Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis ( k VR ), capture structure–activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF–aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF–aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterization of a mock up nuclear waste package using energy resolved MeV neutron analysis

Reliable radiographic methods for characterizing nuclear waste packages non-destructively (without the need to open containers) have the potential to significantly contribute to safe handling and future disposal options, particularly for legacy waste of unknown content. Due to required shielding of waste containers and the need to characterize materials consisting of light elements, X-ray methods are not suitable. Here, energy-resolved MeV neutron radiography is demonstrated as a first-of-its-kind application for non-destructive and remote examination of mock up nuclear waste packages from a safe position using time-of-flight techniques enabled by a novel event-mode imaging detector system. Energy-resolved neutron transmission spectra were measured spatially, permitting the detection of analogue materials to actual nuclear waste such as water, melamine, and ion exchange resin within a 2.54 cm wall thickness steel pipe. The results demonstrate the capability to locate the materials through this wall thickness by radiography and tomographic reconstruction, revealing detailed 3D distributions and structural anomalies. The method effectively detects residual water in ion exchange resin, highlighting its sensitivity to moisture content, a crucial parameter for nuclear waste characterization. Monte Carlo simulations are in agreement with the experimental findings, providing a pathway to simulate waste forms more difficult to tackle experimentally. This work paves the way to apply sub-nanosecond intense MeV neutron sources, such as laser-driven neutron sources under development, to nuclear waste characterization.

36 MATERIALS SCIENCE↗

Resolved Resonance Evaluation for Neutron Interactions with 103 Rh up to 8 keV

A neutron cross-section evaluation for the n + 103 Rh reaction in the resolved resonance region was carried out in the energy range 10−5 eV to 8 keV encompassing thermal energy at 0.0253 eV. The scope of this work is to generate resonance parameters and resonance parameter covariances based on the Reich-Moore reduced R-matrix formalism using the code SAMMY. Some features of the new evaluation are the inclusion of high-resolution capture data in the SAMMY evaluation process and the extension of the resolved resonance range from 4 to 8 keV. Furthermore, the evaluation employs more accurate resonance parameter representation by exploring the use of the LRF = 7 ENDF feature and also the use of the LCOMP = 2 compact format for resonance parameter covariance representation. Included in the SAMMY evaluation are transmission data, capture cross-section data, and neutron scattering length information. Thermal cross-section values listed in the literature, as well as capture resonance integrals, were also incorporated into the evaluation process.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Enhancing transfer learning in angle-resolved photoemission spectroscopy (ARPES) with spatially-aware representations via graph convolution

A recent application of machine learning has been to spatially-resolved angle-resolved photoemission spectroscopy (ARPES). Here we advance the state-of-the-art by applying representational learning to transform ARPES data into an embedding space of a pre-trained self-supervised learning model, thus enhancing the pipeline that improves the bandstructure classification and domain assignment/segmentation performance compared to a k-means clustering method. In the current iteration, the real-space information is entered into the domain assignment through the graph convolution method, which improves the transfer learning performance of the original self-supervised model. Lastly, an unsupervised automated tool is developed that incorporates these techniques to enable automatic domain assignment.

ARPES↗

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗

Momentum-Resolved Direct Observation of Chiral Phonons in Elemental Tellurium

Chiral phonons carry finite phonon angular momentum, yet their momentum-resolved behavior in acoustic branches remains largely unexplored. In this work, we report the direct detection of chiral acoustic phonons in elemental Te. Through a combination of high-energy-resolution inelastic x-ray scattering experiments and atomistic modeling, we confirm that longitudinal acoustic modes develop pronounced circular atomic motion by mixing with transverse modes. Our results establish a direct link between unexpected scattering intensity in nominally forbidden geometries and circular phonons, offering a framework for characterizing momentum-resolved phonon chirality and highlighting the emergence of intrinsic phonon angular momentum in acoustic branches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Disentangling the physics of the attractive Hubbard model as a fully interacting model of fermions via the accessible and symmetry-resolved entanglement entropies

The complicated ways in which electrons interact in many-body systems such as molecules and materials have long been viewed through the lens of local electron correlation and associated correlation functions. However, quantum information science has demonstrated that more global diagnostics of quantum states like the entanglement entropy can provide a complementary and clarifying lens on electronic behavior. One particularly useful measure that can be used to distinguish between quantum and classical sources of entanglement is the accessible entanglement, the entanglement available as a quantum resource for systems subject to conservation laws, such as fixed particle number, due to superselection rules. In this work, we introduce an algorithm and demonstrate how to compute accessible and symmetry-resolved entanglements for interacting fermion systems. This is accomplished by combining an incremental version of the swap algorithm with a recursive auxiliary field quantum Monte Carlo algorithm recently developed by the authors. We apply these tools to study the pairing and charge density waves exhibited in the paradigmatic attractive Hubbard model via entanglement. We find that the particle and spin symmetry-resolved entanglements and their related full probability distribution functions show very clear—and unique—signatures of the underlying electronic behavior even when those features are less pronounced in conventional correlation functions. Altogether, this work provides a systematic means of characterizing the entanglement within quantum systems that can grant a deeper understanding of the complicated electronic behavior that underlies quantum phase transitions and crossovers in many-body systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Instrumentation and methods for efficient time-resolved X-ray crystallography of biomolecular systems with sub-10 ms time resolution

Time-resolved X-ray crystallography has great promise to illuminate structure–function relations and key steps of enzymatic reactions with atomic resolution. The dominant methods for chemically-initiated reactions require complex instrumentation at the X-ray beamline, significant effort to operate and maintain this instrumentation, and enormous numbers (∼10 5 –10 9 ) of crystals per time point. We describe instrumentation and methods that enable high-throughput time-resolved study of biomolecular systems using standard crystallography sample supports and mail-in X-ray data collection at standard high-throughput cryocrystallography synchrotron beamlines. The instrumentation allows rapid reaction initiation by mixing of crystals and substrate/ligand solution, rapid capture of structural states via thermal quenching with no pre-cooling perturbations, and yields time resolutions in the single-millisecond range, comparable to the best achieved by any non-photo-initiated method in both crystallography and cryo-electron microscopy. Our approach to reaction initiation has the advantages of simplicity, robustness, low cost, adaptability to diverse ligand solutions and small minimum volume requirements, making it well suited to routine laboratory use and to high-throughput screening. We report the detailed characterization of instrument performance, present structures of binding of N -acetylglucosamine to lysozyme at time points from 8 ms to 2 s determined using only one crystal per time point, and discuss additional improvements that will push time resolution toward 1 ms.

Indergaard, John A. (ORCID:000000022367699X)↗

Optimization of X-ray event screening using ground and in-orbit data for the Resolve instrument onboard the XRISM satellite

The X-Ray Imaging and Spectroscopy Mission (XRISM) satellite was successfully launched and put into a low-Earth orbit on September 6, 2023 (UT). The Resolve instrument onboard XRISM hosts an X-ray microcalorimeter detector, which was designed to achieve a high-resolution ( ≤ 7 eV FWHM at 6 keV), high-throughput, and non-dispersive spectroscopy over a wide energy range. It also excels in a low background with a requirement of < 2 × 10 -3 s -1 keV -1 (0.3 to 12.0 keV), which is equivalent to only one background event per spectral bin per 100-ks exposure. Event screening to discriminate X-ray events from background is a key to meeting the requirement. We present the result of the Resolve event screening using data sets recorded on the ground and in orbit based on the heritage of the preceding X-ray microcalorimeter missions, in particular, the Soft X-ray Spectrometer onboard ASTRO-H. We optimize and evaluate 19 screening items of three types based on (1) the event pulse shape, (2) relative arrival times among multiple events, and (3) good time intervals. We show that the initial screening, which is applied for science data products in the performance verification phase, reduces the background rate to 1.8 × 10 -3 s -1 keV -1 meeting the requirement. We further evaluate the additional screening utilizing the correlation among some pulse shape properties of X-ray events and show that it further reduces the background rate, particularly in the < 2 keV band. Over 0.3 to 12 keV, the background rate becomes 1.0 × 10 -3 s -1 keV -1 .

47 OTHER INSTRUMENTATION↗

Resolve instrument onboard XRISM: design, integration, and instrument test results

The Resolve instrument onboard the X-Ray Imaging and Spectroscopy Mission (XRISM) consists of an array of 6 × 6 silicon-thermistor microcalorimeters cooled down to 50 mK and a high-throughput X-ray mirror assembly (XMA) with a focal length of 5.6 m. XRISM is a recovery mission of ASTRO-H/Hitomi, and the Resolve instrument is a rebuild of the ASTRO-H Soft X-ray spectrometer (SXS) and the Soft X-ray Telescope (SXT) that achieved energy resolution of ∼ 5 eV FWHM on orbit, with several important changes based on lessons learned from ASTRO-H. The flight models of the Dewar and the electronics boxes were fabricated, and the instrument test and calibration were conducted in 2021. By tuning the cryocooler frequencies, energy resolution better than 4.9 eV FWHM at 6 keV was demonstrated for all 36 pixels and high-resolution grade events, as well as energy-scale accuracy better than 2 eV up to 30 keV. The immunity of the detectors to microvibration, electrical conduction, and radiation was evaluated. The instrument was delivered to the spacecraft system in April 2022. The XMA was tested and calibrated separately. Its angular resolution is 1.27′, and the effective area of the mirror itself is 570 cm 2 at 1 keV and 424 cm 2 at 6 keV. We report the design and the major changes from the ASTRO-H SXS, the integration, and the results of the instrument test.

X-ray↗

Resolve instrument onboard the X-Ray Imaging and Spectroscopy Mission

We present an overview of the design and in-flight performance of the Resolve soft X-ray spectrometer on the X-Ray Imaging and Spectroscopy Mission that was successfully launched on September 7, 2023, on a JAXA H-IIA rocket from the Tanegashima Space Center of Japan. The instrument has a 36-pixel array of microcalorimeters, 35 of which are at the focus of a high-throughput grazing-incidence X-ray mirror. The instrument has achieved its required operational base temperature of 0.05 K and a spectral resolution of 4.5 eV (FWHM) at 6 keV. The cooling chain was designed to provide a lifetime of at least 3 years in orbit and operate with and without liquid helium to provide redundancy and the longest operational lifetime for the instrument. Early indications are that the cryogen lifetime may reach 6 years with a cryogen-free mode thereafter. A series of onboard X-ray calibration sources produces energy scale calibration lines simultaneously while observing celestial sources. The overall design and in-flight performance of Resolve are described.

Astronomy and AstroPhysics↗

Depth-Resolved Lithiated Gradients in Pristine and Laser-Ablated Anodes During Fast Charging

Laser ablating 3D electrode microstructures is a technique to improve Li-ion battery fast-charge performance. This technique has been theoretically proposed and electrochemically validated previously in the literature. The fundamental principle underlying laser ablation is that the ablated features reduce Li-ion transport pathways, improving access to the electrode active material near the current collector. This, in turn, promotes more homogeneous electrode utilization. The present study seeks to directly affirm the physics attributed to laser ablation using operando high-speed synchrotron X-ray diffraction. In this study, depth-resolved graphite lithiation gradients are measured operando during high-rate (15 min) charging. The depth-resolved lithiation dynamics of both ablated and non-ablated anodes are compared. The results highlight that the laser-ablated graphite electrode has notably more homogeneous utilization as compared to the non-ablated electrode. Additionally, the ablated electrode has a significant delay in reaching the maximum graphite lithiation at the separator, indicating less propensity for lithium plating. During low rate delithiation/discharge (2 hr), the two cells' lithiation gradients converge. Notably, a calibrated physics-based electrochemical model accurately reflects experimental findings, suggesting the potential to use pseudo-4D models not only to optimize laser ablation parameters in fast-charge capable electrodes but also to guide fast charging protocols that avoid lithium plating.

25 ENERGY STORAGE↗

Spatially Resolved Raman Spectroscopic Investigation of Uranyl Fluoride: A Case Study in the Importance of Instrument Optimization

Raman spectroscopy is an emerging technique for rapid and nondestructive analysis of nuclear materials for forensic and nonproliferation applications as it is a powerful tool for distinguishing multiple chemical forms of materials with similar stoichiometries. Recent developments in spectroscopic software have enabled rapid data collection with high-speed Raman spectroscopic mapping capabilities. However, some uranium-rich materials are susceptible to degradation in humid air and/or laser-induced phase transformations. To mitigate environmental or measurement-related sample degradation of potential samples of interest, we have taken a systematic approach to define optimized data collection parameters for high-throughput measurements of uranyl fluoride (UO 2 F 2 ), which is an important intermediate material in the nuclear fuel cycle. First, we systematically describe the influence of optical magnification (5× to 100×), laser power, and exposure time on obtained signal for identical particles of UO 2 F 2 and find that at low laser power and exposure times, comparable signal is obtained regardless of optical magnification. Second, we ensure sample integrity during data collection, and third, collect spectroscopic maps that employ optimized parameters to reduce the time required to obtain spatially resolved spectroscopic information. Reductions of 90% and 99% in measurement times are discussed as they relate to differences in resolving spectroscopic features of particles in identical mapping areas. Finally, during this work, we found that additional data processing options were needed and thus developed a customized Python script for importing, processing, analyzing, and visualizing Raman spectroscopic map data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

High temporal frequency data from a four turbine, blade-resolved wind farm simulation with ExaWind

The data was generated with ExaWind (https://github.com/Exawind) which couples AMR-Wind (https://github.com/Exawind/amr-wind/), Nalu-Wind (https://github.com/Exawind/nalu-wind), TIOGA (https://github.com/Exawind/tioga), and OpenFAST (https://github.com/OpenFAST/openfast). This is a large-scale simulation of a blade-resolved wind farm using the ExaWind software stack. ExaWind couples together a background flow solver, AMR-Wind, and a near-body solver, Nalu-Wind, through an overset technique from the TIOGA application. Another application, OpenFAST, handles the structural dynamics of the turbine blades and towers, which informs the fluid-structure interaction of the wind turbines with the flow solvers. This particular simulation includes four blade-resolved wind turbines operating in a turbulent atmospheric boundary layer. The AMR-Wind solver uses 500 million cells and is being solved on 256 AMD GPUs of the Oakridge Leadership Computing Facility Frontier supercomputer. Each turbine is assigned its own Nalu-Wind solver with over 13 million elements per turbine and solved using 448 CPU cores, for a total of 1792 CPU cores. For each node, 56 cores contain Nalu-Wind, while 8 cores correspond to AMR-Wind operations on the GPUs. Consequently, ExaWind is entirely utilizing the CPUs and the GPUs of the nodes concurrently. The data used in the visualization is full flow field data output from the simulation. It is lossy-compressed to a specific accuracy using ZFP and written to disk every 16 time-steps to enable real-time flow visualization. The flow fields are sampled at a high temporal frequency to enable real-time, 24fps visualization. The flow fields are sampled every 12 simulation time steps (every 0.04132s).

17 WIND ENERGY↗

High-harmonic spin-shearing interferometry for spatially resolved EUV magneto-optical spectroscopy

We present a method for achieving hyperspectral magnetic imaging in the extreme ultraviolet (EUV) region based on high-harmonic generation (HHG). By interfering two mutually coherent orthogonally-polarized and laterally-sheared HHG sources, we create an EUV illumination beam with spatially-dependent ellipticity. By placing a magnetic sample in the beamline and sweeping the relative time delay between the two sources, we record a spatially resolved interferogram that is sensitive to the EUV magnetic circular dichroism of the sample. This image contains the spatially-resolved magneto-optical response of the sample at each harmonic order, and can be used to measure the magnetic properties of spatially inhomogeneous magnetic samples.

Optics↗

Dual-frequency-comb UV spectroscopy with one million resolved comb lines

We present high-resolution dual-comb spectroscopy across two broad UV spectral regions spanning 372–410 nm and 325–342 nm. This is achieved by generating sixth and seventh harmonics, respectively, from a low-noise 2.35 µm Cr:ZnS dual-comb laser system. The sixth harmonic band contains approximately 1,000,000 spectrally resolved comb lines, while the seventh harmonic band—around 550,000 comb lines. With the line spacing of 80 MHz, this corresponds to a resolving power of up to 10 million, offering remarkable spectral resolution.

Muraviev, Andrey↗

Resolving femtosecond photoinduced energy flow: capture of nonadiabatic reaction pathway topography and wavepacket dynamics from photoexcitation through the conical intersection seam (Final Technical Report)

The dynamics that take place within just tens to hundreds of femtoseconds following the absorption of light by a molecule can play a critical role in how the absorbed energy is directed, allowing it to be used for a specific function or dissipated harmlessly. The form of chemical change that occurs rapidly in these molecules is called a “nonadiabatic electronic transition.” Such transitions are known to mediate energy flow in natural biological systems such as the ultraviolet photoprotection mechanism of DNA and the first step of the human vision response. Understanding how these mechanisms work precisely may help scientists achieve controlled manipulation of solar energy or optical control of a wide range of energy management functions in artificial systems. Experimental methods, however, have not yet allowed a precisely resolved and complete measurement of nonadiabatic electronic transitions. This constitutes a major obstacle to progress in the field. For progress to occur that would inform a wide body of research aiming to efficiently harness the energy of light for practical purposes, it is especially important to benchmark computational models of the molecules undergoing these rapid changes with experimental measurements, in order to learn which models are accurate. With Dept. of Energy funding, we have made strong progress towards establishing a new optical method for experimentally detecting the full nonadiabatic electronic transition. This requires having coordinated pulses of light covering the visible through the mid-infrared range of the electromagnetic spectrum that last only ten femtoseconds. We have developed a new, relatively simple approach for generating such pulses of laser light, and have incorporated them into a time-resolved spectrometer for measuring rapid changes in molecules. These tools can provide the greater precision and new types of data that are needed to benchmark computational models of molecular change and thus to make progress in the field. Our tools were tested on graphene, an excellent solid-state sample for verifying the capabilities and limitations of our instrumentation. The investment made in these tools by the Dept. of Energy Office of Science will allow new fundamental scientific understanding of energy dynamics in molecules in future studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗