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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

Removing Atmospheric Fringes from Zwicky Transient Facility i-band Images using Principal Component Analysis

The Zwicky Transient Facility is a time-domain optical survey that has substantially increased our ability to observe and construct massive catalogs of astronomical objects by use of its 47 square degree camera that can observe in multiple filters. However the telescope’s i-band filter suffers from significant atmospheric fringes that reduce photometric precision, especially for faint sources and in multi-epoch co-additions. Here we present a method for constructing models of these atmospheric fringes using Principal Component Analysis that can be used to identify and remove these artifacts from contaminated images. In addition, we present the Uniform Background Indicator as a quantitative measurement of the reduced correlated background noise and photometric error present after removing fringes. We conclude by evaluating the effect of our method on measuring faint sources through the injection and recovery of artificial stars in both single-image epochs and co-additions. Our method for constructing atmospheric fringe models and applying those models to produce cleaned images is available for public download in the open source Python package fringez.

79 ASTRONOMY AND ASTROPHYSICS↗

Revealing room temperature ferromagnetism in exfoliated Fe 5 GeTe 2 flakes with quantum magnetic imaging

Van der Waals (vdW) material Fe 5 GeTe 2 , with its long-range ferromagnetic ordering near room temperature, has significant potential to become an enabling platform for implementing novel spintronic and quantum devices. To pave the way for applications, it is crucial to determine the magnetic properties when the thickness of Fe 5 GeTe 2 reaches the few-layers regime. However, this is highly challenging due to the need for a characterization technique that is local, highly sensitive, artifact-free, and operational with minimal fabrication. Prior studies have indicated that Curie temperature T C can reach up to close to room temperature for exfoliated Fe 5 GeTe 2 flakes, as measured via electrical transport; there is a need to validate these results with a measurement that reveals magnetism more directly. Here, we investigate the magnetic properties of exfoliated thin flakes of vdW magnet Fe 5 GeTe 2 via quantum magnetic imaging technique based on nitrogen vacancy centers in diamond. Through imaging the stray fields, we confirm room-temperature magnetic order in Fe 5 GeTe 2 thin flakes with thickness down to 7 units cell. The stray field patterns and their response to magnetizing fields with different polarities is consistent with previously reported perpendicular easy-axis anisotropy. Furthermore, we perform imaging at different temperatures and determine the Curie temperature of the flakes at ≈300 K. These results provide the basis for realizing a room-temperature monolayer ferromagnet with Fe 5 GeTe 2 . This work also demonstrates that the imaging technique enables rapid screening of multiple flakes simultaneously as well as time-resolved imaging for monitoring time-dependent magnetic behaviors, thereby paving the way towards high throughput characterization of potential two-dimensional (2D) magnets near room temperature and providing critical insights into the evolution of domain behaviors in 2D magnets due to degradation.

2D magnet↗

Deep learning-based spatiotemporal multi-event reconstruction for delay line detectors

Abstract Accurate observation of two or more particles within a very narrow time window has always been a challenge in modern physics. It creates the possibility of correlation experiments, such as the ground-breaking Hanbury Brown–Twiss experiment, leading to new physical insights. For low-energy electrons, one possibility is to use a Microchannel plate with subsequent delay lines for the readout of the incident particle hits, a setup called a Delay Line Detector. The spatial and temporal coordinates of more than one particle can be fully reconstructed outside a region called the dead radius. For interesting events, where two electrons are close in space and time, the determination of the individual positions of the electrons requires elaborate peak finding algorithms. While classical methods work well with single particle hits, they fail to identify and reconstruct events caused by multiple nearby particles. To address this challenge, we present a new spatiotemporal machine learning model to identify and reconstruct the position and time of such multi-hit particle signals. This model achieves a much better resolution for nearby particle hits compared to the classical approach, removing some of the artifacts and reducing the dead radius a factor of eight. We show that machine learning models can be effective in improving the spatiotemporal performance of delay line detectors.

Computer Science↗

KG-Hub—building and exchanging biological knowledge graphs

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract–transform–load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial–environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of Electron Tomography Capabilities for Shale Imaging

Despite the advantageous resolution of electron tomography (ET), reconstruction of three-dimensional (3D) images from multiple two-dimensional (2D) projections presents several challenges, including small signal-to-noise ratios, and a limited projection range. This study evaluates the capabilities of ET for thin sections of shale, a complex nanoporous medium. A numerical phantom with 1.24 nm pixel size is constructed based on the tomographic reconstruction of a Barnett shale. A dataset of 2D projection images is numerically generated from the 3D phantom and studied over a range of conditions. First, common reconstruction techniques are used to reconstruct the shale structure. The reconstruction uncertainty is quantified by comparing overall values of storage and transport metrics, as well as the misclassification of pore voxels compared to the phantom. We then select the most robust reconstruction technique and we vary the acquisition conditions to quantify the effect of artifacts. We find a strong agreement for large pores over the different acquisition workflows, while a wider variability exists for nanometer-scale features. Furthermore, the limited projection range and reconstruction are identified as the main experimental bottlenecks, thereby suggesting that sample thinning, advanced holders, and advanced reconstruction algorithms offer opportunities for improvement.

3D scanning transmission electron microscopy↗

Multimodal imaging of hemorrhagic transformation biomarkers in an ischemic stroke model.

Abstract Hemorrhagic transformation of ischemic stroke has devastating consequences, with high mortality and poor functional outcomes. Animal models of ischemic stroke also demonstrate the potential for hemorrhagic transformation, which complicates biochemical characterization, treatment studies, and hinders poststroke functional outcomes in affected subjects. The incidence of hemorrhagic transformation of ischemic stroke in animal model research is not commonly reported. The postmortem brain of such cases presents a complex milieu of biomarkers due to the presence of healthy cells, regions of varying degrees of ischemia, dead and dying cells, dysregulated metabolites, and blood components (especially reactive Fe species released from lysed erythrocytes). To improve the characterization of hemorrhage biomarkers on an ischemic stroke background, we have employed a combination of histology, X-ray fluorescence imaging (XFI), and Fourier transform infrared (FTIR) spectroscopic imaging to assess 122 photothrombotic (ischemic) stroke brains. Rapid freezing preserves brain biomarkers in situ and minimizes metabolic artifacts due to postmortem ischemia. Analysis revealed that 25% of the photothrombotic models had clear signs of hemorrhagic transformation. The XFI and FTIR metabolites provided a quantitative method to differentiate key metabolic regions in these models. Across all hemorrhage cases, it was possible to consistently differentiate otherwise healthy tissue from other metabolically distinct regions, including the ischemic infarct, the ischemic penumbra, blood vessels, sites of hemorrhage, and a region surrounding the hemorrhage core that contained elevated lipid oxidation. Chemical speciation of deposited Fe demonstrates the presence of heme-Fe and accumulation of ferritin.

Pushie, M. J. (ORCID:0000000174945427)↗

X-ray fluorescence microscopy methods for biological tissues

Abstract Synchrotron-based X-ray fluorescence microscopy is a flexible tool for identifying the distribution of trace elements in biological specimens across a broad range of sample sizes. The technique is not particularly limited by sample type and can be performed on ancient fossils, fixed or fresh tissue specimens, and in some cases even live tissue and live cells can be studied. The technique can also be expanded to provide chemical specificity to elemental maps, either at individual points of interest in a map or across a large field of view. While virtually any sample type can be characterized with X-ray fluorescence microscopy, common biological sample preparation methods (often borrowed from other fields, such as histology) can lead to unforeseen pitfalls, resulting in altered element distributions and concentrations. A general overview of sample preparation and data-acquisition methods for X-ray fluorescence microscopy is presented, along with outlining the general approach for applying this technique to a new field of investigation for prospective new users. Considerations for improving data acquisition and quality are reviewed as well as the effects of sample preparation, with a particular focus on soft tissues. The effects of common sample pretreatment steps as well as the underlying factors that govern which, and to what extent, specific elements are likely to be altered are reviewed along with common artifacts observed in X-ray fluorescence microscopy data.

Pushie, M. Jake (ORCID:0000000174945427)↗

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. In this work, we demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗

Direct structural retrieval from gas-phase ultrafast diffraction data using a genetic algorithm

Ultrafast scattering techniques such as ultrafast electron diffraction and ultrafast x-ray diffraction have been utilized to elucidate the structural dynamics, reaction intermediates, and final products in molecular reactions following photoexcitation. The time-dependent structures are typically not directly retrieved from the experimental data, but they rely on comparison with calculations. The genetic algorithm (GA), a global optimization strategy, can be used to retrieve the molecular structures directly from diffraction patterns without any theoretical input. However, the robustness of the GA with respect to real experimental conditions such as a limited momentum transfer range, noise, and artifacts has not been studied in detail. In this work, we characterize the performance of the GA with simulated data that mimic realistic experimental conditions. We have developed and implemented a variant of the GA specific to diffraction measurements which performs better in the presence of imperfect data compared to the standard implementation of the GA. We demonstrate this method with both synthetic data and experimental ultrafast electron diffraction data on the UV-induced photodissociation of trifluoroiodomethane (C⁢F 3⁡ I) molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗

Importance of finite-size corrections for accurate ab initio modeling of carrier capture at semiconductor defects: A case study of substitutional C N in GaN

In ab initio studies of carrier-capture processes in defective semiconductor materials, the single-effective-mode formalism and the static-coupling approximation have become the predominant theoretical approaches for determining carrier-capture coefficients. The single-mode formalism relies on accurate nonequilibrium defect energies obtained from density-functional theory (DFT), where required inputs are a series of configurationally displaced, defect-containing supercells obtained using an interpolative ansatz, and where the DFT outputs are corresponding total energies that have traditionally been postprocessed using a long-established ground-state formulation of finite-size corrections and defect-formation energies. This formulation remains commonly used even though the defects that form a configuration-coordinate (CC) diagram typically exist as structures that are displaced from the ground state. To remedy this inconsistency, Kumagai has recently proposed novel methods for implementing finite-size corrections specifically intended for DFT calculations of the defect energies used to construct CC diagrams and implement the single-mode formalism [Y. Kumagai, Phys. Rev. B 107, L220101 (2023)]. Kumagai's approach builds on the latest finite-size-correction methods introduced to describe vertical charge-state transitions for charge-localizing point defects in semiconductors and insulators [T. Gake et al., Phys. Rev. B 101, 020102 (2020); S. Falletta et al., Phys. Rev. B 102, 041115 (2020)]. The newly identified finite-size artifact treated in these studies is the polarization charge induced on a configurationally frozen defect and its subsequent interaction with a vertical transition in charge state. In this work, we evaluate Kumagai's proposed methodology by applying it in a high-precision DFT study of carrier capture by substitutional C N in GaN, a well-characterized and technologically relevant defect and material. We have rigorously calculated C N defect energies across various supercell sizes for each defect configuration and charge state on the hole-capture CC diagram of C N (𝑞=−1), enabling a direct comparison of the slopes of the defect energies versus inverse cell size with those predicted by Kumagai. The most consequential prediction of Kumagai's method is that these slopes distinctly vary as the square of the linear-interpolation parameter used to construct the nonequilibrium defect configurations. Our results quantitatively support this prediction. Moreover, with these new finite-size corrections and multiple-cell-size DFT calculations in place, we find that the classical energy barrier for hole capture by C N (𝑞=−1) in GaN decreases to 0.092–0.127 eV. This finding confirms the recent ≈ 0.1 eV prediction of Reshchikov based on the weak temperature dependence for hole capture observed in photoluminescence experiments [M. A. Reshchikov, J. Appl. Phys. 129, 121101 (2021)]. These results stand in stark contrast to previously calculated barriers of 0.486 and 0.73 eV, which also used the single-mode formalism but were obtained by instead using ground-state-based finite-size corrections. Our reduced classical barrier for capture increases the temperature-dependent hole-capture coefficient of a C N (𝑞=−1) defect by more than two to four orders of magnitude for temperatures of 100–600 K, compared to the previous 0.486 eV results. While other defects may not be as dramatically affected as here, we suggest that incorporating proper finite-size corrections for the vertical-transition-like states embedded within CC diagrams is an essential, yet previously unrecognized, component of accurate modeling of carrier-capture when using the single-effective-mode formalism.

dielectric properties↗

Agentic artificial intelligence for multistage physics experiments at a large-scale user facility particle accelerator

We present a language-model-driven agentic artificial intelligence (AI) system to autonomously execute multistage physics experiments on a production synchrotron light source. Implemented at the Advanced Light Source particle accelerator, the system translates natural language user prompts into structured execution plans that combine archive data retrieval, control-system channel resolution, automated script generation, controlled machine interaction, and analysis. In a representative machine physics task, we show that preparation time was reduced by 2 orders of magnitude relative to manual scripting even for a system expert, while operator-standard safety constraints were strictly upheld. Core architectural features, plan-first orchestration, bounded tool access, and dynamic capability selection, enable transparent, auditable execution with fully reproducible artifacts. These results establish a blueprint for the safe integration of agentic AI into accelerator experiments and demanding machine physics studies, as well as routine operations, with direct portability across accelerators worldwide and, more broadly, to other large-scale scientific infrastructures.

Accelerator/storage ring control systems↗

Fixed-point quantum circuits for quantum field theories

Renormalization group ideas and effective operators are introduced to efficiently prepare ground states of massive lattice field theories on digital quantum devices. This is accomplished with a systematic approximation through localized unitaries that removes an exponentially costly barrier in the spatial volume of the quantum simulation. With these methods, classically computed ground states in a spatial volume L, containing a few Compton wavelengths, can be used to determine operators for preparing the ground state toward the thermodynamic limit with a precision improving as e –mL on beyond-classical quantum registers. Here, due to the exponential spatial decay of correlations in massive theories and the double exponential suppression of digitization artifacts in the number of qubits representing the scalar field, the derived fixed-point quantum circuits are expected to be relevant for simulations of quantum field theories throughout the evolution from small-scale near-term quantum devices to large-scale fault-tolerant quantum computers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Mixed-strategy approach to band-edge analysis and modeling in semiconductors

In semiconductor physics, the Urbach rule describes an exponential dependence of the UV-Vis absorption coefficient on photon energy at the band edge. The rule is so ubiquitously applied that a single common mechanism, variability in the local potential, is generally considered to be the cause of exponential band edges. Variability in the local potential may be caused by alloy inhomogeneity, structural defects, impurities, thermal excitation, or any other mechanism that interrupts ideal crystallinity and creates disorder. A crucial point of the Urbach rule is its development for band edges which approach linearity when plotted on a logarithmic scale. The rule was not developed in the context of nonlinear band edges with complex fine structure. Even so, this model has been applied extensively to band edges with such features. Using differential analysis and deconvolution, we develop an analytical technique capable of separating the components responsible for the fine structure observed. This approach reduces challenging signal-artifact convolution problems to a simple linear combination. Furthermore, we develop a model that can be applied to the nonlinear band-edge signals extracted. In this work, we show that in the limiting case of linearity, our model is consistent with and produces the same results as the linear Urbach model. Our model is capable of bypassing “tailing” as an indirect measure of the spread in the local potential and gives a direct measure of this quantity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Analytical continuation of matrix-valued functions: Carathéodory formalism

Finite-temperature quantum field theories are formulated in terms of Green's functions and self-energies on the Matsubara axis. In multiorbital systems, these quantities are related to positive semidefinite matrix-valued functions of the Carathéodory and Schur class. Analysis, interpretation, and evaluation of derived quantities such as real-frequency response functions requires analytic continuation of the off-diagonal elements to the real axis. Here we derive the criteria under which such functions exist for given Matsubara data and present an interpolation algorithm that intrinsically respects their mathematical properties. For small systems with precise Matsubara data, we find that the continuation exactly recovers all off-diagonal and diagonal elements. In real-materials systems, we show that the precision of the continuation is sufficient for the analytic continuation to commute with the Dyson equation, and we show that the truncation of the off-diagonal self-energy elements leads to considerable approximation artifacts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Spreading resistance effects in tunneling spectroscopy of α–RuCl 3 and Ir 0.5 Ru 0.5 Cl 3

The Mott insulating state is the progenitor of many interesting quantum phases of matter including the famous high-temperature superconductors and quantum spin liquids. A recent candidate for novel spin liquid phenomena is α–RuCl 3 , a layered honeycomb Mott insulator whose electronic structure has been a source of mystery. In particular, scanning tunneling spectroscopy has indicated a Mott gap in α–RuCl 3 that is much lower than the 2-eV value observed in photoemission measurements. Here, we show that the origin of this discrepancy is a spreading resistance artifact associated with tunneling into highly resistive materials by comparing with prior experiments and numerical modeling. Furthermore, a similar phenomenon is also observed in a substitutional alloy, Ir 0.5 Ru 0.5 Cl 3 , that has a higher resistivity than the parent compound. While the tunneling measurements cannot be used to accurately measure the sample density of states for these materials, we can take advantage of the spreading resistance sensitivity to quantify the anisotropic resistivity of these layered materials and connect to previous macroscopic transport observations.

2-dimensional systems↗

Imaging interfacial topography with coherent x-ray reflectivity

The use of coherent x-ray reflectivity to image interfaces is illustrated using model calculations for three cases: a thin film, a semi-infinite substrate, and a coherently strained epitaxial thin film. The intensities and phases of the coherent scattering signals are calculated based on a fully atomistic model (where the phases are assumed to have been recovered by a phasing algorithm). Here, we describe the characteristics of the effective density that are obtained by direct inverse Fourier transformation of the complex structure factors, using a window function to define the data range. These effective densities include significant artifacts like oscillations and negative values derived from the finite vertical momentum transfer of the window function. Two approaches are described to extract the surface topography from the effective densities for three-dimensional visualization: (i) multiplying the effective density by a phase factor and (ii) analyzing the data as a hybrid structure factor F(x, Q z ). The explicit surface sensitivity and specificity of measurements is illustrated when the film or substrate Bragg peaks are excluded. These considerations show that images of interfacial topography can be obtained using currently available experimental capabilities with parameters corresponding to epitaxial thin films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Topological Hall-like behavior of multidomain ferromagnets

Here, we investigate the emergence of topological Hall-like signals in disordered multidomain ferromagnets. Nonmonotonic behavior in Hall resistivity, commonly attributed to topological spin textures such as skyrmions, is produced in a random resistor network model without any chirality. It arises from simple mechanisms of the anomalous Hall effect in combination with the domain wall scattering. By varying domain configurations and domain wall resistances, we explore the conditions under which the nonmonotonic resistivity can be enhanced. Our results emphasize the need for careful analysis in distinguishing between true topological Hall effects and artifacts caused by domain disorders.

anomalous Hall effect↗