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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 1,243 records · Page 69
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Operation and performance of a dual-phase crystalline/vapor xenon time projection chamber

We have built and operated a crystalline/vapor xenon TPC, with the goal of improving searches for dark matter. The motivation for this instrument is the fact that beta decays from the radon decay chain to the ground state presently limit the state-of-the-art liquid/vapor xenon experiments. In contrast, a crystalline xenon target has the potential to exclude, or tag and reject radon-chain backgrounds. As a preamble to demonstrating such capabilities, the present article makes a first demonstration of the operation of a crystalline/vapor xenon TPC with electroluminescence (gas gain) for the electron signal readout. It also shows that the scintillation yield in crystalline xenon appears to be identical to that in liquid xenon, in contrast to previous results.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Impact of ocean model resolution on understanding the delayed warming of the Southern Ocean

Abstract Currently available historical climate change simulations indicate a relatively delayed Southern Ocean warming, particularly poleward of the Antarctic Circumpolar Current (ACC) compared much of the rest of the globe. However, even this simulated delayed warming is inconsistent with observational estimates which show a cooling trend poleward of the ACC for the period 1979–2014. A fully coupled model run at two resolutions, i.e. ocean eddy parameterized and ocean eddy resolving, driven by historical and fixed CO2 concentration is used to investigate forced trends south of the ACC. We analyze the 1961–2005 Southern Ocean surface and upper ocean temperatures trends simulated by the model and observational estimates to understand the observed trends in the SO. At both resolutions, the models successfully reproduce the observed warming response for the northern flank of the ACC. The eddy resolving simulations, however, are able to reproduce the observed near Antarctic cooling in contrast to the eddy parameterized simulation which shows a warming trend. The cause of this inconsistency between the observations and the ocean eddy parameterized climate models is still a matter of debate, and we show here results that suggest resolved ocean meso-scale processes may be an integral part of capturing the observed trends in the Southern Ocean.

Environmental Sciences & Ecology↗
DOE OSTI2020

Atomic force microscopy phase imaging of epitaxial graphene films

Abstract Dynamic mode atomic force microscopy phase imaging is known to produce distinct contrast between graphene areas of different atomic thickness. But the intrinsic complexity of the processes controlling the tip motion and the phase angle shift excludes its use as an independent technique for a quantitative type of analysis. By investigating the relationship between the phase shift, the tip-surface interaction, and the thickness of the epitaxial graphene areas grown on silicon carbide, we shed light on the origin of such phase contrast, and on the complex energy dissipation processes underlying phase imaging. In particular, we study the behavior of phase shift and energy dissipation when imaging the interfacial buffer layer, single-layer, and bilayer graphene regions as a function of the tip-surface separation and the interaction forces. Finally, we compare these results with those obtained on differently-grown quasi free standing single- and bilayer graphene samples.

Lavini, Francesco (ORCID:0000000257223040)↗
DOE OSTI2024

Maven: a multimodal foundation model for supernova science

Abstract A common setting in astronomy is the availability of a small number of high-quality observations, and larger amounts of either lower-quality observations or synthetic data from simplified models. Time-domain astrophysics is a canonical example of this imbalance, with the number of supernovae observed photometrically outpacing the number observed spectroscopically by multiple orders of magnitude. At the same time, no data-driven models exist to understand these photometric and spectroscopic observables in a common context. Contrastive learning objectives, which have grown in popularity for aligning distinct data modalities in a shared embedding space, provide a potential solution to extract information from these modalities. We present Maven, the first foundation model for supernova science. To construct Maven, we first pre-train our model to align photometry and spectroscopy from 0.5 M synthetic supernovae using a contrastive objective. We then fine-tune the model on 4702 observed supernovae from the Zwicky transient facility. Maven reaches state-of-the-art performance on both classification and redshift estimation, despite the embeddings not being explicitly optimized for these tasks. Through ablation studies, we show that pre-training with synthetic data improves overall performance. In the upcoming era of the Vera C. Rubin observatory, Maven will serve as a valuable tool for leveraging large, unlabeled and multimodal time-domain datasets.

Zhang, Gemma (ORCID:0000000280198082)↗
DOE OSTI2023

Starch depletion in the xylem and phloem ray parenchyma of grapevine stems under drought

Abstract While nonstructural carbohydrate (NSC) storage can support long-lived woody plants during abiotic stress, the timing and extent of their use are less understood, as are the thresholds for cell mortality as NSCs and water supplies are consumed. Here, we combine physiological and imaging tools to study the response of Vitis riparia to a 6-week experimental drought. We focused on the spatial and temporal dynamics of starch consumption and cell viability in the xylem and phloem of the stem. Starch dynamics were further corroborated with enzymatic starch digestion and X-ray microcomputed tomography imaging. Starch depletion in the stems of droughted plants was detected after 2 weeks and continued over time. We observed distinct differences in starch content and cell viability in the xylem and phloem. By the end of the drought, nearly all the starch was consumed in the phloem ray parenchyma (98 % decrease), and there were almost no metabolically active cells in the phloem. In contrast, less starch was consumed in the xylem ray parenchyma (30 % decrease), and metabolically active cells remained in the ray and vessel-associated parenchyma in the xylem. Our data suggest that the higher proportion of living cells in the phloem and cambium, combined with smaller potential NSC storage area, rapidly depleted starch, which led to cell death. In contrast, the larger cross-sectional area of the xylem ray parenchyma with higher NSC storage and lower metabolically active cell populations depleted starch at a slower pace. Why NSC source-sink relationships between xylem and phloem do not allow for a more uniform depletion of starch in ray parenchyma over time is unclear. Our data help to pinpoint the proximate and ultimate causes of plant death during prolonged drought exposure and highlight the need to consider the influence of within-organ starch dynamics and cell mortality on abiotic stress response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗
DOE OSTI2022

Spatial resolution in secondary-electron microscopy

Here, we first review the significance of resolution and contrast in electron microscopy, and the effect of the electron optics on these two quantities. We then outline the physics of the generation of secondary electrons (SE) and their transport and emission from the surface of a specimen. Contrast and resolution are discussed for different kinds of SE imaging in scanning (SEM) and scanning-transmission (STEM) instruments, with some emphasis on the observation of individual atoms and atomic columns in a thin specimen. The possibility of achieving atomic resolution from a bulk specimen at SEM energies is also considered.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Differential response of the photosynthetic machinery to dehydration in older and younger resurrection plants

Abstract A group of vascular plants called homoiochlorophyllous resurrection plants evolved unique capabilities to protect their photosynthetic machinery against desiccation-induced damage. This study examined whether the ontogenetic status of the resurrection plant Craterostigma pumilum has an impact on how the plant responds to dehydration at the thylakoid membrane level to prepare cells for the desiccated state. Thus, younger plants (<4 months) were compared with their older (>6 months) counterparts. Ultrastructural analysis provided evidence that younger plants suppressed senescence-like programs that are realized in older plants. During dehydration, older plants degrade specific subunits of the photosynthetic apparatus such as the D1 subunit of PSII and subunits of the cytochrome b6f complex. The latter leads to a controlled down-regulation of linear electron transport. In contrast, younger plants increased photoprotective high-energy quenching mechanisms and maintained a high capability to replace damaged D1 subunits. It follows that depending on the ontogenetic state, either more degradation-based or more photoprotective mechanisms are employed during dehydration of Craterostigma pumilum.

Plant Sciences↗
DOE OSTI2024

Application of Weak-Beam Dark-Field STEM for Dislocation Loop Analysis

Nanoscale dislocation loops formed by irradiation can significantly contribute to both irradiation hardening and embrittlement of materials when subjected to extreme nuclear reactor environments. Here, this study explores the application of weak-beam dark-field (WBDF) scanning transmission electron microscopy (STEM) methods for quantitative irradiation-induced defect analysis in crystalline materials, with a specific focus on dislocation loop imaging and analysis. A high-purity Fe-5 wt% Cr model alloy was irradiated with 8 MeV Fe 2+ ions at 450°C to a fluence of 8.8 × 10 19 m -2 , inducing dislocation loops for analysis. While transmission electron microscopy (TEM) has traditionally been the primary tool for dislocation imaging, recent advancements in STEM technology have reignited interest in using STEM for defect imaging. This study introduces and compares three WBDF STEM methods, demonstrating their effectiveness in suppressing background contrasts, isolating defect information for dislocation loop type classification, providing finer dislocation line images for small loop analysis, and presenting inside–outside contrast for identifying loop nature. Experimental findings indicate that WBDF STEM methods surpass traditional TEM approaches, yielding clearer and more detailed images of dislocation loops. The study concludes by discussing the potential applications of WBDF STEM techniques in defect analysis, emphasizing their adaptability across various material systems beyond nuclear materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Single Electron Self-coherence and Its Wave/Particle Duality in the Electron Microscope

Intensities in high-resolution phase-contrast images from electron microscopes build up discretely in time by detecting single electrons. A wave description of pulse-like coherent-inelastic interaction of an electron with matter implies a time-dependent coexistence of coherent partial waves. Their superposition forms a wave package by phase decoherence of 0.5 - 1 radian with Heisenbergs energy uncertainty ΔE H = $\hbar$/2 Δt -1 matching the energy loss ΔE of a coherent-inelastic interaction and sets the interaction time Δt. In these circumstances, the product of Planck's constant and the speed of light hc is given by the product of the expression for temporal coherence λ 2 /Δλ and the energy loss ΔE. Experimentally, the self-coherence length was measured by detecting the energy-dependent localization of scattered, plane matter waves in surface proximity exploiting the Goos–Hänchen shift. Chromatic-aberration Cc-corrected electron microscopy on boron nitride (BN) proves that the coherent crystal illumination and phase contrast are lost if the self-coherence length shrinks below the size of the crystal unit cell at ΔE > 200 eV. Finally, in perspective, the interaction time of any matter wave compares with the lifetime of a virtual particle of any elemental interaction, suggesting the present concept of coherent-inelastic interactions of matter waves might be generalizable.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Super-Resolution Ptychography with Small Segmented Detectors

To overcome the spatial resolution limit set by aperture-limited diffraction in traditional scanning transmission electron microscopy, microscopists have developed ptychography enabled by iterative phase retrieval algorithms and high-dynamic-range pixel array detectors. Current detector designs are limited by the data rate off chip, so a high-pixel-count detector has a proportionally lower frame rate than the few-segment detectors used for differential phase contrast (DPC) imaging. This slower acquisition speed leads to heightened vulnerability to scan noise, drift, and potential sample damage. This creates opportunities for repurposing fast segmented detectors for ptychography by trading a reduction in reciprocal space pixels for an increase in real space pixels. Here, we explore a strategy of oversampling in real space and instead apply detector pixel upsampling during the reconstruction process. Further, we demonstrate the viability of achieving super-resolution ptychography on thin objects using only 2 × 2 detector pixels, surpassing the resolution of integrated DPC (iDPC) imaging. With optimization using simulated datasets and experiments on MoTe 2 /WSe 2 bilayer moiré superlattices, we achieved super-resolution ptychography reconstructions under rapid acquisition conditions (37.5 pA, 1 μs dwell time), yielding over 50% improvements in contrast and information limit compared to annular dark field and iDPC imaging on the same detectors.

2D materials↗
DOE OSTI2020

Revisiting the reactivity between HCO and CH 3 on interstellar grain surfaces

The formation of interstellar complex organic molecules is currently thought to be dominated by the barrierless coupling between radicals on the interstellar icy grain surfaces. Previous standard density functional theory (DFT) results on the reactivity between CH 3 and HCO on amorphous water surfaces showed that the formation of CH 4 + CO by H transfer from HCO to CH 3 assisted by water molecules of the ice was the dominant channel. In contrast, the adopted description of the electronic structure of the biradical (i.e. CH 3 /HCO) system was inadequate [without the broken-symmetry (BS) approach]. In this work, we revisit the original results by means of BS-DFT both in gas phase and with one water molecule simulating the role of the ice. Results indicate that the adoption of BS-DFT is mandatory to describe properly biradical systems. In the presence of the single water molecule, the water-assisted H transfer exhibits a high energy barrier. In contrast, CH 3 CHO formation is found to be barrierless. Yet, direct H transfer from HCO to CH 3 to give CO and CH 4 presents a very low energy barrier, hence being a potential competitive channel to the radical coupling and indicating, moreover, that the physical insights of the original work remain valid.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Spectral variability of a sample of extreme variability quasars and implications for the MgII broad-line region

We present new Gemini/GMOS optical spectroscopy of 16 extreme variability quasars (EVQs) that dimmed bymore than 1.5mag in the g band between the Sloan Digital Sky Survey (SDSS) and the Dark Energy Survey epochs (separated by a few years in the quasar rest frame). These EVQs are selected from quasars in the SDSS Stripe 82 region, covering a redshift range of 0.5 < z < 2.1. Nearly half of these EVQs brightened significantly (by more than 0.5 mag in the g band) in a few years after reaching their previous faintest state, and some EVQs showed rapid (non-blazar) variations of greater than 1-2 mag on time-scales of only months. To increase sample statistics, we use a supplemental sample of 33 EVQs with multi-epoch spectra from SDSS that cover the broad Mg II lambda 2798 line. Leveraging on the large dynamic range in continuum variability between the multi-epoch spectra, we explore the associated variations in the broad MgII line, whose variability properties have not been well studied before. The broad MgII flux varies in the same direction as the continuum flux, albeit with a smaller amplitude, which indicates at least some portion of Mg II is reverberating to continuum changes. However, the full width at half-maximum (FWHM) of Mg II does not vary accordingly as continuum changes for most objects in the sample, in contrast to the case of the broad Balmer lines. Using the width of broad MgII to estimate the black hole mass with single epoch spectra therefore introduces a luminosity-dependent bias.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Quantifying the impact of the Si/O interface in CCSN explosions using the Force Explosion Condition

ABSTRACT The explosion mechanism of a core-collapse supernova (SN) is a complex interplay between neutrino heating and cooling (including the effects of neutrino-driven convection), the gravitational potential, and the ram pressure of the infalling material. To analyse the post-bounce phase of an SN, one can use the generalized force explosion condition (FEC+), which succinctly formalizes the interplay among these four phenomena in an analytical condition, consistent with realistic simulations. In this paper, we use the FEC+ to study the post-bounce phase of 341 spherically symmetric simulations, where convection is included through a time-dependent mixing-length approach. We find that the accretion of the Si/O interface through the expanding shock can significantly change the outcome of the SN by driving the FEC+ above the explosion threshold. We systematically explore this by (i) artificially smoothing the pre-SN density profile, and (ii) artificially varying the mixing length. In both cases, we find that large-enough density contrasts at the Si/O interface lead to successful shock revival only if the FEC+ is already close to the explosion threshold. Furthermore, we find that the accretion of the Si/O interface has a substantial effect on the critical condition for SN explosions, contributing between 5 and 15 per cent, depending on how pronounced the density contrast at the interface is. Earlier studies showed that convection affects the critical condition by 25–30 per cent, which demonstrates that the accretion of the Si/O interface through the shock can play a nearly comparable role in influencing shock dynamics.

Boccioli, Luca (ORCID:000000024819310X)↗
DOE OSTI2022

Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager’s activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1

UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Two interacting ethylene response factors regulate heat stress response

Abstract The ethylene response factor (ERF) transcription factors are integral components of environmental stress signaling cascades, regulating a wide variety of downstream genes related to stress responses and plant development. However, the mechanisms by which ERF genes regulate the heat stress response are not well understood. Here, we uncover the positive role of ethylene signaling, ERF95 and ERF97 in basal thermotolerance of Arabidopsis thaliana. We demonstrate that ethylene signaling-defective mutants exhibit compromised basal thermotolerance, whereas plants with constitutively activated ethylene response show enhanced basal thermotolerance. EIN3 physically binds to the promoters of ERF95 and ERF97. Ectopic constitutive expression of ERF95 or ERF97 increases the basal thermotolerance of plants. In contrast, erf95 erf96 erf97 erf98 quadruple mutants exhibit decreased basal thermotolerance. ERF95 and ERF97 genetically function downstream of EIN3. ERF95 can physically interact with ERF97, and this interaction is heat inducible. ERF95 and ERF97 regulate a common set of target genes, including known heat-responsive genes and directly bind to the promoter of HSFA2. Thus, our study reveals that the EIN3-ERF95/ERF97-HSFA2 transcriptional cascade may play an important role in the heat stress response, thereby establishing a connection between ethylene and its downstream regulation in basal thermotolerance of plants.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Short- and long-term responses of photosynthetic capacity to temperature in four boreal tree species in a free-air warming and rainfall manipulation experiment

Abstract High latitude forests cope with considerable variation in moisture and temperature at multiple temporal scales. To assess how their photosynthetic physiology responds to short- and long-term temperature variation, we measured photosynthetic capacity for four tree species growing in an open-air experiment in the boreal-temperate ecotone `Boreal Forest Warming at an Ecotone in Danger' (B4WarmED). The experiment factorially manipulated temperature above- and below-ground (ambient, +3.2 °C) and summer rainfall (ambient, 40% removal). We measured A/Ci curves at 18, 25 and 32 °C for individuals of two boreal (Pinus banksiana Lamb., Betula papyrifera Marsh.) and two temperate species (Pinus strobus L., Acer rubrum L.) experiencing the long-term warming and/or reduced-rainfall conditions induced by our experimental treatments. We calculated the apparent photosynthetic capacity descriptors VCmax,Ci and Jmax,Ci and their ratio for each measurement temperate. We hypothesized that (i) VCmax,Ci and Jmax,Ci would be down-regulated in plants experiencing longer term (e.g., weeks to months) warming and reduced rainfall (i.e., have lower values at a given measurement temperature), as is sometimes found in the literature, and that (ii) plants growing at warmer temperatures or from warmer ranges would show greater sensitivity (steeper slope) to short-term (minutes to hours) temperature variation. Neither hypothesis was supported as a general trend across the four species, as there was not a significant main effect (across species) of either warming or rainfall reduction on VCmax,Ci and Jmax,Ci. All species markedly increased VCmax,Ci and Jmax,Ci (and decreased their ratio) with short-term increases in temperature (i.e., contrasting values at 18, 25 and 32 °C), and those responses were independent of long-term treatments and did not differ among species. The Jmax,Ci:VCmax,Ci ratio was, however, significantly lower across species in warmed and reduced rainfall treatments. Collectively, these results suggest that boreal trees possess considerable short-term plasticity that may allow homeostasis of VCmax,Ci and Jmax,Ci to a longer term temperature treatment. Our results also caution against extrapolating results obtained under controlled and markedly contrasting temperature treatments to responses of photosynthetic parameters to more modest temperature changes expected in the near-term with climate warming in field conditions.

Forestry↗