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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Emergence of flat bands and ferromagnetic fluctuations via orbital-selective electron correlations in Mn-based kagome metal

Kagome lattice has been actively studied for the possible realization of frustration-induced two-dimensional flat bands and a number of correlation-induced phases. Currently, the search for kagome systems with a nearly dispersionless flat band close to the Fermi level is ongoing. Here, by combining theoretical and experimental tools, we present Sc 3 Mn 3 Al 7 Si 5 as a novel realization of correlation-induced almost-flat bands in the kagome lattice in the vicinity of the Fermi level. Our magnetic susceptibility, 27 Al nuclear magnetic resonance, transport, and optical conductivity measurements provide signatures of a correlated metallic phase with tantalizing ferromagnetic instability. Our dynamical mean-field calculations suggest that such ferromagnetic instability observed originates from the formation of nearly flat dispersions close to the Fermi level, where electron correlations induce strong orbital-selective renormalization and manifestation of the kagome-frustrated bands. In addition, a significant negative magnetoresistance signal is observed, which can be attributed to the suppression of flat-band-induced ferromagnetic fluctuation, which further supports the formation of flat bands in this compound. These findings broaden a new prospect to harness correlated topological phases via multiorbital correlations in 3d-based kagome systems.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Polymorphisms in Fibronectin Binding Protein A of Staphylococcus Aureus are Associated with Infection of Cardiovascular Devices

Medical implants, like cardiovascular devices, improve the quality of life for countless individuals but may become infected with bacteria like Staphylococcus aureus. Such infections take the form of a bio-film, a structured community of bacterial cells adherent to the surface of a solid substrate. Every bio-film begins with an attractive force or bond between bacterium and substratum. We used atomic force microscopy to probe experimentally forces between a fibronectin-coated surface (i.e., proxy for an implanted cardiac device) and fibronectin-binding receptors on the surface of individual living bacteria from each of 80 clinical isolates of S. aureus. These isolates originated from humans with infected cardiac devices (CDI; n = 26), uninfected cardiac devices (n = 20), and the anterior nares of asymptomatic subjects (n = 34). CDI isolates exhibited a distinct bindingforce signature and had speci!c single amino acid polymorphisms in fibronectin-binding protein A corresponding to E652D, H782Q, and K786N. In silico molecular dynamics simulations demonstrate that residues D652, Q782, and N786 in fibronectin-binding protein A form extra hydrogen bonds with fibronectin, complementing the higher binding force and energy measured by atomic force microscopy for the CDI isolates. This study is significant, because it links pathogenic bacteria biofilms from the length scale of bonds acting across a nanometer-scale space to the clinical presentation of disease at the human dimension.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2019

Multichannel charge Kondo effect and non-Fermi-liquid fixed points in conventional and topological superconductor islands

We study multiterminal Majorana and conventional superconducting islands in the vicinity of the charge degeneracy point using bosonization and the numerical renormalization group. Both models map to the multichannel charge Kondo problem, but for noninteracting normal leads they flow to different non-Fermi-liquid fixed points at low temperatures. We compare and contrast both cases by numerically obtaining the full crossover to the low-temperature regime, and we predict distinctive transport signatures. Here, the differences between the two types of islands result from a crucial distinction between charge-2e and charge-e transfer in the conventional and topological case, respectively. In the conventional case, our results establish s-wave islands as a platform to study the intermediate multichannel Kondo fixed point. In the topological setup, the crossover temperature to non-Fermi-liquid behavior is relatively high as it is proportional to the level broadening, and the transport results are not sensitive to channel coupling anisotropy, moving away from the charge degeneracy point or including a small Majorana hybridization, which makes our proposal experimentally feasible.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Transposon signatures of allopolyploid genome evolution

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

Significance In mammals, when and where a gene is transcribed are primarily regulated by the activity of regulatory DNA elements, or enhancers. Genetic mutation disrupting enhancer function is emerging as one of the major causes of human diseases. However, our knowledge remains limited about the location and activity of enhancers in the numerous and distinct cell types and tissues. Here, we develop a computational approach, regulatory element prediction based on tissue-specific local epigenetic marks (REPTILE), to precisely locate enhancers based on genome-wide DNA methylation and histone modification profiling. We systematically tested REPTILE on a variety of human and mouse cell types and tissues. Compared with existing methods, we found that enhancer predictions from REPTILE are more likely to be active in vivo and the predicted locations are more accurate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses

Antibodies capable of neutralizing divergent influenza A viruses could form the basis of a universal vaccine. Here, from subjects enrolled in an H5N1 DNA/MIV-prime-boost influenza vaccine trial, we sorted hemagglutinin cross-reactive memory B cells and identified three antibody classes, each capable of neutralizing diverse subtypes of group 1 and group 2 influenza A viruses. Co-crystal structures with hemagglutinin revealed that each class utilized characteristic germline genes and convergent sequence motifs to recognize overlapping epitopes in the hemagglutinin stem. All six analyzed subjects had sequences from at least one multidonor class, and—in half the subjects—multidonor-class sequences were recovered from >40% of cross-reactive B cells. By contrast, these multidonor-class sequences were rare in published antibody datasets. Vaccination with a divergent hemagglutinin can thus increase the frequency of B cells encoding broad influenza A-neutralizing antibodies. We propose the sequence signature-quantified prevalence of these B cells as a metric to guide universal influenza A immunization strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Genomics of sorghum local adaptation to a parasitic plant

Host–parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR–Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis

The SMARCA4 (also known as BRG1 in humans) chromatin remodeling factor is critical for establishing lineage-specific chromatin states during early mammalian development. However, the role of SMARCA4 in tissue-specific gene regulation during embryogenesis remains poorly defined. To investigate the genome-wide binding landscape of SMARCA4 in differentiating tissues, we engineered a Smarca4FLAG knock-in mouse line. Using ChIP-seq, we identified ~51,000 SMARCA4- associated regions across six embryonic mouse tissues (forebrain, hindbrain, neural tube, heart, limb, and face) at midgestation (E11.5). The majority of these regions was distal from promoters and showed dynamic occupancy, with most distal SMARCA4 sites (73%) confined to a single or limited subset of tissues. To further characterize these regions, we profiled active and repressive histone marks in the same tissues and examined the intersection of informative chromatin states and SMARCA4 binding. This revealed distinct classes of distal SMARCA4-associated elements characterized by activating and repressive chromatin signatures that were associated with tissue-specific up- or down-regulation of gene expression and relevant active/repressed biological pathways. We further demonstrate the predicted active regulatory properties of SMARCA4- associated elements by retrospective analysis of tissue-specific enhancers and direct testing of SMARCA4-bound regions in transgenic mouse assays. Our results indicate a dual active/repressive function of SMARCA4 at distal regulatory sequences in vivo and support its role in tissue-specific gene regulation during embryonic development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Self-stabilizing exchange-mediated spin transport

We report that long-range spin transport in magnetic systems can be achieved by means of exchange-mediated spin textures with robust topological winding, a phenomenon referred to as spin superfluidity. Its experimental signatures have been discussed in antiferromagnets, which are nearly free of dipolar interaction. However, in ferromagnets, which possess non-negligible dipole fields, realization of such spin transport has remained a challenge. Using micromagnetic simulations, we investigate coherent exchange-mediated spin transport in extended thin ferromagnetic films. We uncover a two-fluid state in which the long-range spin transport by spin textures coexists with spin waves, as well as a soliton-screened spin transport regime at high spin injection biases. Both states are associated with distinct spin texture reconstructions near the spin injection region and sustain spin transport over large distances.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Sci—Fri AM: Mountain — 04: Label-free Raman spectroscopy of single tumour cells detects early radiation-induced glycogen synthesis associated with increased radiation resistance

Purpose: To use label-free Raman spectroscopy (RS) for early treatment monitoring of tumour cell radioresistance. Methods: Three human tumour cell lines, two radioresistant (H460, SF{sub 2} = 0.57 and MCF7, SF{sub 2} = 0.70) and one radiosensitive (LNCaP, SF{sub 2} = 0.36), were irradiated with single fractions of 2, 4, 6, 8 or 10 Gy. In additional experiments, H460 and MCF7 cells were irradiated under co-treatment with the anti-diabetic drug metformin, a known radiosensitizing agent. Treated and control cultures were analyzed with RS daily for 3 days post-treatment. Single-cell Raman spectra were acquired from 20 live cells per sample, and experiments were repeated in triplicate. The combined data sets were analyzed with principal component analysis using standard algorithms. Cells from each culture were also subjected to standard assays for viability, proliferation, cell cycle, and radiation clonogenic survival. Results: The radioresistant cells (H460, MCF7) exhibited a RS molecular radiation response signature, detectable as early as 1 day post-treatment, of which radiation-induced glycogen synthesis is a significant contributor. The radiosensitive cells (LNCaP) exhibited negligible glycogen synthesis. Co-treatment with metformin in MCF7 cells blocked glycogen synthesis, reduced viability and proliferation, and increased radiosensitivity. Conversely, metformin co-treatment in H460 cells did not produce these same effects; importantly, both radiation-induced synthesis of glycogen and radiosensitivity were unaffected. Conclusions: Label-free RS can detect early glycogen synthesis post-irradiation, a previously undocumented metabolic mechanism associated with tumour cell radioresistance that can be targeted to increase radiosensitivity. RS monitoring of intratumoral glycogen may provide new opportunities for personalized combined modality radiotherapy treatments.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Genomic fingerprints of the world’s soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Extending Classification Algorithms to Case-Control Studies

Classification is a common technique applied to ’omics data to build predictive models and identify potential markers of biomedical outcomes. Despite the prevalence of case-control studies, the number of classification methods available to analyze data generated by such studies is extremely limited. Conditional logistic regression is the most commonly used technique, but the associated modeling assumptions limit its ability to identify a large class of sufficiently complicated ’omic signatures. We propose a data preprocessing step which generalizes and makes any linear or nonlinear classification algorithm, even those typically not appropriate for matched design data, available to be used to model case-control data and identify relevant biomarkers in these study designs. We demonstrate on simulated case-control data that both the classification and variable selection accuracy of each method is improved after applying this processing step and that the proposed methods are comparable to or outperform existing variable selection methods. Finally, we demonstrate the impact of conditional classification algorithms on a large cohort study of children with islet autoimmunity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

DNA Persistence in a Sink Drain Environment

Biofilms are organized structures composed mainly of cells and extracellular polymeric substances produced by the constituent microorganisms. Ubiquitous in nature, biofilms have an innate ability to capture and retain passing material and may therefore act as natural collectors of contaminants or signatures of upstream activities. To determine the persistence and detectability of DNA passing through a sink drain environment, Bacillus anthracis strain Ames35 was cultured (6.35 x 10 7 CFU/mL), sterilized, and disposed of by addition to a sink drain apparatus with an established biofilm. The sink drain apparatus was sampled before and for several days after the addition of the sterilized B. anthracis culture to detect the presence of B. anthracis DNA. Multiple PCR primer pairs were used to screen for chromosomal and plasmid DNA with primers targeting shorter sequences showing greater amplification efficiency and success. PCR amplification and detection of target sequences indicate persistence of chromosomal DNA and plasmid DNA in the biofilm for 5 or more and 14 or more days, respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Final Report for Wetlands as a Source of Atmospheric Methane: A Multiscale and Multidisciplinary Approach

Boreal peatlands contain large amounts of old carbon, protected by anaerobic and cold conditions. Climate change could result in favorable conditions for the microbial decomposition and release of this old peat carbon as CO2 or CH4 back into the atmosphere. Our goal was to test the potential for this positive biological feedback to climate change at SPRUCE (Spruce and Peatland Response Under Climatic and Environmental Change), a manipulation experiment funded by DOE and occurring in a forested bog in Minnesota. Taking advantage of LLNL’s capabilities and expertise in chemical and isotopic signatures we found that carbon emissions from peat were dominated by recently fixed photosynthates, even after short-term experimental warming. We also found that subsurface hydrologic transport was surprisingly rapid at SPRUCE, supplying microbes with young dissolved organic carbon (DOC). We also identified which microbes oxidize CH4 to CO2 at SPRUCE and found that the most active of these also fix N2 (which means they can utilize atmospheric N, making it accessible for other microbes and plants). These results reflect important interactions between hydrology, carbon cycling, and nitrogen cycling present at the bog and relevant to interpreting experimental results and modeling the wetland response to experimental treatments. LLNL involvement at SPRUCE continues through collaborations and a small contract with ORNL, the lead lab for the SPRUCE experiment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Strategic Survey of Antineutrino-based Nonproliferation Technologies

Antineutrinos carry approximately 3% of the total energy released in fission processes. As a consequence, nuclear energy production provides by far the brightest antineutrino sources on Earth. Antineutrino interactions with ordinary matter are weak and these particles cannot be shielded, making them an ideal signature of fissioning systems. However, the same property makes antineutrinos difficult to detect. Antineutrino detection technologies have matured in recent years, and emerging detection approaches warrant further investment. For near-field applications, the major enabling technological advancement, reported in 2018, is the conclusive detection of the antineutrino spectrum in segmented detectors operating at the surface with minimal shielding. For far-field applications, the highlights are the routine detection of reactor antineutrinos at hundreds of kilometer standoff in the kiloton-scale KamLAND and Borexino liquid scintillator detectors, and in particular the observation of the residual South Korean reactor antineutrino flux in KamLAND following the Fukushima disaster that led to shutdown of reactors in Japan

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRSDate not supplied

Identifying Chemical and Optical Smoke Signatures in Suborbital Observations to Improve Model Projections

Biomass Burning (BB) fires are expected to occur more frequently in the future due to climate change, the build‐up of fuels due to fire suppression, and the expansion of the wildland‐urban interface [Schoennagel et al., 2017; Shivdenko & Schepaschenko, 2013; Stevens et al., 2014; Turner et al., 2019; Yue et al., 2015; Tilman et al., 2001]. Accurate knowledge of the abundance, distribution, and optical properties of absorbing aerosols such as BB smoke is essential to understanding regional and global aerosol radiative effects [Boucher et al., 2013]. It is recognized that differing fuel types (e.g., rice straw, ponderosa pine), combustion modes (i.e., flaming, smoldering or both) and temperature/ moisture content produce smoke with differing optical characteristics (e.g., aerosol light scattering and absorption) and component mixing ratios [e.g., BC, OC and inorganic species such as sulfate, potassium, chloride; Streets et al. 2003; Reid et al., 2005a, b; Janhäll et al., 2010; Sayer et al., 2014]. However, climate models often ascribe a fixed set of emission factors [i.e., amount of particulate for a given species released in the atmosphere per unit dry fuel burned; Darmenov and Dasilva, 2013] and optical properties [Hess et al., 1998] to all BB aerosol plumes, inherently limiting accurate representation of the global and regional heterogeneity of BB. The overarching goal of the proposed work is to improve the microphysical and optical representation of different types of Biomass Burning in Chemistry Transport Models. Our strategy is to capitalize on multiple airborne campaigns (e.g., ARCTAS, SEAC4RS, ORACLES, FIREX-AQ), which sampled different types of BB plumes at different aging stages. Models, when improved and combined with satellite, airborne, and ground observations will help address many aerosol science objectives from the NASA Decadal survey [National Academies of Sciences, Engineering, and Medicine. 2018].

Meloe Shenandoah F Kacenelenbogen↗
DOE OSTI2018

Egress of murine regulatory T cells from the thymus requires TIPE2

Highlights: • TIPE2 deficiency leads to the accumulation of Tregs in the thymus. • TIPE2 deficiency doesn't affect the development and apoptosis of tTregs. • TIPE2 promotes the chemotaxis of tTregs in vitro. • TIPE2 promotes the polarization of pAKT and F-actin in tTregs undergoing directed migration. Regulatory T cells (Tregs) can be divided into thymus-derived Treg (tTregs) and peripheral induced Tregs (pTregs) in vivo according to their origins and are essential for the maintenance of immune hemostasis and immune tolerance. Tumor necrosis factor-α-induced protein 8 like 2 (TIPE2) is expressed primarily by immune cells and is a negative regulator of the innate and adaptive immune response. Previous studies indicate that TIPE2 is required for the expression of Treg signature genes and promotes leading-edge formation in neutrophils through cytoskeleton remodeling. In the current study, we showed that TIPE2 deficient mice accumulate more Treg cells in the thymus. Further studies revealed that TIPE2 deficiency doesn't affect the development and apoptosis of tTregs. Instead, TIPE2 promotes the chemotaxis of tTregs in vitro, which may account for the accumulation of Tregs in the thymus of TIPE2 deficient mice. Mechanistic study revealed that TIPE2 promotes the polarization of pAKT and F-actin in tTregs undergoing directed migration. Taken together, these results demonstrated that TIPE2 enhances the cytoskeleton remodeling and promotes the thymus egress of tTregs, which may play an important role in the maintenance of self-tolerance.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Radiation Effects on Uranyl Tetrachloro Coordination Compounds: Impact of Lattice Water

Nuclear materials, such as uranium-bearing solids, are exposed to high levels of ionizing radiation throughout the nuclear fuel cycle; thus, it is important to develop a molecular-level understanding of how these materials behave and degrade in the presence of gamma (γ) irradiation. In the current study, three U(VI) tetrachloride complexes, M 2 [UO 2 Cl 4 ]·xH 2 O (where M = K + , Rb + , or Cs + and x = 0 or 2), and their respective chloride salts were exposed to 1–50 kGy of γ radiation using a 60 Co source. Irradiated materials were evaluated by using electron paramagnetic resonance (EPR) and Raman spectroscopy and were further explored by using density functional theory (DFT) methods. EPR spectra of the irradiated materials suggest the formation of a Cl-based radical for both the alkali salts and the uranyl tetrachloride compounds, and DFT calculations provide evidence that the Cl 2 –• radical is formed within these materials. The presence of water in the K + and Rb + compounds leads to additional spectroscopic signatures that could be traced back to water radiolysis and the formation of peroxide and superoxide species. DFT results support the formation of HO 2 • in the lattice and potentially the formation of a [UO 2 Cl 3 (O 2 )] 3– species, highlighting the impact of water within the hydrated material to alter U(VI) speciation by radiolysis.

36 MATERIALS SCIENCE↗