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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes

Abstract McrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis activity is stimulated by its partner nuclease McrC. Here, we report cryo-EM structures of Thermococcus gammatolerans McrB and McrBC, and E. coli McrBC. The McrB hexamers, containing the necessary catalytic machinery for basal GTP hydrolysis, are intrinsically asymmetric. This asymmetry directs McrC binding so that it engages a single active site, where it then uses an arginine/lysine-mediated hydrogen-bonding network to reposition the asparagine in the McrB signature motif for optimal catalytic function. While the two McrBC complexes use different DNA-binding domains, these contribute to the same general GTP-recognition mechanism employed by all G proteins. Asymmetry also induces distinct inter-subunit interactions around the ring, suggesting a coordinated and directional GTP-hydrolysis cycle. Our data provide insights into the conserved molecular mechanisms governing McrB family AAA + motors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Continent-wide tree fecundity driven by indirect climate effects

Indirect climate effects on tree fecundity that come through variation in size and growth (climate-condition interactions) are not currently part of models used to predict future forests. Trends in species abundances predicted from meta-analyses and species distribution models will be misleading if they depend on the conditions of individuals. Here we find from a synthesis of tree species in North America that climate-condition interactions dominate responses through two pathways, i) effects of growth that depend on climate, and ii) effects of climate that depend on tree size. Because tree fecundity first increases and then declines with size, climate change that stimulates growth promotes a shift of small trees to more fecund sizes, but the opposite can be true for large sizes. Change the depresses growth also affects fecundity. We find a biogeographic divide, with these interactions reducing fecundity in the West and increasing it in the East. Continental-scale responses of these forests are thus driven largely by indirect effects, recommending management for climate change that considers multiple demographic rates.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry

Campylobacter jejuni is a foodborne pathogen that binds to and invades the epithelial cells lining the human intestinal tract. Maximal invasion of host cells by C. jejuni requires cell binding as well as delivery of the Cia proteins (Campylobacter invasion antigens) to the host cell cytosol via the flagellum. Here, we show that CiaD binds to the host cell protein IQGAP1 (a Ras GTPase-activating-like protein), thus displacing RacGAP1 from the IQGAP1 complex. This, in turn, leads to the unconstrained activity of the small GTPase Rac1, which is known to have roles in actin reorganization and internalization of C. jejuni. Our results represent the identification of a host cell protein targeted by a flagellar secreted effector protein and demonstrate that C. jejuni-stimulated Rac signaling is dependent on IQGAP1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Creation and observation of Hopfions in magnetic multilayer systems

Among topological solitons, magnetic skyrmions are two-dimensional particle-like objects with a continuous winding of the magnetization, and magnetic Hopfions are three-dimensional objects that can be formed from a closed loop of twisted skyrmion strings. Theoretical models suggest that magnetic Hopfions can be stabilized in frustrated or chiral magnetic systems, and target skymions can be transformed into Hopfions by adapting their perpendicular magnetic anisotropy, but their experimental verification has been elusive so far. Here, we present an experimental study of magnetic Hopfions that are created in Ir/Co/Pt multilayers shaped into nanoscale disks, known to host target skyrmions. To characterize three-dimensional spin textures that distinguish Hopfions from target skyrmions magnetic images are recorded with surface-sensitive X-ray photoemission electron microscopy and bulk-sensitive soft X-ray transmission microscopy using element-specific X-ray magnetic circular dichroism effects as magnetic contrast. These results could stimulate further investigations of Hopfions and their potential application in three-dimensional spintronics devices.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile—but to a greater extent in the subsoil—physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Sugar phosphate activation of the stress sensor eIF2B

The multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. The eIF2B regulatory subcomplex is evolutionarily related to sugar-metabolizing enzymes, but the biological relevance of this relationship was unknown. To identify natural ligands that might regulate eIF2B, we conduct unbiased binding- and activity-based screens followed by structural studies. We find that sugar phosphates occupy the ancestral catalytic site in the eIF2Bα subunit, promote eIF2B holoenzyme formation and enhance enzymatic activity towards eIF2. A mutant in the eIF2Bα ligand pocket that causes Vanishing White Matter disease fails to engage and is not stimulated by sugar phosphates. These data underscore the importance of allosteric metabolite modulation for proper eIF2B function. We propose that eIF2B evolved to couple nutrient status via sugar phosphate sensing with the rate of protein synthesis, one of the most energetically costly cellular processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

In situ observation of thermal-driven degradation and safety concerns of lithiated graphite anode

Abstract Graphite, a robust host for reversible lithium storage, enabled the first commercially viable lithium-ion batteries. However, the thermal degradation pathway and the safety hazards of lithiated graphite remain elusive. Here, solid-electrolyte interphase (SEI) decomposition, lithium leaching, and gas release of the lithiated graphite anode during heating were examined by in situ synchrotron X-ray techniques and in situ mass spectroscopy. The source of flammable gas such as H 2 was identified and quantitively analyzed. Also, the existence of highly reactive residual lithium on the graphite surface was identified at high temperatures. Our results emphasized the critical role of the SEI in anode thermal stability and uncovered the potential safety hazards of the flammable gases and leached lithium. The anode thermal degradation mechanism revealed in the present work will stimulate more efforts in the rational design of anodes to enable safe energy storage.

25 ENERGY STORAGE↗
DOE OSTI2021

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Probing atom dynamics of excited Co-Mo-S nanocrystals in 3D

Advances in electron microscopy have enabled visualizations of the three-dimensional (3D) atom arrangements in nano-scale objects. The observations are, however, prone to electron-beam-induced object alterations, so tracking of single atoms in space and time becomes key to unravel inherent structures and properties. Here, we introduce an analytical approach to quantitatively account for atom dynamics in 3D atomic-resolution imaging. The approach is showcased for a Co-Mo-S nanocrystal by analysis of time-resolved in-line holograms achieving ~1.5 Å resolution in 3D. The analysis reveals a decay of phase image contrast towards the nanocrystal edges and meta-stable edge motifs with crystallographic dependence. These findings are explained by beam-stimulated vibrations that exceed Debye-Waller factors and cause chemical transformations at catalytically relevant edges. This ability to simultaneously probe atom vibrations and displacements enables a recovery of the pristine Co-Mo-S structure and establishes, in turn, a foundation to understand heterogeneous chemical functionality of nanostructures, surfaces and molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Superconductivity up to 243 K in the yttrium-hydrogen system under high pressure

The discovery of superconducting H 3 S with a critical temperature T c ~200 K opened a door to room temperature superconductivity and stimulated further extensive studies of hydrogen-rich compounds stabilized by high pressure. Here, we report a comprehensive study of the yttrium-hydrogen system with the highest predicted T c s among binary compounds and discuss the contradictions between different theoretical calculations and experimental data. We synthesized yttrium hydrides with the compositions of YH 3 , YH 4 , YH 6 and YH 9 in a diamond anvil cell and studied their crystal structures, electrical and magnetic transport properties, and isotopic effects. We found superconductivity in the Im-3m YH 6 and P6 3 /mmc YH 9 phases with maximal T c s of ~220 K at 183 GPa and ~243 K at 201 GPa, respectively. Fm-3m YH 10 with the highest predicted T c > 300 K was not observed in our experiments, and instead, YH 9 was found to be the hydrogen-richest yttrium hydride in the studied pressure and temperature range up to record 410 GPa and 2250 K.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Cas9-derived peptides presented by MHC Class II that elicit proliferation of CD4 + T-cells

CRISPR–Cas9 mediated genome editing offers unprecedented opportunities for treating human diseases. There are several reports that demonstrate pre-existing immune responses to Cas9 which may have implications for clinical development of CRISPR-Cas9 mediated gene therapy. Here we use 209 overlapping peptides that span the entire sequence of Staphylococcus aureus Cas9 (SaCas9) and human peripheral blood mononuclear cells (PBMCs) from a cohort of donors with a distribution of Major Histocompatibility Complex (MHC) alleles comparable to that in the North American (NA) population to identify the immunodominant regions of the SaCas9 protein. We also use an MHC Associated Peptide Proteomics (MAPPs) assay to identify SaCas9 peptides presented by MHC Class II (MHC-II) proteins on dendritic cells. Using these two data sets we identify 22 SaCas9 peptides that are both presented by MHC-II proteins and stimulate CD4 + T-cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Observation of the modification of quantum statistics of plasmonic systems

Abstract For almost two decades, researchers have observed the preservation of the quantum statistical properties of bosons in a large variety of plasmonic systems. In addition, the possibility of preserving nonclassical correlations in light-matter interactions mediated by scattering among photons and plasmons stimulated the idea of the conservation of quantum statistics in plasmonic systems. It has also been assumed that similar dynamics underlie the conservation of the quantum fluctuations that define the nature of light sources. So far, plasmonic experiments have been performed in nanoscale systems in which complex multiparticle interactions are restrained. Here, we demonstrate that the quantum statistics of multiparticle systems are not always preserved in plasmonic platforms and report the observation of their modification. Moreover, we show that optical near fields provide additional scattering paths that can induce complex multiparticle interactions. Remarkably, the resulting multiparticle dynamics can, in turn, lead to the modification of the excitation mode of plasmonic systems. These observations are validated through the quantum theory of optical coherence for single- and multi-mode plasmonic systems. Our findings unveil the possibility of using multiparticle scattering to perform exquisite control of quantum plasmonic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Fast-decaying plant litter enhances soil carbon in temperate forests but not through microbial physiological traits

Abstract Conceptual and empirical advances in soil biogeochemistry have challenged long-held assumptions about the role of soil micro-organisms in soil organic carbon (SOC) dynamics; yet, rigorous tests of emerging concepts remain sparse. Recent hypotheses suggest that microbial necromass production links plant inputs to SOC accumulation, with high-quality (i.e., rapidly decomposing) plant litter promoting microbial carbon use efficiency, growth, and turnover leading to more mineral stabilization of necromass. We test this hypothesis experimentally and with observations across six eastern US forests, using stable isotopes to measure microbial traits and SOC dynamics. Here we show, in both studies, that microbial growth, efficiency, and turnover are negatively (not positively) related to mineral-associated SOC. In the experiment, stimulation of microbial growth by high-quality litter enhances SOC decomposition, offsetting the positive effect of litter quality on SOC stabilization. We suggest that microbial necromass production is not the primary driver of SOC persistence in temperate forests. Factors such as microbial necromass origin, alternative SOC formation pathways, priming effects, and soil abiotic properties can strongly decouple microbial growth, efficiency, and turnover from mineral-associated SOC.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Dielectric catastrophe at the Wigner-Mott transition in a moiré superlattice

The bandwidth-tuned Wigner-Mott transition is an interaction-driven phase transition from a generalized Wigner crystal to a Fermi liquid. Because the transition is generally accompanied by both magnetic and charge-order instabilities, it remains unclear if a continuous Wigner-Mott transition exists. Here, we demonstrate bandwidth-tuned metal-insulator transitions at fixed fractional fillings of a MoSe 2 /WS 2 moiré superlattice. The bandwidth is controlled by an out-of-plane electric field. The dielectric response is probed optically with the 2s exciton in a remote WSe 2 sensor layer. The exciton spectral weight is negligible for the metallic state with a large negative dielectric constant. It continuously vanishes when the transition is approached from the insulating side, corresponding to a diverging dielectric constant or a ‘dielectric catastrophe’ driven by the critical charge dynamics near the transition. Our results support the scenario of continuous Wigner-Mott transitions in two-dimensional triangular lattices and stimulate future explorations of exotic quantum phases in their vicinities.

42 ENGINEERING↗
DOE OSTI2023

Element- and enantiomer-selective visualization of molecular motion in real-time

Ultrafast optical-domain spectroscopies allow to monitor in real time the motion of nuclei in molecules. Achieving element-selectivity had to await the advent of time resolved X-ray spectroscopy, which is now commonly carried at X-ray free electron lasers. However, detecting light element that are commonly encountered in organic molecules, remained elusive due to the need to work under vacuum. Here, we present an impulsive stimulated Raman scattering (ISRS) pump/carbon K-edge absorption probe investigation, which allowed observation of the low-frequency vibrational modes involving specific selected carbon atoms in the Ibuprofen RS dimer. Remarkably, by controlling the probe light polarization we can preferentially access the enantiomer of the dimer to which the carbon atoms belong.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2

Abstract Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with k inact /K I = 9,600 M −1 s −1 , achieves sub-μM EC 50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A sensitive high repetition rate arrival time monitor for X-ray free electron lasers

X-ray free-electron laser sources enable time-resolved X-ray studies with unmatched temporal resolution. To fully exploit ultrashort X-ray pulses, timing tools are essential. However, new high repetition rate X-ray facilities present challenges for currently used timing tool schemes. Here we address this issue by demonstrating a sensitive timing tool scheme to enhance experimental time resolution in pump-probe experiments at very high pulse repetition rates. Our method employs a self-referenced detection scheme using a time-sheared chirped optical pulse traversing an X-ray stimulated diamond plate. By formulating an effective medium theory, we confirm subtle refractive index changes, induced by sub-milli-Joule intense X-ray pulses, that are measured in our experiment. The system utilizes a Common-Path-Interferometer to detect X-ray-induced phase shifts of the optical probe pulse transmitted through the diamond sample. Owing to the thermal stability of diamond, our approach is well-suited for MHz pulse repetition rates in superconducting linear accelerator-based free-electron lasers.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Mineral reactivity determines root effects on soil organic carbon

Modern conceptual models of soil organic carbon (SOC) cycling focus heavily on the microbe-mineral interactions that regulate C stabilization. However, the formation of ‘stable’ (i.e. slowly cycling) soil organic matter, which consists mainly of microbial residues associated with mineral surfaces, is inextricably linked to C loss through microbial respiration. Therefore, what is the net impact of microbial metabolism on the total quantity of C held in the soil? To address this question, we constructed artificial root-soil systems to identify controls on C cycling across the plant-microbe-mineral continuum, simultaneously quantifying the formation of mineral-associated C and SOC losses to respiration. Here we show that root exudates and minerals interacted to regulate these processes: while roots stimulated respiratory C losses and depleted mineral-associated C pools in low-activity clays, root exudates triggered formation of stable C in high-activity clays. Moreover, we observed a positive correlation between the formation of mineral-associated C and respiration. This suggests that the growth of slow-cycling C pools comes at the expense of C loss from the system.

54 ENVIRONMENTAL SCIENCES↗