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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography

The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5'-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2'-O position of the first nucleotide. To investigate the conformational changes of the complex during 2'-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog ( m7 GpppA m2'-O ). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Large-scale analysis of structural brain asymmetries in schizophrenia via the ENIGMA consortium

Left–right asymmetry is an important organizing feature of the healthy brain that may be altered in schizophrenia, but most studies have used relatively small samples and heterogeneous approaches, resulting in equivocal findings. We carried out the largest case–control study of structural brain asymmetries in schizophrenia, with MRI data from 5,080 affected individuals and 6,015 controls across 46 datasets, using a single image analysis protocol. Asymmetry indexes were calculated for global and regional cortical thickness, surface area, and subcortical volume measures. Differences of asymmetry were calculated between affected individuals and controls per dataset, and effect sizes were meta-analyzed across datasets. Small average case–control differences were observed for thickness asymmetries of the rostral anterior cingulate and the middle temporal gyrus, both driven by thinner left-hemispheric cortices in schizophrenia. Analyses of these asymmetries with respect to the use of antipsychotic medication and other clinical variables did not show any significant associations. Assessment of age- and sex-specific effects revealed a stronger average leftward asymmetry of pallidum volume between older cases and controls. Case–control differences in a multivariate context were assessed in a subset of the data (N = 2,029), which revealed that 7% of the variance across all structural asymmetries was explained by case–control status. Subtle case–control differences of brain macrostructural asymmetry may reflect differences at the molecular, cytoarchitectonic, or circuit levels that have functional relevance for the disorder. Reduced left middle temporal cortical thickness is consistent with altered left-hemisphere language network organization in schizophrenia.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Probing FeSi, a d -electron topological Kondo insulator candidate, with magnetic field, pressure, and microwaves

Recently, evidence for a conducting surface state (CSS) below 19 K was reported for the correlated d -electron small gap semiconductor FeSi. In the work reported herein, the CSS and the bulk phase of FeSi were probed via electrical resistivity ρ measurements as a function of temperature T , magnetic field B to 60 T, and pressure P to 7.6 GPa, and by means of a magnetic field-modulated microwave spectroscopy (MFMMS) technique. The properties of FeSi were also compared with those of the Kondo insulator SmB 6 to address the question of whether FeSi is a d -electron analogue of an f -electron Kondo insulator and, in addition, a “topological Kondo insulator” (TKI). The overall behavior of the magnetoresistance of FeSi at temperatures above and below the onset temperature T S = 19 K of the CSS is similar to that of SmB 6 . The two energy gaps, inferred from the ρ( T ) data in the semiconducting regime, increase with pressure up to about 7 GPa, followed by a drop which coincides with a sharp suppression of T S . Several studies of ρ( T ) under pressure on SmB 6 reveal behavior similar to that of FeSi in which the two energy gaps vanish at a critical pressure near the pressure at which T S vanishes, although the energy gaps in SmB 6 initially decrease with pressure, whereas in FeSi they increase with pressure. The MFMMS measurements showed a sharp feature at T S ≈ 19 K for FeSi, which could be due to ferromagnetic ordering of the CSS. However, no such feature was observed at T S ≈ 4.5 K for SmB 6 .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy

Vibrio vulnificus causes life-threatening wound and gastrointestinal infections, mediated primarily by the production of a Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The most commonly present MARTX effector domain, the Makes Caterpillars Floppy-like (MCF) toxin, is a cysteine protease stimulated by host adenosine diphosphate (ADP) ribosylation factors (ARFs) to autoprocess. Here, we show processed MCF then binds and cleaves host Ra s-related proteins in b rain (Rab) guanosine triphosphatases within their C-terminal tails resulting in Rab degradation. We demonstrate MCF binds Rabs at the same interface occupied by ARFs. Moreover, we show MCF preferentially binds to ARF1 prior to autoprocessing and is active to cleave Rabs only subsequent to autoprocessing. We then use structure prediction algorithms to demonstrate that structural composition, rather than sequence, determines Rab target specificity. We further determine a crystal structure of aMCF as a swapped dimer, revealing an alternative conformation we suggest represents the open, activated state of MCF with reorganized active site residues. The cleavage of Rabs results in Rab1B dispersal within cells and loss of Rab1B density in the intestinal tissue of infected mice. Collectively, our work describes an extracellular bacterial mechanism whereby MCF is activated by ARFs and subsequently induces the degradation of another small host guanosine triphosphatase (GTPase), Rabs, to drive organelle damage, cell death, and promote pathogenesis of these rapidly fatal infections.

Science & Technology - Other Topics↗
DOE OSTI2025

Realizing a topological diode effect on the surface of a topological Kondo insulator

Introducing the concept of topology into material science has sparked a revolution from classic electronic and optoelectronic devices to topological quantum devices. The latter has potential for transferring energy and information with unprecedented efficiency. Here, we demonstrate a topological diode effect on the surface of a three-dimensional material, SmB 6 , a candidate topological Kondo insulator. The diode effect is evidenced by pronounced rectification and photogalvanic effects under electromagnetic modulation and radiation at radio frequency. Our experimental results and modeling suggest that these prominent effects are intimately tied to the spatially inhomogeneous formation of topological surface states (TSS) at the intermediate temperature. This work provides a manner of breaking the mirror symmetry (in addition to the inversion symmetry), resulting in the formation of pn-junctions between puddles of metallic TSS. Further, this effect paves the way for efficient current rectifiers or energy-harvesting devices working down to radio frequency range at low temperature, which could be extended to high temperatures using other topological insulators with large bulk gap.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The shard test and nanoporomechanics reverse classical paradigm of cement hydration being contractive

Le Chatelier in 1887 and Powers in 1947 demonstrated that the volume of nanoscale C-S-H (calcium silicate hydrate) particles formed during hydration is smaller than the combined volume of the reactants—the anhydrous Portland cement and water. Hydration has thus been considered as contractive. An experiment shows that the opposite is true above the nanoscale. The porous skeleton of cement paste expands as the growing C-S-H particles push each other apart, similar to crystal growth pressure. This is significant for high-performance concretes (HPC) with low water-cement ratios (w/c ≤ 0.4), where chemical self-desiccation lowers pore relative humidity by 40%, compared to just 1% in traditional concretes (w/c ≈ 0.5). Standard American Society for Testing and Materials (ASTM) C1608 tests, using 10 mm thick water-immersed specimens, show large shrinkage because the half-time of water ingress is many decades, unable to offset shrinkage-causing self-desiccation. The present experiment, using a laser microscopy-topography technique, proves the opposite—expansion, evidenced by measuring the length changes of water-immersed HPC shards 0.5 mm thick in which the diffusion halftime, only about one hour, allows continuous resaturation of pores, canceling self-desiccation. The faster diffusion (halftime of one hour) enables continuous pore resaturation, preventing shrinkage. When sealed with paraffin oil, the shards self-desiccate and shrink. These findings align with studies since 2015, showing that models excluding hydration expansion cannot fit test data across various specimen sizes and sealing conditions. The results suggest that standardized ASTM tests for the so-called chemical shrinkage in modern concretes with very low water-cement ratios are misleading and need revision.

Science & Technology - Other Topics↗
DOE OSTI2025

Apomixis in Farmers’ Fields: Overview, Case Studies from Forage Grasses and Considerations for Future Apomictic Crops

Apomixis occurs naturally in several commercially important species from diverse plant families. While in some of these species apomixis is yet to be exploited in breeding schemes aimed at fixing heterosis, genetic progress and cultivar development, in other species apomixis has been integrated at different stages of breeding. Some of the most relevant examples come from the subfamily Panicoideae, the second largest subfamily of the Poaceae, and are the main focus of this review. The subfamily encompasses many tropical and sub-tropical grasses and grains of worldwide economic importance. Apomictic tropical forages are prime examples of how apomixis can be used and exploited in the development of marketable cultivars, which are essential to the meat and milk production industries globally. The main commercial forages used as grass pastures covering millions of hectares in tropical and sub-tropical regions are polyploids exhibiting gametophytic apomixis that belong to the genus Urochloa spp. (brachiariagrasses) and to the species Megathyrsus maximus (guineagrass). Buffel grass (Cenchrus ciliaris) and Paspalum spp. are other important apomictic forages bred and used in these regions. Breeding involves large germplasm collections from the centers of origin of the species, and for most of them, sexually reproducing diploid plants have been found. Chromosomically duplicated plants that maintain sexual reproduction are used in crosses with apomictic genotypes for the development and selection of cultivars to be marketed or used as progenitors in subsequent breeding cycles. The peculiarities of each genus/species breeding programs, the cultivars obtained from these programs, and the impact of use of marker assisted selection in cultivar development are presented. In addition, the test or implementation of new technologies such as high throughput phenotyping, and the use of machine learning methods for trait prediction and genomic selection are positively impacting the selection and speed of development of new polyploid apomictic cultivars. Furthermore, genetic transformation techniques, including genome editing, provide an additional layer for design of tailor-made, customer-oriented cultivars.

Cenchrus↗
DOE OSTI2020

Millimeter wave traveling wave tubes for the 21st Century

Traveling wave tubes are rapidly evolving to provide unprecedented power level in comparison to solid state devices in the millimeter waves region of the spectrum (80–300 GHz) thus enabling a wide range of applications. Wireless communications, imaging, plasma diagnostics, healthcare and many others will gain substantial features if high power at millimeter waves would be available from compact sources. The development of fabrication technologies is proving crucial for introducing new topologies and structures for millimeter wave vacuum electronic devices, compatible with the dimensions dictated by the short wavelength that poses substantial manufacturing challenges due to tight tolerances. This review paper will provide an overview of the principles, evolution and state of the art of one of the most widely utilized vacuum electronic device, the traveling wave tube (TWT). The wide band, high gain features of TWTs make those devices the most promising solutions for high power at millimeter waves and THz frequencies.

42 ENGINEERING↗
DOE OSTI2019

Exploring itinerant states in divalent hexaborides using rare-earth L edge resonant inelastic x-ray scattering

We present a study of resonant inelastic x-ray scattering (RIXS) spectra collected at the rare-earth L edges of divalent hexaborides YbB 6 and EuB 6 . In both systems, RIXS-active features are observed at two distinct resonances separated by ~10 eV in incident energy, with angle-dependence suggestive of distinct photon scattering processes. RIXS spectra collected at the divalent absorption peak resemble the unoccupied 5d density of states calculated using density functional theory. We discuss possible origins of this correspondence including a scenario which changes the 4f valence. In addition, anomalous resonant scattering is observed at higher incident energy, where no corresponding absorption feature is present. Our results demonstrate the potential for L-edge RIXS to assess the itinerant-state properties of -electron materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Perturbative second-order optical susceptibility of bulk materials: a symmetry-enforced return to non-orthogonal localized basis sets

The second-order optical susceptibility of semiconductors $\chi^{(2)}_{ijk}(-2\omega;\omega,\omega)$ finds application in metrology, spectroscopy, telecommunications, material characterization, and quantum information. Pioneering calculations of $\chi^{(2)}_{ijk}(-2\omega;\omega,\omega)$ utilized non-orthogonal Gaussian orbitals centered at atoms. That formulation transitioned into plane-wave-based algorithms as time went by. As of late, nevertheless, multiple tools for calculating optical susceptibilities have recast the problem using Wannier (i.e. localized) orbitals, making a comeback onto frameworks based on localized basis sets. Here, in this work, we present an approach for calculating $\chi^{(2)}_{ijk}(-2\omega;\omega,\omega)$ reliant on numerical pseudo-atomic orbitals (PAOs) within perturbation theory in the velocity gauge. Its salient feature is a calculation of ‘Slater–Koster-like’ two-center integrals of the momentum operator in between PAOs identified by symmetry. The approach was successfully tested on paradigmatic cubic silicon carbide (3C-SiC) and gallium arsenide, for which linear responses are contributed as well.

Huamán, Angiolo [Univ. of Arkansas, Fayetteville, ↗
DOE OSTI2021

Sensitivity of future liquid argon dark matter search experiments to core-collapse supernova neutrinos

Future liquid-argon DarkSide-20k and Argo detectors, designed for direct dark matter search, will be sensitive also to core-collapse supernova neutrinos, via coherent elastic neutrino-nucleus scattering. This interaction channel is flavor-insensitive with a high-cross section, enabling for a high-statistics neutrino detection with target masses of ~50 t and ~360 t for DarkSide-20k and Argo respectively. Thanks to the low-energy threshold of ~0.5 keVnr achievable by exploiting the ionization channel, DarkSide-20k and Argo have the potential to discover supernova bursts throughout our galaxy and up to the Small Magellanic Cloud, respectively, assuming a 11-M progenitor star. In this work, we report also on the sensitivity to the neutronization burst, whose electron neutrino flux is suppressed by oscillations when detected via charged current and elastic scattering. Finally, the accuracies in the reconstruction of the average and total neutrino energy in the different phases of the supernova burst, as well as its time profile, are also discussed, taking into account the expected background and the detector response.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Superradiant pion clouds around primordial black holes

Here, we show that highly spinning primordial black holes of mass M ~ 10 12 kg, potentially born in a matter-dominated era after inflation, can produce clouds of pions in their vicinity via the superradiant instability, with densities up to that of nuclear matter. We discuss the electromagnetic signatures of this process, via neutral pion decay and charged pion annihilation into photons, computing in particular their contribution to the isotropic gamma-ray background. This allows us to place upper bounds on the abundance of such primordial black holes that are comparable to the ones obtained from Hawking evaporation. We also discuss the possibility of directly observing such clouds in high-redshift superclusters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

An optimized search for dark matter in the galactic halo with HAWC

The Galactic Halo is a key target for indirect dark matter detection. The High Altitude Water Cherenkov (HAWC) observatory is a high-energy (~300 GeV to >100 TeV) gamma-ray detector located in central Mexico. HAWC operates via the water Cherenkov technique and has both a wide field of view of ~ 2 sr and a >95% duty cycle, making it ideal for analyses of highly extended sources. We made use of these properties of HAWC and a new background-estimation technique optimized for extended sources to probe a large region of the Galactic Halo for dark matter signals. With this approach, we set improved constraints on dark matter annihilation and decay between masses of 10 and 100 TeV. Due to the large spatial extent of the HAWC field of view, these constraints are robust against uncertainties in the Galactic dark matter spatial profile.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Constraining explosive nucleosynthesis by indirect reaction methods at storage rings using unstable beams in batch mode

Nuclear reaction studies on unstable isotopes can strongly help in improving our understanding of nucleosynthesis in stars. Indirect approaches to determining astrophysical reaction rates are increasingly common-place and undergoing continuous refinement. Of particular interest is the use of such indirect techniques at storage rings, which, among other aspects, allow to recycle rare unstable beams. Here, we propose to investigate the reaction rates of astrophysical interest using indirect methods (surrogate, Trojan horse, etc.) in reverse kinematics at the IMP-CAS storage ring. Long lived radioactive ion beams, produced remotely, can be accelerated, and made to interact with light targets. The proposed reactions are 85 Kr(p, p’γ), 85 Kr(d, pγ), constraining the neutron flux in an s-process branching point, 79 Se(p, p’γ), 79 Se(d, pγ), constraining the temperature in s-process nucleosyntheses, and 59 Fe(d, pγ), constraining core collapse supernovae.

Angelis, G. de [National Inst. of Nuclear Physics ↗
DOE OSTI2022

Scintillator ageing of the T2K near detectors from 2010 to 2021

The T2K experiment widely uses plastic scintillator as a target for neutrino interactions and an active medium for the measurement of charged particles produced in neutrino interactions at its near detector complex. Over 10 years of operation the measured light yield recorded by the scintillator based subsystems has been observed to degrade by 0.9–2.2% per year. Extrapolation of the degradation rate through to 2040 indicates the recorded light yield should remain above the lower threshold used by the current reconstruction algorithms for all subsystems. This will allow the near detectors to continue contributing to important physics measurements during the T2K-II and Hyper-Kamiokande eras. Additionally, work to disentangle the degradation of the plastic scintillator and wavelength shifting fibres shows that the reduction in light yield can be attributed to the ageing of the plastic scintillator. The long component of the attenuation length of the wavelength shifting fibres was observed to degrade by 1.3–5.4% per year, while the short component of the attenuation length did not show any conclusive degradation.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Development of a new CEDAR for kaon identification at the NA62 experiment at CERN

The NA62 experiment at CERN utilises a differential Cherenkov counter with achromatic ring focus (CEDAR) for tagging kaons within an unseparated monochromatic beam of charged hadrons. The CEDAR-H detector was developed to minimise the amount of material in the path of the beam by using hydrogen gas as the radiator medium. The detector was shown to satisfy the kaon tagging requirements in a test-beam before installation and commissioning at the experiment. The CEDAR-H performance was measured using NA62 data collected in 2023.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Long-term temporal stability of the DarkSide-50 dark matter detector

The stability of a dark matter detector on the timescale of a few years is a key requirement due to the large exposure needed to achieve a competitive sensitivity. It is especially crucial to enable the detector to potentially detect any annual event rate modulation, an expected dark matter signature. Here, in this work, we present the performance history of the DarkSide-50 dual-phase argon time projection chamber over its almost three-year low-radioactivity argon run. In particular, we focus on the electroluminescence signal that enables sensitivity to sub-keV energy depositions. The stability of the electroluminescence yield is found to be better than 0.5%. Finally, we show the temporal evolution of the observed event rate around the sub-keV region being consistent to the background prediction.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗