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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Tertiary folds of the SL5 RNA from the 5 ' proximal region of SARS-CoV-2 and related coronaviruses

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T’s “arms.” Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Primordial non-Gaussianity from the completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey – I: Catalogue preparation and systematic mitigation

ABSTRACT We investigate the large-scale clustering of the final spectroscopic sample of quasars from the recently completed extended Baryon Oscillation Spectroscopic Survey (eBOSS). The sample contains 343 708 objects in the redshift range 0.8 < z < 2.2 and 72 667 objects with redshifts 2.2 < z < 3.5, covering an effective area of $4699\, {\rm deg}^{2}$. We develop a neural network-based approach to mitigate spurious fluctuations in the density field caused by spatial variations in the quality of the imaging data used to select targets for follow-up spectroscopy. Simulations are used with the same angular and radial distributions as the real data to estimate covariance matrices, perform error analyses, and assess residual systematic uncertainties. We measure the mean density contrast and cross-correlations of the eBOSS quasars against maps of potential sources of imaging systematics to address algorithm effectiveness, finding that the neural network-based approach outperforms standard linear regression. Stellar density is one of the most important sources of spurious fluctuations, and a new template constructed using data from the Gaia spacecraft provides the best match to the observed quasar clustering. The end-product from this work is a new value-added quasar catalogue with the improved weights to correct for non-linear imaging systematic effects, which will be made public. Our quasar catalogue is used to measure the local-type primordial non-Gaussianity in a companion paper.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Exploring the onset of collectivity approaching 𝑁=40 with masses of manganese isotopes

Isotopes in the region of the nuclear chart below 68 Ni have been the subject of intense experimental and theoretical effort due to the potential onset of a new “island of inversion” when crossing the harmonic oscillator subshell closure at 𝑁=40. Here, we have measured the masses of 64−68 Mn using TITAN's multiple-reflection time-of-flight mass spectrometer, resulting in the first precision mass measurements of 67 Mn and 68 Mn. These results are compared to ab initio calculations and modern shell model calculations and show an increase in collectivity approaching 𝑁=40.

binding energy & masses↗
DOE OSTI2025

Dark matter hail: Detecting macroscopic dark matter with asteroids, planetary rings, and craters

Dark matter could be composed of macroscopic objects with large masses and geometric cross-sections spanning many decades. Here, we investigate the potential interaction of such “stuff-sized” dark matter by considering its interactions with asteroids, planetary rings, and terrestrial bodies. This hail of dark matter could catastrophically destroy these Solar System objects, evaporate them from their orbits, or cause substantial cratering. We estimate these effects and use them to place competitive bounds on a wide, previously unconstrained swathe of the dark matter parameter space.

asteroids, meteors, & meteorites↗
DOE OSTI2020

A Predictive Model for Survival of Escherichia coli O157:H7 and Generic E. coli in Soil Amended with Untreated Animal Manure

Abstract This study aimed at developing a predictive model that captures the influences of a variety of agricultural and environmental variables and is able to predict the concentrations of enteric bacteria in soil amended with untreated Biological Soil Amendments of Animal Origin (BSAAO) under dynamic conditions. We developed and validated a Random Forest model using data from a longitudinal field study conducted in mid‐Atlantic United States investigating the survival of Escherichia coli O157:H7 and generic E. coli in soils amended with untreated dairy manure, horse manure, or poultry litter. Amendment type, days of rain since the previous sampling day, and soil moisture content were identified as the most influential agricultural and environmental variables impacting concentrations of viable E. coli O157:H7 and generic E. coli recovered from amended soils. Our model results also indicated that E. coli O157:H7 and generic E. coli declined at similar rates in amended soils under dynamic field conditions.The Random Forest model accurately predicted changes in viable E. coli concentrations over time under different agricultural and environmental conditions. Our model also accurately characterized the variability of E. coli concentration in amended soil over time by providing upper and lower prediction bound estimates. Cross‐validation results indicated that our model can be potentially generalized to other geographic regions and incorporated into a risk assessment for evaluating the risks associated with application of untreated BSAAO. Our model can be validated for other regions and predictive performance also can be enhanced when data sets from additional geographic regions become available.

Pang, Hao↗
DOE OSTI2022

Complete Genome Sequence of Human Oral Saccharibacterium “ Candidatus Nanosynbacter sp. HMT352” Strain KC1

“Cand. Nanosynbacter sp. HMT352” strain KC1 is an ectoparasitic saccharibacterium/TM7 that was co-isolated from a human saliva sample with its obligate bacterial host, Schaalia odontolytica. The genome of strain KC1 enables studies of the mechanisms and evolution of interspecies interactions and, for oral species, studies of their potential roles in health and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Performance Investigation of High-temperature Latent Heat Storage for Integration with Advanced Nuclear Reactors

Integrating thermal energy storage (TES) with advanced nuclear reactors enhances the flexible use of nuclear energy, facilitating its expansion beyond conventional electricity generation. High-temperature TES, capable of storing heat above 400 degree C, emerges as a vital carbon-free energy solution for decarbonizing industrial sector, especially when combined with low-emission energy sources like advanced nuclear reactors. Idaho National Laboratory (INL) has recently developed a novel design for high-temperature latent heat storage system, called Heat pipe Integrated Thermal Battery (HITB), and efforts are underway to experimentally demonstrate the concept. HITB employs liquid-metal heat pipes to establish thermal linkage between TES and nuclear systems without direct fluid exchange, minimizing the potential risk of the integrated systems such as cross-contamination. HITB is designed to achieve high charging and discharging efficiency as well as high energy storage density by employing metal alloys as Phase Change Material (PCM). Initial proof-of-concept experiments are being undertaken using an aluminum alloy (Al59%-Mg35%-Zn6%). This paper discusses current progress of the HITB project at INL, seeking to develop high-temperature TES for versatile integration with advanced nuclear reactors, and shares insights from the performance evaluations via numerical modeling and analysis.

25 ENERGY STORAGE↗
DOE OSTI2021

Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects

SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterize 198 antibodies isolated from four COVID-19+ subjects and identify 14 SARS-CoV-2 neutralizing antibodies. One targets the N-terminal domain (NTD), one recognizes an epitope in S2, and 11 bind the receptor-binding domain (RBD). Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency and antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. All four cross-neutralizing antibodies neutralize the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Determining the Hubble constant through cross-correlation of galaxies and gravitational waves

Gravitational-wave (GW) standard sirens have the potential to measure the Hubble constant 𝐻 0 in the local Universe independent of the distance ladder and thus offer unique insights into the Hubble tension. A key challenge with standard sirens is detecting their electromagnetic counterparts and therefore assigning redshifts to the measured distances. One promising way to proceed is to utilize GW dark sirens—events without an identified electromagnetic counterpart—and cross-correlate their angular distribution with that of galaxies. We present a quantitative study of how precisely the Hubble constant can be measured using tomographic cross-correlation between galaxies and GW sources. Altogether, we find that the constraints on 𝐻 0 will be limited by the quality and quantity of GW data. We find that percent-level constraints on 𝐻 0 will primarily depend on achieving small distance uncertainties (𝜎 𝑑𝐿 = 0.1⁢𝑑 𝐿 ), obtaining a large number of GW dark sirens (≳ 5⁢000) and accurate sky localization in the tomographic analysis.

Cosmological parameters↗
DOE OSTI2023

Quantifying uncertainties due to optical potentials in one-neutron knockout reactions

One-neutron knockout reactions have been widely used to extract information about the single-particle structure of nuclei from the valley of stability to the drip lines. The interpretation of knockout data relies on reaction models, where the uncertainties are typically not accounted for. In this work, we quantify uncertainties of optical potentials used in these reaction models and propagate them, for the first time, to knockout observables using a Bayesian analysis. We study two reactions in the present paper, the first of which involves a loosely bound halo projectile, 11 Be, and the second a tightly bound projectile, 12 C. We first quantify the parametric uncertainties associated with phenomenological optical potentials. Complementing this approach, we also quantify the model uncertainties associated with the chiral forces that can be used to construct microscopic optical potentials. For the phenomenological study, we investigate the impact of the imaginary terms of the optical potential on the breakup and stripping components of the knockout cross sections as well as the impact of the angular range. For the 11 Be case, the theoretical uncertainty from the phenomenological method is on the order of the experimental uncertainty of the knockout observables; however, for the 12 C case, the theoretical uncertainty is significantly larger. Additionally, the widths of the uncertainty bands for the knockout observables obtained for the microscopic study and the phenomenological approach are of similar orders of magnitude. Based on this work we conclude that structure information inferred from the ratio of the knockout cross sections will carry a theoretical uncertainty of at least 20% for halo nuclei and at least 40% for tightly bound nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Λ Baryon Production in ν¯µ Interactions in the MicroBooNE Detector

The Cabibbo suppressed production of $\Lambda$ baryons in anti-neutrino interactions with nuclei is a rare process that is yet to be measured with a modern neutrino detector with automated reconstruction. The cross section for this process is sensitive to a number of unique nuclear effects, most notably the secondary interactions of the produced hyperon while attempting to escape from the nucleus. Other interactions within the nuclear remnant can impact the estimation of neutrino energy in oscillation measurements, and thus an accurate description of the nuclear environment is required. The strangeness violating hyperon production process is only available to anti-neutrinos. The model of this interaction is implemented into the NuWro neutrino interaction Monte Carlo simulation, and some predictions are presented, focusing on the role of nuclear effects. This model introduces a hyperon-nucleus potential, which calculations from hypernuclear theory permit to be strongly repulsive in th e case of $\Sigma$ baryons. The presence of this potential is found to sculpt the shape of the differential cross section in some variables. The MicroBooNE detector will be described, followed by a description of a measurement of the flux averaged, restricted phase space cross section of Cabibbo suppressed $\Lambda$ baryon production. A sophisticated event selection is employed, as a very large quantity of background neutrino interactions must be removed to perform the measurement with any sensitivity. This selection introduces some novel techniques such as the island finding method, and achieves a background reduction of $\sim 10^6$, with an efficiency of around 7\%. The calculation of the systematic uncertainties will be explained, including two procedures explored to handle sources of background with extremely poor simulation statistics: an in-situ constraint using data from sidebands, and a visual inspection of the data and simulation to remove the troublesome background events. The sensitivity to the $\Lambda$ baryon production cross section is calculated in the form of Bayesian posterior probability distributions, combining the systematic uncertainties with data and simulation statistical uncertainties. As a rare process, the statistical uncertainties are highly non-Gaussian, and the Bayesian approach is applied to include the full shapes of these uncertainties. Data corresponding to $2.2 \times 10^{20}$ protons on target of neutrino mode running and $4.9 \times 10^{20}$ protons on target of anti-neutrino running is analysed. When the data was unblinded, five $\Lambda$ production candidates were selected from the data, consistent with the MC simulation prediction of $5.3 \pm 1.1$ events. The final estimated cross section is $1.8^{+2.0}_{-1.6} \times 10^{-40}$cm$^2/$Ar when employing the sideband constraint procedure. A similar result of $2.0^{+2.2}_{-1.8} \times 10^{-40}$cm$^2/$Ar is obtained when performing the visual scan instead. The methods used in t his analysis are intended to be easily exported to other LArTPC detectors such as the Short Baseline Near Detector.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

The Entropic Braiding Index ( eBI ): A Robust Metric to Account for the Diversity of Channel Scales in Multi‐Thread Rivers

Abstract The Braiding Index ( BI ), defined as the average count of intercepted channels per cross‐section, is a widely used metric for characterizing multi‐thread river systems. However, it does not account for the diversity of channels (e.g., in terms of water discharge) within different cross‐sections, omitting important information related to system complexity. Here we present a modification of BI, the Entropic Braiding Index ( eBI ), which augments the information content in BI by using Shannon Entropy to encode the diversity of channels in each cross section. eBI is interpreted as the number of “effective channels” per cross‐section, allowing a direct comparison with the traditional BI . We demonstrate the potential of the ratio BI/eBI to quantify channel disparity, differentiate types of multi‐thread systems (braided vs. anastomosed), and assess the effect of discharge variability, such as seasonal flooding, on river cross‐section stability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Exclusive $J/ψ$ photoproduction on nuclei

Motivated by the recent experimental developments, the Pom-CQM model of the γ+N → J/ψ+N reaction of Lee et al. [Eur. Phys. J. A. 58, 252 (2022)] and Sakinah et al. [Phys. Rev. C. 109, 065204 (2024)] has been applied to predict the exclusive J/ψ photo-production on nuclei (A). Within the multiple scattering theory, the calculations have been performed by including the impulse amplitude $T^{\textrm{IMP}}_{J/ψA,γA}$ and the J/ψ-nucleus final state interaction (FSI) amplitude $T^{\textrm{FSI}}_{J/ψA,γA}$. For the deuteron target, $T^{\textrm{IMP}}_{J/ψd,γd}$ is calculated exactly using the wave function generated from the realistic nucleon-nucleon potentials. Here, it is found that, near the threshold region, the J/ψ photoproduction cross sections depend sensitively on the d-state of the deuteron wave function. The FSI amplitude $T^{\textrm{FSI}}_{J/ψA,γA}$ is calculated using the first-order optical potential constructed from the J/ψ-N scattering amplitude generated from the employed Pom-CQM model. It turns out that the FSI has significant effects in the large momentum-transfer region. By using the conventional fixed scatter approximation (FSA) and the nuclear form factors from the variational Monte-Carlo (VMC) calculations of Lonardoni et al. [Phys. Rev.C. 96, 024326 (2017)], the cross sections of the J/ψ photo-production on 4 He, 16 O, and 40 Ca are also predicted for future experimental investigations at JLab and EIC.

Kim, Sang-Ho [Soongsil University, Seoul (Korea, R↗
DOE OSTI2026

Photoenzymatic Csp 3 –Csp 3 bond formation via enzyme-templated radical–radical coupling

Cross-couplings are essential reactions in modern chemical synthesis, enabling the rapid construction of complex molecules from simple precursors. Transition metal catalysts are prized for these transformations because their reactivity and selectivity can be tuned via judicious selection of the metal and ligand. Although enzymes offer analogous opportunities for tuning via protein engineering, their application to cross-coupling remains limited, as nature relies on alternative paradigms for building molecular complexity. Here, we report the cross-coupling of alkyl halides and benzylic carboxylic acids using an engineered flavin-dependent lactate monooxygenase—a photoenzyme. The enzyme achieves this feat by exploiting the redox versatility of the flavin cofactor. Stoichiometric experiments, ultrafast spectroscopy, and computational studies support a mechanism in which photoexcited flavin quinone initiates the reaction via oxidative decarboxylation to generate a benzylic radical. The resulting flavin semiquinone can reduce the alkyl halide to form a second organic radical within the protein active site, which rapidly engages in C(sp 3 )–C(sp 3 ) bond formation. A variant was engineered to control the stereochemical outcome of this radical–radical coupling event, highlighting the ability of the protein to alter the energetic barrier for a mechanistic step that is traditionally understood to be near barrierless. This work demonstrates that the scope for nonnative reaction mechanisms in biocatalysis far exceeds previously established bounds and has potential to solve a variety of reactivity challenges in cross-coupling chemistry.

biocatalysis↗
DOE OSTI2024

Ab initio translationally invariant nucleon-nucleus optical potentials

We combine the ab initio symmetry-adapted no-core shell model (SA-NCSM) with the single-particle Green's function approach to construct optical potentials rooted in first principles. Specifically, we show that total cross sections and phase shifts for neutron elastic scattering from a 4 He target with projectile energies between 0.5 and 10 MeV closely reproduce the experiment. In addition, we discuss an important new development that resolves a long-standing issue with spurious center-of-mass motion in the Green's function formalism for many-body approaches. Furthermore, the new development opens a path for first-principle predictions of cross sections for elastic scattering of single-nucleon projectiles, nucleon capture, and deuteron breakup reactions, feasible for a broad range of open-shell spherical and deformed nuclei in the SA-NCSM approach.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Holographic Constraints on the String Landscape

We show that holography imposes strong and general constraints on scalar field potentials in the string landscape, determined by the asymptotic structure of the underlying spacetime. Applying these holographic consistency conditions, we identify broad classes of scalar potentials that are incompatible with a well-defined dual description. These include potentials with extended plateaus, excessively steep or shallow asymptotics, certain zero crossings, and specific alignments of stable AdS minima in moduli space. In particular, making the standard assumption that the CFT dual to a stable AdS vacuum must be realized as a worldvolume theory of a brane in string theory, we show that the brane selects an infinite-distance limit in moduli space where parametric scale separation is forbidden. Furthermore, the steepness and positivity of the potential are restricted in that infinite distance direction. We also find that requiring the validity of the effective theory in the future vacuum, a natural holographic criterion, automatically enforces the Trans-Planckian Censorship Conjecture (TCC) for classical cosmological solutions with positive potentials. Taken together, these constraints exclude the leading proposals to realize scale-separated AdS vacua and metastable de Sitter vacua in the string theory landscape such as DGKT and KKLT.

Cosmology and Nongalactic Astrophysics (astro-ph.C↗
DOE OSTI2025

Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere

Interactions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, 13 C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant 13 CO 2 labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background. We found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly 13 C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all 13 C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web. To date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Cross-correlation Study of High-energy Neutrinos and Tracers of Large-scale Structure

The origin of the bulk of the astrophysical neutrinos detected by the IceCube Observatory remains a mystery. Previous source-finding analyses compared the directions of IceCube events and individual sources in astrophysical catalogs. The source association method is technically challenging when the number of source candidates is much larger than the number of the observed astrophysical neutrinos. In this paper, we show that in this large source number regime, a two-point cross-correlation analysis of neutrino data and source catalog can instead be used to constrain potential source populations for the high-energy astrophysical neutrinos, and provide spatial evidence for the existence of astrophysical neutrinos. We present an analysis of the cross-correlation of the IceCube 2010–2012 point-source data and a WISE–2MASS galaxy sample. While we find no significant detection of cross-correlation with the publicly available neutrino data set, we show that, when applied to the full IceCube data, which has a longer observation time and higher astrophysical neutrino purity, our method has sufficient statistical power to detect a cross-correlation signal if the neutrino sources trace the large-scale structure of the universe.

79 ASTRONOMY AND ASTROPHYSICS↗