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At least 991 records · Page 55

All sources NASA NTRS DOE OSTI

DOE OSTI2021

Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography

Single-domain Variable New Antigen Receptors (VNARs) from the immune system of sharks are the smallest naturally occurring binding domains found in nature. Possessing flexible paratopes that can recognize protein motifs inaccessible to classical antibodies, VNARs have yet to be exploited for the development of SARS-CoV-2 therapeutics. Here, we detail the identification of a series of VNARs from a VNAR phage display library screened against the SARS-CoV-2 receptor binding domain (RBD). The ability of the VNARs to neutralize pseudotype and authentic live SARS-CoV-2 virus rivalled or exceeded that of full-length immunoglobulins and other single-domain antibodies. Crystallographic analysis of two VNARs found that they recognized separate epitopes on the RBD and had distinctly different mechanisms of virus neutralization unique to VNARs. Structural and biochemical data suggest that VNARs would be effective therapeutic agents against emerging SARS-CoV-2 mutants, including the Delta variant, and coronaviruses across multiple phylogenetic lineages. This study highlights the utility of VNARs as effective therapeutics against coronaviruses and may serve as a critical milestone for nearing a paradigm shift of the greater biologic landscape.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

The role of Co valence in charge transport in the entropy‐stabilized oxide (Mg 0.2 Co 0.2 Ni 0.2 Cu 0.2 Zn 0.2 )O

Abstract Many of the studies on the entropy‐stabilized oxide (Mg 0.2 Co 0.2 Ni 0.2 Cu 0.2 Zn 0.2 )O have been heavily application‐based. Previous works have studied effects of cation stoichiometry on the entropy‐driven reaction to form a single phase, but a fundamental exploration of the effects of anion stoichiometry and/or redox chemistry on electrical properties is lacking. Using near‐edge X‐ray absorption fine structure (NEXAFS) and electrical measurements, we show that oxidizing thin film samples of (Mg 0.2 Co 0.2 Ni 0.2 Cu 0.2 Zn 0.2 )O affects primarily the valence of Co, leaving the other cations in this high‐entropy system unchanged. This oxidation increases electrical conduction in these thin films, which occurs via small polaron hopping mediated by the Co valence shift from 2+ to a mixed 2+/3+ state. In parallel, we show that bulk samples sintered in an oxygen‐rich atmosphere have a lower activation energy for electrical conduction than those equilibrated in a nitrogen (reducing) atmosphere. Combining feasible defect compensation scenarios with electrical impedance measurements and NEXAFS data, we propose a self‐consistent interpretation of Co redox‐mediated small polaron conduction as the dominant method of charge transfer in this system.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Singularity-EOS: Performance Portable Equations of State and Mixed Cell Closures

We present Singularity-EOS, a new performance-portable library for equations of state and related capabilities. Singularity-EOS provides a large set of analytic equations of state, such as the Gruneisen equation of state, and tabulated equation of state data under a unified interface. It also provides support capabilities around these equations of state, such as Python wrappers, solvers for finding pressure-temperature equilibrium between multiple equations of state, and a unique modifier framework, allowing the user to transform a base equation of state, for example by shifting or scaling the specific internal energy. All capabilities are performance portable, meaning they compile and run on both CPU and GPU for a wide variety of architectures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Fundamental 235 Uranium Nuclear Resonance Spectroscopy (End of Year Report)

Uranium-235 is ubiquitous in the nuclear industry however, detailed characterization by magnetic resonance spectroscopy has remained largely elusive to-date. Conventional nuclear magnetic resonance techniques are ill-suited for characterizing 235 U due to the small gyromagnetic ratio and extremely large quadrupole moment of this spin$^{7}$ /2 isotope. Thus, we have designed and built a high-frequency nuclear quadrupole resonance spectrometer for measuring the quadrupole resonance of this important isotope. A successful nuclear quadrupole resonance measurement of 235 U would be a significant accomplishment and could yield valuable physical parameters such as chemical shifts, local electric field gradients, and through-bond and through-space internuclear couplings, all of which are directly related to local structure. These terms can be used to understand structural details of poorly characterized uranium materials and can improve computational models of uranium for which accurate reference data is lacking

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2023

Geomagnetic Storm Effects on Ionospheric Irregularities: Insights from SuperDARN, Madrigal GPS TEC, and ISR Data [Slides]

Geomagnetic disturbances trigger an influx of electrons from the magnetosphere, leading to an increase electron density (even in lower altitudes), amplified ionospheric currents, and subsequently, increased conductance. A surge in the AE index, indicating heightened auroral currents, correlates with a rise in precipitated charged particles, including electrons, into the polar ionosphere. This correlation is detectable through increased parameter values measured by SuperDARN. The downward flow of electron density towards lower altitudes, as observed in PFISR data, potentially obstructs the transmission frequency from radar stations passing through the PFISR location (just like we saw in the KOD station). During the geomagnetic storm, there is increased backscatter power (increased amount of ionospheric irregularities), and the plasma flow draws closer to the radar, suggesting a possible southward shift in the auroral oval as a result of the heightened auroral activity. Increased geomagnetic activity correlates with an elevation in average TEC and induces the occurrence of SED (Storm Enhanced Density).

58 GEOSCIENCES↗

DOE OSTI2025

Study of Quadrupole Fringe Fields in the Interaction Region of the Hadron Storage Ring of the Electron Ion Collider

Fringe fields in quadrupole magnets are usually neglected in studies of beam dynamics at accelerators. However, the extreme optical parameters present in the final focus of a collider such as the Electron–Ion Collider (EIC) may give rise to effects that should not be overlooked. The calculation of quadrupole fringe fields presented in this study follows the procedure outlined in Ref. [1], specialized to the case of a straight reference orbit (i.e., with no dipole field component). A right-handed Cartesian coordinate system is employed, with the $z$-axis aligned with the quadrupole axis and $x$ and $y$ denoting the horizontal and vertical transverse coordinates, respectively. The magnetic quadrupole field gradient, $G = \partial B_y / \partial x$, transitions from its peak value inside the quadrupole—where it is nearly independent of the longitudinal coordinate $z$—to zero at some distance beyond the magnet edge. Consequently, $G$ is treated as a function of $z$. The region over which this variation occurs is defined as the quadrupole fringe field region. The study begins with the development of a description of the magnetic field in the fringe region using a power-series expansion in the transverse coordinates $x$and $y$, consistent with the longitudinally varying gradient. A model for the $z$-dependence of the gradient is then proposed and adjusted to reproduce magnetic field data obtained from three-dimensional field calculations. To evaluate the impact of the fringe fields on beam dynamics, the corresponding vector potential is derived and incorporated into a Hamiltonian formulation of particle motion. The significance of the fringe fields is quantified by calculating the amplitude-dependent tune shift from the Hamiltonian. Using linear beam optics parameters of the Hadron Storage Ring (HSR) of the EIC, the tune shift due to the fringe fields of all quadrupole magnets in the IR-6 interaction region is evaluated. Finally, the resulting tune shifts are compared with those arising from other nonlinear field components present in the HSR.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

The Inducible Accumulation of Cell Wall-Bound p -Hydroxybenzoates Is Involved in the Regulation of Gravitropic Response of Poplar

Lignin in Populus species is acylated with p-hydroxybenzoate. Monolignol p-hydroxybenzoyltransferase 1 (PHBMT1) mediates p-hydroxybenzoylation of sinapyl alcohol, eventually leading to the modification of syringyl lignin subunits. Angiosperm trees upon gravistimulation undergo the re-orientation of their growth along with the production of specialized secondary xylem, i.e., tension wood (TW), that generates tensile force to pull the inclined stem or leaning branch upward. Sporadic evidence suggests that angiosperm TW contains relatively a high percentage of syringyl lignin and lignin-bound p-hydroxybenzoate. However, whether such lignin modification plays a role in gravitropic response remains unclear. By imposing mechanical bending and/or gravitropic stimuli to the hybrid aspens in the wild type (WT), lignin p-hydroxybenzoate deficient, and p-hydroxybenzoate overproduction plants, we examined the responses of plants to gravitropic/mechanical stress and their cell wall composition changes. We revealed that mechanical bending or gravitropic stimulation not only induced the overproduction of crystalline cellulose fibers and increased the relative abundance of syringyl lignin, but also significantly induced the expression of PHBMT1 and the increased accumulation of p-hydroxybenzoates in TW. Furthermore, we found that although disturbing lignin-bound p-hydroxybenzoate accumulation in the PHBMT1 knockout and overexpression (OE) poplars did not affect the major chemical composition shifts of the cell walls in their TW as occurred in the WT plants, depletion of p-hydroxybenzoates intensified the gravitropic curving of the plantlets in response to gravistimulation, evident with the enhanced stem secant bending angle. By contrast, hyperaccumulation of p-hydroxybenzoates mitigated gravitropic response. These data suggest that PHBMT1-mediated lignin modification is involved in the regulation of poplar gravitropic response and, likely by compromising gravitropism and/or enhancing autotropism, negatively coordinates the action of TW cellulose fibers to control the poplar wood deformation and plant growth.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

TRACER-CAT-UCDAVIS Aerosol Optical Properties and Sizing - smps

Aerosol size distribution and optical properties collected in La Port TX, during TRACER-CAT-UCDavis, July 2022. Speciated particle composition measurements are reported separately. All sampling was conducted with an identical aerosol inlet as the standard ARM-AOS systems. The TRacking Aerosol Convection interactions ExpeRiment Carbonaceous Aerosols Thrust by UC Davis (TRACER-CAT-UCDavis, July 2022) was designed to complement the larger ARM TRACER science goals to understand convective cloud lifecycles and aerosol-convection interactions. TRACER-CAT-UCDavis is focused on understanding the relationship between particle composition and light absorption and the influence of water uptake on this relationship. This aerosol data can be used to understand the relationship between particle composition and light absorption and the influence of water uptake on this relationship. Instruments include: UC Davis two-wavelength cavity ringdown-photoacoustic spectrometer (CRD-PAS); Brechtel scanning electrical mobility sizer (SEMS); modified humidified cavity attenuated phase shift spectrometer with single scatter albedo (H-CAPS-SSA)

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

TRACER-CAT-UCDAVIS Aerosol Optical Properties and Sizing - crdps

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Numerical Investigation of High Delta T Sensible Storage Integrated CO2 Heat Pump: Preprint

To assist building heating electrification, this paper numerically investigates a load flexible heat pump system for commercial buildings. The system consists of a CO2 vapor compression cycle, a sensible thermal storage tank, and an air handling unit. The thermal storage medium is inexpensive, non-toxic and stable anti-freeze solution (30% potassium acetate). The air handing unit has an indoor coil and a ventilation coil. The system can be used to manage building electric load. During peak hours, the heat pump is off and the hot solution water is discharged from the tank to heat up the indoor air and ventilation air. During the hour of charge, the heat pump delivers hot solution water to the tank and to the air. The tank can also stand by while the heat pump provides space heating directly. We selected a medium sized office building located in Minnesota as the representative building and used EnergyPlus to obtain its 24 hour load data. We designed three storage tank volumes assuming 50 degrees C, 65 degrees C and 80 degrees C tank temperatures to independently provide the building load for 4 hours in the morning. The higher the tank temperature, the smaller the required volume, and thus higher energy density. The effective energy density is 78 with an 80 degrees C tank, and 40 kWhth/m3 with 50 degrees C. We simulated the tank integrated heat pump performance subjected to the 24-hour building load profile and ambient data. The baseline is the same system without storage tank. There was a trade-off between the storage energy density and the charging COP. The charge hour COP was 2.77 to charge the tank to 80 degrees C, and 3.01 to 50 degrees C. The proposed system could shift building load from the peak hours (8:00 - 12:00) to off-business hour (23:00 - 7:00+1). It eliminated 100% compressor electricity use during the peak hours, and avoided a peak electric power of 34 kW. The 65 degrees C tank saved 9.5 kWhe (4%) considering all day operation, which was the best balance between energy density and the system operation efficiency among the three options.

CO2 heat pump↗

DOE OSTI2023

Uncovering a CF 3 Effect on X‐ray Absorption Energies of [Cu(CF 3 ) 4 ] − and Related Copper Compounds by Using Resonant Diffraction Anomalous Fine Structure (DAFS) Measurements**

Abstract Understanding the electronic structures of high‐valent metal complexes aids the advancement of metal‐catalyzed cross coupling methodologies. A prototypical complex with formally high valency is [Cu(CF 3 ) 4 ] − (1), which has a formal Cu(III) oxidation state but whose physical analysis has led some to a Cu(I) assignment in an inverted ligand field model. Recent examinations of1by X‐ray spectroscopies have led previous authors to contradictory conclusions, motivating the re‐examination of its X‐ray absorption profile here by a complementary method, resonant diffraction anomalous fine structure (DAFS). From analysis of DAFS measurements for a series of seven mononuclear Cu complexes including1, here it is shown that there is a systematic trifluoromethyl effect on X‐ray absorption that blue shifts the resonant Cu K‐edge energy by 2–3 eV per CF 3 , completely accounting for observed changes in DAFS profiles between formally Cu(III) complexes like1and formally Cu(I) complexes like (Ph 3 P) 3 CuCF 3 (3). Thus, in agreement with the inverted ligand field model, the data presented herein imply that1is best described as containing a Cu(I) ion with d n count approaching 10.

Chemistry↗

DOE OSTI2021

The denatured state of HIV ‐1 protease under native conditions

Abstract The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

The roles of three-nucleon force and continuum coupling in mirror symmetry breaking of oxygen mass region

With both three-nucleon force and continuum coupling included, we have developed a self-consistent ab initio Gamow shell model within the Gamow Hartree-Fock (GHF) basis obtained by the realistic interaction itself. With the chiral two-nucleon N 3 LO and three-nucleon N 2 LO interactions, the Gamow shell model has been applied to the mirror systems of Z = 8 neutron-rich isotopes and N = 8 proton-rich isotones, giving good agreements with data in binding energies, dripline positions and excitation spectra. The GHF calculated that the 0 ds/2 , 1 S1/2 and 1 p3/2 orbitals are resonances. The resonance states and their interplay with nonresonant continua play a crucial role in the descriptions of nuclei around driplines. Excitation spectra and Thomas-Ehrman shifts observed can be better described when both three-nucleon force and continuum coupling are considered in calculations. The three-nucleon force and continuum coupling produce a combined effect on the Thomas-Ehrman shift, e.g., for the 1/2 + resonance level of 19Na. The calculations help the understandings of related nuclear astrophysical processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

X-ray phase contrast and absorption imaging for the quantification of transient cavitation in high-speed nozzle flows

In this work, high-flux synchrotron radiation has been employed in a time-resolved manner to characterise the distinct topology features and dynamics of different cavitation regimes arising in a throttle orifice with an abrupt flow-entry contraction. Radiographs obtained though both X-ray phase- contrast and absorption imaging have been captured at 67,890 frames per second. The flow lied in the turbulent regime (Re=35,500), while moderate (CN=2.0) to well-established (CN=6.0) cavitation conditions were examined encompassing the cloud and vortical cavitation regimes with pertinent transient features, such as cloud-cavity shedding. X-ray Phase-Contrast Imaging (XPCI), exploiting the shift in the X-ray wave phase during interactions with matter, offers sharp-refractive index gradients in the interface region. Hence, it is suitable for capturing fine morphological fluctuations of transient cavitation structures. Nevertheless, the technique cannot provide information on the quantity of vapour within the orifice. Such data have been obtained utilising absorption imaging, where beam attenuation is not associated with scattering and refraction events, and hence can be explicitly correlated with the projected vapour thickness in line-of-sight measurements. A combination of the two methods is proposed, as it has been found is capable of quantifying the vapour content arising in the complex nozzle flow, while also faithfully illustrating the dynamics of the highly-transient cavitation features.

42 ENGINEERING↗

DOE OSTI2024

Gauge Theory Bootstrap

We propose the gauge theory bootstrap, a method to compute the pion S matrix that describes the low-energy physics of the strong interaction and other similar gauge theories. The phase shifts of the S 0 , P 1 , and S 2 waves obtained are in good agreement with experimental results. The only numerical inputs are the quark mass m q , the QCD scale Λ QCD , the pion mass m π , and the pion decay constant f π without any other experimental data. We make use of the form-factor bootstrap recently proposed by Karateev, Kuhn, and Penedones together with a finite energy version of the Shifman-Veinshtein-Zakharov sum rules. Published by the American Physical Society 2024

He, Yifei (ORCID:0000000213666157)↗

DOE OSTI2026

SpaceNet 9—Cross-Sensor Alignment of Optical and SAR Imagery

Precise registration of high-resolution synthetic aperture radar (SAR) and optical imagery is necessary for realizing the full potential and benefits of multimodal image analysis. However, two significant challenges presently exist. First, there is a lack of annotated datasets and benchmarks available for high-resolution SAR–optical image registration. Second, an assessment of efficient and reliable image registration methods that can precisely align these modalities is lacking. Here, we present a holistic description of the SpaceNet 9 Challenge and its results. We present a description of the dataset and baseline algorithm along with the results of the challenge, including a description of the winning algorithms. We release the SpaceNet 9 dataset along with open-sourcing the winning algorithms and baseline. The objective of SpaceNet 9 was to compute a dense displacement map that indicates the shift needed to align pixels in an optical image to the pixels in a SAR image. The challenge launched in April 2025 and was active for approximately two months. The top five solutions reduced image alignment error from approximately 34 m to under 13 m for public and private test data, with the best results obtaining a registration error of only 8.5 and 6.7 m on the public testing and private testing dataset, respectively. Usage of pretrained image matching models, robust outlier rejection with RANSAC, and estimating local displacement were common among the top solutions. The results of this challenge provide insight into high-resolution SAR–optical image registration and offer opportunities for future benchmarking in this domain. The baseline algorithm, winning solutions, and datasets are available at https://spacenet.ai/sn9-challenge/.

benchmark datasets↗

DOE OSTI2024

In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance

To facilitate the detection and management of potential clinical antiviral resistance, in vitro selection of drug-resistant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) against the virus M pro inhibitor nirmatrelvir (Paxlovid active component) was conducted. Six M pro mutation patterns containing T304I alone or in combination with T21I, L50F, T135I, S144A, or A173V emerged, with A173V+T304I and T21I+S144A+T304I mutations showing >20-fold resistance each. Biochemical analyses indicated inhibition constant shifts aligned to antiviral results, with S144A and A173V each markedly reducing nirmatrelvir inhibition and M pro activity. SARS-CoV-2 surveillance revealed that in vitro resistance–associated mutations from our studies and those reported in the literature were rarely detected in the Global Initiative on Sharing All Influenza Data database. In the Paxlovid Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients trial, E166V was the only emergent resistance mutation, observed in three Paxlovid-treated patients, none of whom experienced COVID-19–related hospitalization or death.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Redesign of the Timeline Generator at Fermilab using a web-based Flutter application, GraphQL API and an IOC

The control system at Fermilab is undergoing an evolution with a shift towards web-based applications with connections to the EPICS infrastructure. The Timeline Generator (TLG) is an application that serves to coordinate events across the lab using different timing links. These links include the Tevatron clock (TCLK), a 10 MHz serial link with events encoded at 20Hz and Machine Data (MDAT), a communication link with states encoded at 720Hz. This paper covers the redesign of the major components of the TLG. This includes a web-based Flutter application for building timelines. A placement service is in use that has a GraphQL interface and uses a timeline input to compute a schedule of events and states. The Flutter application sends this computed schedule to the TLG IOC via a GraphQL interface to the Data Pool Manager (DPM). The TLG IOC runs on an Arria FPGA, the Accelerator Clock Generator (ACLK-GEN), which is responsible for writing the events and states on to the different timing links.

Carmichael, Linden [Fermilab]↗