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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

IGM damping wing constraints on the tail end of reionization from the enlarged XQR-30 sample

ABSTRACT The attenuation of Lyα photons by neutral hydrogen in the intergalactic medium (IGM) at z ≳ 5 continues to be a powerful probe for studying the epoch of reionization. Given a framework to estimate the intrinsic (true) Lyα emission of high-z sources, one can infer the ionization state of the IGM during reionization. In this work, we use the enlarged XQR-30 sample of 42 high-resolution and high signal-to-noise quasar spectra between $5.8\lesssim \, z\lesssim \, 6.6$ obtained with VLT/X-shooter to place constraints on the IGM neutral fraction. This is achieved using our existing Bayesian QSO reconstruction framework which accounts for uncertainties such as the: (i) posterior distribution of predicted intrinsic Lyα emission profiles (obtained via covariance matrix reconstruction of the Lyα and N v emission lines from unattenuated high-ionization emission line profiles; C iv, Si iv + O iv], and C iii]) and (ii) distribution of ionized regions within the IGM using synthetic damping wing profiles drawn from a 1.63 Gpc3 reionization simulation. Following careful quality control, we used 23 of the 42 available QSOs to obtain constraints/limits on the IGM neutral fraction during the tail-end of reionization. Our median and 68th percentile constraints on the IGM neutral fraction are: $0.20\substack{+0.14 -0.12}$ and $0.29\substack{+0.14 -0.13}$ at z = 6.15 and 6.35. Further, we also report 68th percentile upper limits of $\bar{x}_{\mathrm{H\, {\small I}}{}} \lt 0.21$, 0.20, 0.21, and 0.18 at z = 5.8, 5.95, 6.05, and 6.55. These results imply reionization is still ongoing at $5.8\lesssim \, z\lesssim \, 6.55$, consistent with previous results from XQR-30 (dark fraction and Lyα forest) along with other observational probes considered in the literature.

Greig, B. (ORCID:0000000240852094)↗
DOE OSTI2024

Uncovering the truth about M101, NGC 3938, and their significant others through radiative transfer

ABSTRACT Solving the inverse problem in spiral galaxies, that allows the derivation of the spatial distribution of dust, gas, and stars, together with their associated physical properties, directly from panchromatic imaging observations, is one of the main goals of this work. To this end, we used radiative transfer models to decode the spatial and spectral distributions of the nearby face-on galaxies M101 and NGC 3938. In both cases, we provide excellent fits to the surface-brightness distributions derived from GALEX, SDSS, 2MASS, Spitzer, and Herschel imaging observations. Together with previous results from M33, NGC 628, M51, and the Milky Way, we obtain a small statistical sample of modelled nearby galaxies that we analyse in this work. We find that in all cases Milky Way-type dust with Draine-like optical properties provide consistent and successful solutions. We do not find any ‘submm excess’, and no need for modified dust-grain properties. Intrinsic fundamental quantities like star-formation rates (SFR), specific SFR (sSFR), dust opacities, and attenuations are derived as a function of position in the galaxy and overall trends are discussed. In the SFR surface density versus stellar mass surface density space, we find a structurally resolved relation (SRR) for the morphological components of our galaxies, that is steeper than the main sequence (MS). Exception to this is for NGC 628, where the SRR is parallel to the MS.

Pricopi, D.↗
DOE OSTI2024

Properties of a fading AGN from SDSS-IV MaNGA

ABSTRACT We identify a fading AGN SDSS J220141.64+115124.3 from the internal Product Launch-11 (MPL-11) in Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey. The central region with a projected radius of $\sim$2.4 kpc is characterized as LINER-like line ratios while the outskirts extended to $\sim$15 kpc show Seyfert-like line ratios. The ${\rm{[O {\small III}]}}$$\lambda$5007 luminosity of the Seyfert regions is a factor of 37 (2) higher than the LINER regions without (with) dust attenuation correction, suggesting that the AGN activity decreases at least $\sim$8 $\times$ 10$^3$ yr ($\sim$2.4 kpc/light-speed) ago. We model the emission line spectra in the central region with double Gaussian components (a narrow core and a broad wing) and analyse the properties of each component. The narrow core component mostly co-rotates with the stellar disc, whereas the broad wing component with a median of the velocity dispersion $\sim$300 km s$^{-1}$ is related to a wind outflow. The kinematic position angle (PA) of the ionized gas shows an $\sim 20^{\circ }$ twist from the galaxy centre to 1.5 effective radius. The median of the PA difference between the gas and stellar components is as large as $\sim 50^{\circ }$ within 0.4 effective radius. The tidal feature in DESI image and star–gas misalignment suggest this galaxy is a merger remnant. Combining all these observational results as well as public available X-ray and MIR luminosities, we confirm this is a fading AGN, the merger process kick-started the central engine to quasar phase which ionized gas composed of tidal debris, and now the activity of the central black hole decreases. The discontinuity in ${\rm{[O {\small III}]}}$$\lambda$5007 flux and EQW maps is due to multiple AGN outbursts triggered by merger remnant gas inflows.

Mo, Hao (ORCID:0000000234430768)↗
DOE OSTI2023

A riboswitch separated from its ribosome-binding site still regulates translation

Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10–G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch—akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A conserved viral RNA fold enables nuclease resistance across kingdoms of life

Abstract Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence variability among xrRNAs from distantly related viruses raises questions about the shared molecular features that enable these RNAs to withstand the strong unwinding forces of exoribonucleases. Here, we present the first structure of a plant-virus xrRNA in its active conformation and uncover universal principles of xrRNA folding. Comparison with the structure of a human-pathogenic flavivirus xrRNA reveals that both share a core structural motif—a protective ring encircling the RNA’s 5′ end—despite lacking sequence similarity. Disrupting this core motif through targeted mutagenesis eliminates exoribonuclease-resistance and attenuates viral infection. We identify hundreds of related structures across multiple virus families, supporting the conservation of this mechanism. Our study demonstrates how distantly related RNA viruses have converged on a common structural strategy to inhibit cellular nucleases, with a universal ring topology as the defining feature of viral xrRNAs.

Biochemistry & Molecular Biology↗
DOE OSTI2022

MECHANISMS OF RADIATION CARCINOGENESIS: WHAT IS REALLY INDUCED?

Abstract It has been difficult to understand why the relative risk for cancer decreases with an increase in time since an exposure to radiation. It was recently recognized that this decline can be explained by a parallel shift of the age-related cancer mortality curve toward younger ages. In fact, it has been known for many years that mouse survival curves exhibit a parallel shift toward younger ages following an exposure to radiation, but it was not recognized that the mutation induction theory is incompatible with this parallel shift. This is because a parallel shift in the survival curve implies that all the irradiated individuals are affected, but the mutation induction theory assumes that only a fraction of the irradiated individuals is affected following an exposure to radiation. Thus, it seems likely that the target of radiation action, which leads to carcinogenesis, is not restricted to epithelial cells but includes all of the surrounding cells leading to an altered microenvironment. Since it is repeatedly observed that radiation-exposed normal tissues can stimulate transplanted or spontaneously arising tumor cells to grow faster, worsen the malignant phenotypes and finally kill the host earlier than usual, an exposure to radiation seems most likely to cause tissue inflammation, which creates conditions favorable for the growth of spontaneously arising tumor cells. This new concept suggests that it might be possible to attenuate the extent of radiation carcinogenesis by intervening in tissue inflammatory processes.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Perturbation of tonoplast sucrose transport alters carbohydrate utilization for seasonal growth and defense metabolism in coppiced poplar

Abstract Nonstructural carbohydrate reserves of stems and roots underpin overall tree fitness and productivity under short-rotation management practices such as coppicing for bioenergy. While sucrose and starch comprise the predominant stem carbohydrate reserves of Populus, utilization for fitness and agricultural productivity is understood primarily in terms of starch turnover. The tonoplast sucrose transport protein SUT4 modulates sucrose export from source leaves to distant sinks during photoautotrophic growth, but the possibility of its involvement in remobilizing carbohydrates from storage organs during heterotrophic growth has not been explored. Here, we used PtaSUT4-knockout mutants of Populus tremula × P. alba (INRA 717-1B4) in winter (cool) and summer (warm) glasshouse coppicing experiments to assess SUT4 involvement in reserve utilization. Conditions preceding and supporting summer sprouting were considered favorable for growth, while those preceding and supporting cool temperature sprouting were suboptimal akin to conditions associated with coppicing as generally practiced. Epicormic bud emergence was delayed in sut4 mutants following lower temperature ‘winter’ but not summer coppicing. Winter xylem hexose increases were observed in control but not in sut4 stumps after coppicing. The magnitude of starch and sucrose reserve depletion was similar in control and sut4 stumps during the winter and did not explain the sprouting and xylem hexose differences. However, winter maintenance costs appeared higher in sut4 based partly on Krebs cycle intermediate levels. In control plants, bark accrual of abundant defense metabolites, including salicinoids and condensed tannins, was higher in summer than in winter, but this increase of summer defense allocations was attenuated in sut4 mutants. Temperature-sensitive trade-offs between growth and other priorities may therefore depend on SUT4 in Populus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

‘ Candidatus Liberibacter asiaticus’-Encoded BCP Peroxiredoxin Suppresses Lipopolysaccharide-Mediated Defense Signaling and Nitrosative Stress In Planta

The lipopolysaccharides (LPS) of gram-negative bacteria trigger a nitrosative and oxidative burst in both animals and plants during pathogen invasion. Liberibacter crescens strain BT-1 is a surrogate for functional genomic studies of the uncultured pathogenic ‘Candidatus Liberibacter’ spp. that are associated with severe diseases such as citrus greening and potato zebra chip. Structural determination of L. crescens LPS revealed the presence of a very long chain fatty acid modification. L. crescens LPS pretreatment suppressed growth of Xanthomonas perforans on nonhost tobacco (Nicotiana benthamiana) and X. citri subsp. citri on host orange (Citrus sinensis), confirming bioactivity of L. crescens LPS in activation of systemic acquired resistance (SAR). L. crescens LPS elicited a rapid burst of nitric oxide (NO) in suspension cultured tobacco cells. Pharmacological inhibitor assays confirmed that arginine-utilizing NO synthase (NOS) activity was the primary source of NO generation elicited by L. crescens LPS. LPS treatment also resulted in biological markers of NO-mediated SAR activation, including an increase in the glutathione pool, callose deposition, and activation of the salicylic acid and azelaic acid (AzA) signaling networks. Transient expression of ‘Ca. L. asiaticus’ bacterioferritin comigratory protein (BCP) peroxiredoxin in tobacco compromised AzA signaling, a prerequisite for LPS-triggered SAR. Western blot analyses revealed that ‘Ca. L. asiaticus’ BCP peroxiredoxin prevented peroxynitrite-mediated tyrosine nitration in tobacco. ‘Ca. L. asiaticus’ BCP peroxiredoxin (i) attenuates NO-mediated SAR signaling and (ii) scavenges peroxynitrite radicals, which would facilitate repetitive cycles of ‘Ca. L. asiaticus’ acquisition and transmission by fecund psyllids throughout the limited flush period in citrus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Design and Characterization of an Extremely-Sensitive, Large-Volume Gamma-Ray Spectrometer for Environmental Samples

A large volume gamma spectrometer was designed and constructed to analyze foodstuffs and environmental samples having low radionuclide concentrations. This system uses eight 11-cm × 42.5-cm × 5.5-cm NaI(Tl) detectors, chosen due to their relatively high sensitivity and availability and arranged in an octagonal configuration. The sensitive volume of the system is ~28 cm in diameter and ~42 cm deep. Shielding consists of an 86-cm × 86-cm square, 64-cm-tall lead brick enclosure with 18-cm-thick lead walls lined by 0.3-cm-thick copper plates. An aluminum top was machined to suspend the detectors within this shield. The shielding reduces background counts by 72% at 100 keV and 42% at 1,000 keV. The positional variability in sensitivity of the well was determined by both simulation and experiment. A 2.1-L volume of nearly uniform sensitivity, varying less than 10%, exists in the well's center. Energy resolutions of 14.6% and 7.8% were measured for 241 Am and 137 Cs, respectively. Energy resolution shows a 0.2% variation for both 241 Am and 137 Cs as a function of position within all regions of the well’s central sensitive volume. Dead time was also determined to be less than 35% for all sources measured in the system, the largest of which had an activity of 1,760 kBq. Simulated results for various source geometries show higher counts for smaller samples, especially at lower energies due to less attenuation of low energy photons. In conclusion, minimum detectable activities were determined for all source energies used, less than 5.1 Bq kg -1 for reasonable background and sample counting times.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Seeing through noise in power laws

Despite widespread claims of power laws across the natural and social sciences, evidence in data is often equivocal. Modern data and statistical methods reject even classic power laws such as Pareto’s law of wealth and the Gutenberg–Richter law for earthquake magnitudes. We show that the maximum-likelihood estimators and Kolmogorov–Smirnov (K-S) statistics in widespread use are unexpectedly sensitive to ubiquitous errors in data such as measurement noise, quantization noise, heaping and censorship of small values. This sensitivity causes spurious rejection of power laws and biases parameter estimates even in arbitrarily large samples, which explains inconsistencies between theory and data. We show that logarithmic binning by powers of λ > 1 attenuates these errors in a manner analogous to noise averaging in normal statistics and that λ thereby tunes a trade-off between accuracy and precision in estimation. Binning also removes potentially misleading within-scale information while preserving information about the shape of a distribution over powers of λ, and we show that some amount of binning can improve sensitivity and specificity of K-S tests without any cost, while more extreme binning tunes a trade-off between sensitivity and specificity. We therefore advocate logarithmic binning as a simple essential step in power-law inference.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Measurement of the Low-Energy Electron Inelastic Mean Free Path in Monolayer Graphene

Measuring the electron-transport properties of substrate-supported nanomaterials with the traditional two-point comparison method is difficult at electron energies below 50 eV, where core-level signals are too feeble to be detected against the strong secondary-electron background. Herein, a data-driven spectral analysis technique is used to study the low-energy electron-transport properties of substrate-supported target nanomaterials, while eliminating the influence of the substrate signal. Applying this technique, the electron-transport properties of the effective attenuation length and the inelastic mean free path (IMFP) can be determined with extremely high efficiency over the entire measured energy range of 6–600 eV. Further, these results show excellent agreement with other experimental and theoretical results. In this work, significant differences are observed between monolayer graphene and the bulk graphite IMFP, which illustrates the importance of the nanometer effect in the electron-transport properties of the material. Furthermore, this technique is readily applicable to any ultrathin material that can be transferred onto a polycrystalline gold substrate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Experimental Passive-State Preparation for Continuous-Variable Quantum Communications

In the Gaussian-modulated coherent state quantum key distribution (QKD) protocol, the sender first generates Gaussian-distributed random numbers and then encodes them on weak laser pulses actively by performing amplitude and phase modulations. Recently, an equivalent passive QKD scheme has been proposed by exploring the intrinsic field fluctuations of a thermal source [B. Qi, P. G. Evans, and W. P. Grice, Phys. Rev. A 97, 012317 (2018)]. This passive QKD scheme is especially appealing for chip-scale implementation since no active modulation is required. In this paper, we conduct an experimental study of the passively encoded QKD scheme using an off-the-shelf amplified spontaneous emission source operated in continuous-wave mode. Our results show that the excess noise introduced by the passive state preparation scheme can be effectively suppressed by applying optical attenuation and a secure key can be generated over metro-area distances.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Inverse Method for Noninvasive Material Discrimination with Multienergy X-Ray Radiography

Active x-ray inspections have great potential for noninvasive detection of illicit materials. Dual-energy x-ray radiography, in particular, has been used to determine material composition by utilizing the energy-dependence of the x-ray attenuation coefficients. However, current implementations of this method are limited in their ability to determine the material composition of composite objects. Here, in this paper, we present an inverse algorithm that uses multienergy x-ray radiography data to noninvasively reconstruct the contents of a container. A critical feature of the current contribution is that material identification can be performed using conventional detectors and x-ray spectra with different endpoint energies produced by varying nothing more than the tube voltage. Adaptive regularization is used to increase the accuracy of material estimations from multienergy data sets. The utility of these methods is demonstrated with experimentally acquired radiographs obtained using a tunable x-ray source that produces spectra with endpoint energies of 100–450 keV. The object inspected is a scale model of a nuclear materials storage container composed of three-dimensional printed plastic and stainless-steel spheres inside a thin-walled steel container. Reconstructions of the steel sphere thicknesses are within a root-mean-square error of 0.37 cm.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Procrustean entanglement concentration in quantum-classical networking

The success of a future quantum internet will rest in part on the ability of quantum and classical signals to coexist in the same optical fiber infrastructure, a challenging endeavor given the orders of magnitude differences in flux of single-photon-level quantum fields and bright classical traffic. Here, we theoretically describe and experimentally implement Procrustean entanglement concentration for polarization-entangled states contaminated with classical light, showing significant mitigation of crosstalk noise in dense wavelength-division multiplexing. Our approach leverages a pair of polarization-dependent loss emulators to attenuate highly polarized crosstalk that results from imperfect isolation of conventional signals copropagating on shared fiber links. We demonstrate our technique both on the tabletop and over a deployed quantum local area network, finding a substantial improvement of two-qubit entangled state fidelity from approximately 75% to over 92%. This local filtering technique could be used as a preliminary step to reduce asymmetric errors, potentially improving the overall efficiency when combined with more complex error-mitigation techniques in future quantum repeater networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Cooperative response of magnetism and superconductivity in the magnetic superconductor RbEuFe 4 As 4

Herein, we present a study of the magnetic-flux evolution in the magnetic superconductor RbEuFe 4 As 4 performed using magneto-optical imaging and magnetization measurements during field cooling and warming and magnetic field cycling at temperatures above and below the magnetic transition point, T$_m$. The vortex patterns emerging at T ≲ T$_m$ reveal that the Eu-spin subsystem serves as an internal pump of the magnetic flux while the superconducting critical current controls the delivery of magnetic-flux quanta into the bulk. The interplay of magnetic susceptibility amplifying the magnetic induction and vortex pinning attenuating the magnetic-flux entry results in a field- and temperature-dependent critical state that emulates a paramagnetic Meissner effect. The observed vortex dynamics corresponds to a nontrivial spatial current distribution and yields a self-consistent inhomogeneous enhancement of the sample magnetization.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Campbell penetration depth in low carrier density superconductor YPtBi

Magnetic penetration depth, λ m , was measured as a function of temperature and magnetic field in single crystals of low carrier density superconductor YPtBi by using a tunnel-diode oscillator technique. Measurements in zero DC magnetic field yield London penetration depth, λ L ( T ) , but in the applied field the signal includes the Campbell penetration depth, λ C ( T ) , which is the characteristic length of the attenuation of small excitation field, H AC , into the Abrikosov vortex lattice due to its elasticity. Whereas the magnetic field dependent λ C exhibit λ C ~ B p with p = 1 / 2 in most of the conventional and unconventional superconductors, we found that p ≈ 0.23 << 1 / 2 in YPtBi due to rapid suppression of the pinning strength. From the measured λ C ( T , H ) , the critical current density is j c ≈ 40 A / cm 2 at 75 mK. We find that this is orders of magnitude lower than that of conventional superconductors of comparable T c .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Moving vortices in anisotropic superconductors

The magnetic field of moving vortices in anisotropic superconductors is considered in the framework of the time-dependent London approach. It is found that, at distances large relative to the core size, the field may change sign that alludes to a nontrivial intervortex interaction which depends on the crystal anisotropy and on the speed and direction of motion. These effects are caused by the electric fields and corresponding normal currents which appear due to the moving vortex magnetic structure. We find that the motion related part of the magnetic field attenuates at large distances as 1/r 3 unlike the exponential decay of the static vortex field. The electric field induced by the vortex motion decreases as 1/r 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Pearl vortices in anisotropic superconducting films

The magnetic field of vortices in anisotropic superconducting films is considered in the framework of anisotropic London approach. It is found that at distances large relative to the core size, the magnetic field normal to the film surface may change sign. Here, we find that the magnetic field attenuates at large distances as 1/r 3 as it does in isotropic films, but the anisotropy induces an angular dependence to the supercurrents which causes the sign of the field to change for anisotropy parameters γ = λ 2 /λ 1 > $\sqrt{2}$ in some parts of the (x, y) plane.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗