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At least 649 records · Page 36

Ancestral archaea expanded the genetic code with pyrrolysine

The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA Pyl ) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA Pyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA Pyl and reveal the emergence of tRNA Pyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA Pyl species with the more common G73-containing tRNA Pyl will enable future efforts to engineer PylRS systems for further genetic code expansion.

59 BASIC BIOLOGICAL SCIENCES↗

Probing anisotropies of the Stochastic Gravitational Wave Background with LISA

Here, we investigate the sensitivity of the Laser Interferometer Space Antenna (LISA) to the anisotropies of the Stochastic Gravitational Wave Background (SGWB). We first discuss the main astrophysical and cosmological sources of SGWB which are characterized by anisotropies in the GW energy density, and we build a Signal-to-Noise estimator to quantify the sensitivity of LISA to different multipoles. We then perform a Fisher matrix analysis of the prospects of detectability of anisotropic features with LISA for individual multipoles, focusing on a SGWB with a power-law frequency profile. We compute the noise angular spectrum taking into account the specific scan strategy of the LISA detector. We analyze the case of the kinematic dipole and quadrupole generated by Doppler boosting an isotropic SGWB. We find that β Ω GW ~ 2 × 10 -11 is required to observe a dipolar signal with LISA. The detector response to the quadrupole has a factor ~ 10 3 β relative to that of the dipole. The characterization of the anisotropies, both from a theoretical perspective and from a map-making point of view, allows us to extract information that can be used to understand the origin of the SGWB, and to discriminate among distinct superimposed SGWB sources.

79 ASTRONOMY AND ASTROPHYSICS↗

H i asymmetries in LVHIS, VIVA, and HALOGAS galaxies

ABSTRACT We present an analysis of morphological, kinematic, and spectral asymmetries in observations of atomic neutral hydrogen (H i) gas from the Local Volume H i Survey (LVHIS), the VLA Imaging of Virgo in Atomic Gas (VIVA) survey, and the Hydrogen Accretion in Local Galaxies Survey. With the aim of investigating the impact of the local environment density and stellar mass on the measured H i asymmetries in future large H i surveys, we provide recommendations for the most meaningful measures of asymmetry for use in future analysis. After controlling for stellar mass, we find signs of statistically significant trends of increasing asymmetries with local density. The most significant trend we measure is for the normalized flipped spectrum residual (Aspec), with mean LVHIS and VIVA values of 0.204 ± 0.011 and 0.615 ± 0.068 at average weighted 10th nearest-neighbour galaxy number densities of log (ρ10/Mpc−3) = −1.64 and 0.88, respectively. Looking ahead to the Widefield ASKAP L-band Legacy All-sky Blind survey on the Australian Square Kilometre Array Pathfinder, we estimate that the number of detections will be sufficient to provide coverage over 5 orders of magnitude in both local density and stellar mass increasing the dynamic range and accuracy with which we can probe the effect of these properties on the asymmetry in the distribution of atomic gas in galaxies.

Reynolds, T. N.↗

Analyzing the Performance Trade-Off in Implementing User-Level Threads

User-level threads have been widely adopted as a means of achieving lightweight concurrent execution without the costs of OS-level threads. Nevertheless, the costs of managing user-level threads represent a performance barrier that dictates how fine grained the concurrency exposed by an application can be without incurring significant overheads; this in turn may translate into insufficient parallelism to exploit highly parallel systems. This article is a deep dive into the fundamental costs in implementing user-level threads. We first identify that one of the highest sources of fork-join overheads stems from deviations, events that incur context switching during the execution of a thread and disrupt a run-to-completion execution. We then conduct an in-depth investigation of a wide spectrum of methods with respect to how they handle deviations while covering both parent- and child-first scheduling policies. Our methodology involves a comprehensive instruction- and cache-level analysis of all methods on several modern CPU architectures. Finally, the primary finding of our evaluation is that dynamic promotion methods that assume the absence of deviation and dynamically provide context-switching support offer the best trade-off between performance and capability when the likelihood of deviation is low.

97 MATHEMATICS AND COMPUTING↗

Photoluminescence probing of light absorption centers at silica laser damage

We use photoluminescence (PL) imaging to study damage growth precursors within laser damage sites on the surface of silica. Damage site evolution is induced by multiple shots of UV nanosecond pulsed laser at various energy densities and monitored throughout the early stages of growth. Wide-field PL imaging rapidly locates microscopic light absorption centers within the silica damage site. Our quantitative analysis shows that damage sites with strong local PL intensity show a higher probability of growth upon subsequent laser pulses. Scanning electron microscopy (SEM) paired with a study of PL spectrum shows that the strong PL intensity appears from the subsurface fractures with high defect density, which provides a local light absorption center leading to significant damage growth. We believe that this result offers an efficient optical damage mitigation strategy by providing a rapid and non-destructive optical inspection approach.

36 MATERIALS SCIENCE↗

Simplified Approach for Scoping Assessment of Non-LWR Source Terms

This report describes a structure to aid in evaluation of release mitigation strategies across a range of reactor technologies. The assessment performed for example reactor concepts utilizes previous studies of postulated accident sequences for each reactor concept. This simplified approach classifies release mitigation strategies based on a range of barriers, physical attenuation processes, and system performance. It is not, however, intended to develop quantitative estimates of radiological release magnitudes and compositions to the environment. Rather, this approach is intended to identify the characteristics of a reactor design concepts release mitigation strategies that are most important to different classes of accident scenarios. It uses a scoping methodology to provide an approximate, order-of-magnitude, estimate of the radiological release to the environment and associated off-site consequences. This scoping method is applied to different reactor concepts, considering the performance of barriers to fission product release for these concepts under sample accident scenarios. The accident scenarios and sensitivity evaluations are selected in this report to evaluate the role of different fission product barriers in ameliorating the source term to the environment and associated off-site consequences. This report applies this structure to characterize how release mitigation measures are integrated to define overall release mitigation strategies for High Temperature Gas Reactors (HTGRs), Sodium Fast Reactors (SFRs), and liquid fueled Molten Salt Reactors (MSRs). To support this evaluation framework, factors defining a chain of release attenuation stages, and thus an overall mitigation strategy, must be established through mechanistic source term calculations. This has typically required the application of an integral plant analysis code such as MELCOR. At present, there is insufficient evidence to support a priori evaluation of the effectiveness of a release mitigation strategy for advanced reactor concepts across the spectrum of events that could challenge the radiological containment function. While it is clear that these designs have significant margin to radiological release to the environment for the scenarios comprising the design basis, detailed studies have not yet been performed to assess the risk profile for these plants. Such studies would require extensive evaluation across a reasonably complete spectrum of accident scenarios that could lead to radiological release to the environment.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Ultrasound preliminary cyber-physical evaluation

In this assessment, we focused on identifying unwanted RF emissions from the subject devices. This consisted of two major approaches: 1) Monitor for emitted RF during operation and ensure it is within expected bounds. 2) Inspect circuit board construction for any geometry or design patterns that could lead to RF emissions, whether intentional or unintentional. These patterns include: a) Single-ended PCB traces that could operate as an antenna. b) Insufficient shielding around typically “noisy” components such as switching power supplies. c) Free-hanging high-speed signal wires with no shielding that could emit RF. Suspicious components and design patterns were given a plausible reason to be included in the design. Any suspicious components or patterns warranted reason for deeper investigation. After more in-depth analysis no components were found to be intentionally malicious or had unexpected functionality.

42 ENGINEERING↗

A near magnetic-to-kinetic energy equipartition flare from the relativistic jet in AO 0235 + 164 during 2013–2019

ABSTRACT We present the multiwavelength flaring activity of the blazar AO 0235 + 164 during its recent active period from 2013 to 2019. From a discrete correlation function analysis, we find a significant ($\gt 95~{{\ \rm per\ cent}}$) correlation between radio and gamma-ray light curves with flares at longer wavelengths following flares at shorter wavelengths. We identify a new jet component in 43 GHz Very Long Baseline Array data that was ejected from the radio core on MJD $57246^{+26}_{-30}$ (2015 August 12), during the peak of the 2015 radio flare. From the analysis of the jet component, we derived a Doppler factor of δvar = 28.5 ± 8.4, a bulk Lorentz factor of $\Gamma =16.8^{+3.6}_{-3.1}$, and an intrinsic viewing angle of $\theta _{\rm v}=1.42^{+1.07}_{-0.52}\textrm {~degrees}$. Investigation of the quasi-simultaneous radio data revealed a partially absorbed spectrum with the turnover frequency varying in the range of 10−70 GHz and the peak flux density varying in the range of 0.7−4 Jy. We find the synchrotron self-absorption magnetic field strength to be $B_{\rm SSA}=15.3^{+12.6}_{-14.0}\textrm {~mG}$ at the peak of the 2015 radio flare, which is comparable to the equipartition magnetic field strength of $B_{\rm EQ}=43.6^{+10.6}_{-10.4}\textrm {~mG}$ calculated for the same epoch. Additional analysis of the radio emission region in the relativistic jet of AO 0235 + 164 suggests that it did not significantly deviate from equipartition during its recent flaring activity.

Astronomy & Astrophysics↗

Cosmic shear power spectra in practice

Cosmic shear is one of the most powerful probes of Dark Energy, targeted by several current and future galaxy surveys. Lensing shear, however, is only sampled at the positions of galaxies with measured shapes in the catalog, making its associated sky window function one of the most complicated amongst all projected cosmological probes of inhomogeneities, as well as giving rise to inhomogeneous noise. Partly for this reason, cosmic shear analyses have been mostly carried out in real-space, making use of correlation functions, as opposed to Fourier-space power spectra. Since the use of power spectra can yield complementary information and has numerical advantages over real-space pipelines, it is important to develop a complete formalism describing the standard unbiased power spectrum estimators as well as their associated uncertainties. Building on previous work, this paper contains a study of the main complications associated with estimating and interpreting shear power spectra, and presents fast and accurate methods to estimate two key quantities needed for their practical usage: the noise bias and the Gaussian covariance matrix, fully accounting for survey geometry, with some of these results also applicable to other cosmological probes. Here, we demonstrate the performance of these methods by applying them to the latest public data releases of the Hyper Suprime-Cam and the Dark Energy Survey collaborations, quantifying the presence of systematics in our measurements and the validity of the covariance matrix estimate. We make the resulting power spectra, covariance matrices, null tests and all associated data necessary for a full cosmological analysis publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗

Advancing set-conditional set generation: Diffusion models for fast simulation of reconstructed particles

The computational intensity of detector simulation and event reconstruction poses a significant difficulty for data analysis in collider experiments. This challenge inspires the continued development of machine learning techniques to serve as efficient surrogate models. We propose a fast emulation approach that combines simulation and reconstruction. In other words, a neural network generates a set of reconstructed objects conditioned on input particle sets. To make this possible, we advance set-conditional set generation with diffusion models. Using a realistic, generic, and public detector simulation and reconstruction package (COCOA), we show how diffusion models can accurately model the complex spectrum of reconstructed particles inside jets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Precision Local Burnup Assessment Through Dynamic Peak Fitting in Atom Probe Tomography for Depleted, Enriched, and Irradiated Metallic and Ceramic Fuels

Abstract Burnup estimation in nuclear fuels is vital for evaluating fuel performance, transportation, and safe fuel storage. Accurate assessments of burnup from service period and spent fuels involve tracking the consumption of fissile isotopes of uranium (U) offering a direct insight into energy changes within the fuels especially for thermal spectrum reactors. In current approach, mass spectroscopic technique in atom probe tomography (APT) is utilized for accurate quantification of U isotopes. Quantification of U peaks in mass spectrum is performed on asymmetric shapes due to delayed signals, known as thermal tails, particularly for poorly conducting samples analyzed in laser mode. In this study, we introduce a novel quantification tool for isotopic analysis from APT datasets by developing a fitting algorithm based on shapes of the peaks. A MATLAB-based dynamic peak fitting toolbox is developed and designed to adapt to various peak shapes, ensuring accurate quantification of U isotopes. The effectiveness of this approach is demonstrated in standard Ni-Cr sample, depleted and enriched U samples, and U-based fuels with different burnup levels. The viability of this approach for isotopic quantification is demonstrated on both metallic and ceramic fuels.

Burnup↗

Characterization and Optimization of a Spectral Window for Direct Gaseous Uranium Hexafluoride Enrichment Assay Using Laser-Induced Breakdown Spectroscopy

Through a systematic scanning of 235 U and 238 U emission lines between 280 nm and 745 nm, the optimal emission line for direct gaseous uranium hexafluoride (UF 6 ) enrichment assay using laser-induced breakdown spectroscopy (LIBS) was found. Screening for spectral features that are potentially useful for U isotopic analysis was gauged from the magnitude of the 235 U– 238 U isotopic shift and the signal-to-background ratio of the emission line through a parameter termed ΔSBR 235U–238U . The ΔSBR spectrum shows peaks at wavelength positions where there are strong lines with significant 235 U– 238 U shifts. The screening identified 13 spectral-window candidates, which were down selected based on their overall accuracy in predicting the 235 U enrichment of three UF 6 samples of natural (0.720 atom% 235 U) and low-enriched (4.675 atom% and 9.157 atom% 235 U) grades. The U(I) 646.498 nm emission line, with a determined 235 U– 238 U isotopic shift of -17.7 pm, was found to be the optimal spectral window for direct UF 6 enrichment assay. The root mean square error for enrichment assays on the three natural and low-enriched UF 6 samples, with each sample measured in six replicates, was 0.31% in absolute 235 U content. Each measurement comprised LIBS signals accumulated from 3000 laser shots. In conclusion, the analytical bias and precision were better than 0.5% and 0.3%, respectively, in absolute [ 235 U/( 235 U + 238 U)] ratios. Specific for the two low-enriched UF 6 samples, the relative standard deviations from six replicated measurements were around 2%.

47 OTHER INSTRUMENTATION↗

SCALE Modeling of the Sodium Cooled Fast-Spectrum Advanced Burner Test Reactor

This report documents the modeling and simulation of a sodium-cooled fast reactor (SFR) as part of a U.S. Nuclear Regulatory Commission–sponsored project to assess the modeling and simulation capabilities for accident progression, source term, and consequence analysis for advanced reactor technologies with the Oak Ridge National Laboratory code SCALE and the Sandia National Laboratories (SNL) code MELCOR. Based on publicly available benchmark specifications, a fully heterogeneous 3D SCALE model of the 250 MWth Advanced Burner Test Reactor (ABTR) was developed to demonstrate SCALE’s capabilities for full-core reactivity analysis, fuel inventory prediction, and decay heat analysis of an SFR. The benchmark specifications contain modeling details for the ABTR core at the beginning of equilibrium cycle (BOEC) at operating conditions; they were derived from a 2006 preconceptual design report produced by Argonne National Laboratory. The ABTR was designed to demonstrate reactor-based transmutation of transuranics, that is, to “burn” transuranics recovered from light-water reactor (LWR) spent fuel. The ABTR’s fuel is designed to operate in 4 month cycles using uranium/transuranic (U/TRU) metallic fuel, with a TRU content of approximately 20%, at a conversion ratio of approximately 0.6. Various reactivity calculations were performed with SCALE for the ABTR and, where possible, compared with results available in the open literature. Additionally, SCALE was used to perform a full-core depletion calculation over the 4 month cycle to obtain the nuclide inventory at the end of equilibrium cycle (EOEC). These nuclide inventories, decay heat, power profiles, and reactivity feedback coefficients at EOEC represent the initial conditions for analyzing severe accident scenarios with MELCOR.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Fundamental Phenomena and Applications of Swift Heavy Ion Irradiations

This review concentrates on the specific properties and characteristics of damage structures generated with high-energy ions in the electronic energy loss regime. Irradiation experiments with so-called swift heavy ions (SHIs) find applications in many different fields, with examples presented in ion-track nanotechnology, radiation hardness analysis of functional materials, and laboratory tests of cosmic radiation. The basics of the SHI-solid interaction are described with special attention to processes in the electronic subsystem. The broad spectrum of damage phenomena is exemplified for various materials and material classes, along with a description of typical characterization techniques. This review also presents state-of-the-art modeling efforts that try to account for the complexity of the coupled processes of the electronic and atomic subsystems. Lastly, a brief discussion at the end of this review on SHI phenomena induced by fission fragments in nuclear materials will highlight the relevance of energetic ion irradiation in nuclear technology applications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Copper-nickel electroplating of 3D-printed acrylonitrile butadiene styrene for interference and radiation shielding applications

Here, in this study, electromagnetic and radiation shielding structures were fabricated by 3D printing acrylonitrile butadiene styrene (ABS) structures via fused filament fabrication and electroplating with copper (Cu) and nickel (Ni) metals. Prior to electroplating, the printed ABS materials were made conductive by surface electrodeposition of polypyrrole (PPy). ABS adsorbs the pyrrole monomer, which subsequently polymerizes via oxidation forming conductive PPy layer on the printed structures. The successful anchoring of PPy layer can be attributed to its hydrogen bonding and electrostatic interactions with ABS. Thermal analysis, optical, and electron microscopy equipped with energy dispersive X-ray were employed to characterize the printed shielding structures, while the interference and radiation shielding effectiveness were evaluated using a spectrum analyzer and dosimeter, respectively. The interference shielding was found to be effective at 60 ± 5 dB over relatively small frequency range. Shielding was also apparent against gamma and X-ray ionizing rays, but more significantly effective against beta rays. Furthermore, the Cu/Ni coating was able to reduce any heat-induced dimensional changes for the 3D printed ABS substrate without compromising the mechanical integrity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Robust Automatic EXAFS First-Shell Fits

Extended X-ray absorption fine structure (EXAFS) is a widely used technique for atomic structure determination. Fourier transformation connects EXAFS in k space and R space. However, determining the appropriate k-range for the transformation can be challenging, but critical for the first-shell fit. In this study, we present an automatic method to determine the k-range using the Larch package and a Python program. The first step is to estimate spectral noise across a series of k-ranges with a fixed minimum value and identify the optimal maximum value in the k-range (k max ). The k max is determined by an empirical noise threshold that marks the point where the noise level in the Fourier transformed spectrum changes dramatically. Using the obtained k max value, the first shell is modeled to determine the minimum k value (k min ) by optimizing the background function through alignment of the spectrum with theory. The optimal k min corresponds to the point of the minimum R-factor, which quantifies the difference between the experimental and fitted spectrum. Our method was tested on various typical datasets and yielded suitable k-ranges for Fourier transformation and accurate first-shell fits. This approach helps avoid unreliable, irreproducible data analysis, especially for noisy data from diluted samples, and enables robust automatic first-shell EXAFS fitting.

EXAFS analysis↗

STEM Imaging of Materials: Final Report for DE-FG02-08ER46547

This project supported research advancing the state of the art in scanning transmission electron microscopy (STEM) imaging and characterization of materials, especially electronic materials. The project began with studies of point defects in materials using high-resolution Z-contrast STEM, then evolved to including methods in four-dimensional (4D) STEM and machine learning. Highlights include: (1) the discovery of stable, p-type ZnO via Sb doping, (2) demonstration that the high performance of InGaN LEDs is not due to In composition fluctuations as previously proposed, (3) the demonstration of the first sub-pm precision high-resolution STEM images using non-rigid registration of a series of STEM images, (4) the extension of high-precision STEM to low dose imaging and spectrum imaging, (5) discovery of a synthesis method for twisted spiral growth of transition-metal dichalcogenide materials via chemical vapor deposition, and (6) development of machine-learning methods for analysis and denoising of enormous 4D STEM data sets.

36 MATERIALS SCIENCE↗

Utilizing a Database of Simulated Geometric Albedo Spectra for Photometric Characterization of Rocky Exoplanet Atmospheres

In anticipation of future flagship missions focused on the goal of achieving direct imaging of rocky exoplanets, we have developed a database of models to help the community examine the potential spectral characteristics of a broad range of rocky planet atmospheres. Using the publicly available Planetary Spectrum Generator, we have computed a grid of 141,600 rocky exoplanet geometric albedo spectra across a seven-dimensional parameter space. Using this grid, we have performed a color–color analysis seeking to identify the most useful near-UV and red or near-infrared photometric follow-up channels to combine with a green-optical (discovery) spectral channel. We found that a combination of filters at 0.4, 0.58, and ∼0.8 μm were able to distinguish between atmospheres with moderate-to-high concentrations of four different dominant absorbing constituents, given at least 10 hr of observation on a star at 10 parsec with a 15 m class space telescope; however, more moderate abundances similar to those of solar system rocky bodies would be more challenging to detect. We recommend that future missions seeking to characterize directly imaged rocky exoplanets by colors alone further consider multiband photometry as a first discriminator for planetary characteristics.

79 ASTRONOMY AND ASTROPHYSICS↗