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At least 649 records · Page 36

DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes

Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (~0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗

Natural Language Processing-Enhanced Nuclear Industry Operating Experience Data Analysis: Aggregation and Interpretation of Multi-Report Analysis Results

Industry-wide operating experience is a critical source of raw data for reliability and risk model parameter estimations for nuclear power plants. A large portion of operating experience data are failure events stored as reports that contain unstructured data, such as narratives. In current practice, a failure report is usually reviewed and manually coded by analysts. The coding is based on extracting several event characteristics such as system name, component type, sub-part type, failure mode, and failure cause. Event narratives are mostly used to help understand events and extract their characteristics. In this line of research, we aim to maximize the usage of event narratives by leveraging natural language processing (NLP) methods to automatically convert an event narrative to a causal graph. This research has promise to improve physical understanding of failure initiation and propagation and to facilitate use of non-failure data (e.g., near-misses and degradations) to complement the limited data pool of failures. In our previous work, we developed an NLP tool and applied it to analyze a number of licensee event reports submitted by U.S. nuclear power plants to the Nuclear Regulatory Commission. In this paper, we will report our recent research progress in aggregating the results of multiple reports, developing network model(s), and drawing statistical insights.

99 GENERAL AND MISCELLANEOUS↗

End-Use Savings Shapes Measure Documentation: LED Lighting

Building on the successfully completed effort to calibrate and validate the U.S. Department of Energy's ResStock and ComStock models over the past three years, the objective of this work is to produce national data sets that empower analysts working for federal, state, utility, city, and manufacturer stakeholders to answer a broad range of analysis questions. The goal of this work is to develop energy efficiency, electrification, and demand flexibility end-use load shapes (electricity, gas, propane, or fuel oil) that cover a majority of the high-impact, market-ready (or nearly market-ready) measures. "Measures" refers to energy efficiency variables that can be applied to buildings during modeling. An end-use savings shape is the difference in energy consumption between a baseline building and a building with an energy efficiency, electrification, or demand flexibility measure applied. It results in a timeseries profile that is broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each timestep. ComStock is a highly granular, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual subhourly energy consumption of the commercial building stock across the United States. The baseline model intends to represent the U.S. commercial building stock as it existed in 2018. The methodology and results of the baseline model are discussed in the final technical report of the End-Use Load Profiles project. This documentation focuses on a single end-use savings shape measure - LED lighting. The LED lighting measure replaces interior lights with LEDs where applicable. The measure resulted in 1.25 TBtu energy savings across the building stock, with the majority of savings occurring in retail and warehouse buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

$\mathrm{BUDDI}$-$\mathrm{MaNGA}$ $\mathrm{I}$: A statistical sample of cleanly decomposed bulge and disc spectra

Many galaxies display clear bulges and discs, and understanding how these components form is a vital step towards understanding how the galaxy has evolved into what we see today. The BUDDI-MaNGA project aims to study galaxy evolution and morphological transformations through the star-formation histories of the bulges and discs. We have applied our buddi software to galaxies from the MaNGA Survey in the SDSS DR15 in order to isolate their bulge and disc spectra, from which we derived their stellar populations. To date, this work provides the largest sample of clean bulge and disc spectra extracted from IFU datacubes using the galaxies light profile information, and will form the basis for a series of papers aiming to answer open questions on how galaxies have formed and evolved, and the role of their individual structures. Here this paper presents an introduction to the project, including an overview of these fits, a characterization of the sample, and a series of tests on the fits to ensure reliability.

79 ASTRONOMY AND ASTROPHYSICS↗

Statistical inference of collision frequencies from x-ray Thomson scattering spectra

Thomson scattering spectra measure the response of plasma particles to incident radiation. In warm dense matter, which is opaque to visible light, x-ray Thomson scattering (XRTS) enables a detailed probe of the electron distribution and has been used as a diagnostic for electron temperature, density, and plasma ionization. In this work, we examine the sensitivities of inelastic XRTS signatures to modeling details, including the dynamic collision frequency and the electronic density of states. Applying verified Monte Carlo inversion methods to dynamic structure factors obtained from time-dependent density functional theory, we assess the utility of XRTS signals as a way to inform the dynamic collision frequency, especially its direct-current limit, which is directly related to the electrical conductivity.

Collision frequency↗

Learning likelihood ratios with neural network classifiers

The likelihood ratio is a crucial quantity for statistical inference in science that enables hypothesis testing, construction of confidence intervals, reweighting of distributions, and more. Many modern scientific applications, however, make use of data- or simulation-driven models for which computing the likelihood ratio can be very difficult or even impossible. By applying the so-called “likelihood ratio trick,” approximations of the likelihood ratio may be computed using clever parametrizations of neural network-based classifiers. A number of different neural network setups can be defined to satisfy this procedure, each with varying performance in approximating the likelihood ratio when using finite training data. We present a series of empirical studies detailing the performance of several common loss functionals and parametrizations of the classifier output in approximating the likelihood ratio of two univariate and multivariate Gaussian distributions as well as simulated high-energy particle physics datasets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Effects of Different Types of Entrances on Natural Ventilation in a Subway Station

In this study, the natural ventilation of a horizontal entrance of a typical subway station is investigated based on numerical simulations and experiments. In addition, a renormalization group k-e model (RNG k-e model) is applied to compute both the internal and external airflow patterns. Computational fluid dynamics (CFD) simulations are validated based on the experimental results. Furthermore, a multiple variable regression model is employed to study how the different parameters affect the internal airflow rates of the subway station statistically, according to the experimental results. For this typical model, the parameter importance can be ranked as follows: (1) outdoor wind speed; (2) flow resistance of the subway station; (3) height of the wind catcher; and (4) length of the wind catcher. To understand the detailed pressure distribution of the horizontal entrance of the subway station with and without the wind catcher, 3D numerical simulations are conducted for different scenarios. We attempt to alter the size of the wind catcher (including the length and height) to study the characteristics of the pressure on the horizontal entrance of the subway station under outdoor wind-driven conditions. The pressure distributions for the entrance for different scenarios are compared and analyzed. Finally, the interactions between the internal and external flows are investigated by changing the resistance of the subway station. When the internal flow resistance is changed, the pressure coefficient (Cp) of the entrance is different as well. Hence, the Cp is not only affected by the outdoor environment, but is also influenced by the internal airflows.

CFD↗

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model

Abstract Motivation The classic multispecies coalescent (MSC) model provides the means for theoretical justification of incomplete lineage sorting-aware species tree inference methods. This has motivated an extensive body of work on phylogenetic methods that are statistically consistent under MSC. One such particularly popular method is ASTRAL, a quartet-based species tree inference method. Novel studies suggest that ASTRAL also performs well when given multi-locus gene trees in simulation studies. Further, Legried et al. recently demonstrated that ASTRAL is statistically consistent under the gene duplication and loss model (GDL). GDL is prevalent in evolutionary histories and is the first core process in the powerful duplication-loss-coalescence evolutionary model (DLCoal) by Rasmussen and Kellis. Results In this work, we prove that ASTRAL is statistically consistent under the general DLCoal model. Therefore, our result supports the empirical evidence from the simulation-based studies. More broadly, we prove that the quartet-based inference approach is statistically consistent under DLCoal. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Cosmology from weak lensing peaks and minima with Subaru Hyper Suprime-Cam Survey first-year data

We present cosmological constraints derived from peak counts, minimum counts, and the angular power spectrum of the Subaru Hyper Suprime-Cam first-year (HSC Y1) weak lensing shear catalogue. Weak lensing peak and minimum counts contain non-Gaussian information and hence are complementary to the conventional two-point statistics in constraining cosmology. In this work, we forward-model the three summary statistics and their dependence on cosmology, using a suite of N-body simulations tailored to the HSC Y1 data. We investigate systematic and astrophysical effects including intrinsic alignments, baryon feedback, multiplicative bias, and photometric redshift uncertainties. We mitigate the impact of these systematics by applying cuts on angular scales, smoothing scales, signal-to-noise ratio bins, and tomographic redshift bins. By combining peaks, minima, and the power spectrum, assuming a flat-ΛCDM model, we obtain S 8 ≡ σ 8 $\sqrt{Ω_m/0.3}$ = 0.810$^{+0.022}_{-0.026}$⁠, a 35 per cent tighter constraint than that obtained from the angular power spectrum alone. Our results are in agreement with other studies using HSC weak lensing shear data, as well as with Planck 2018 cosmology and recent CMB lensing constraints from the Atacama Cosmology Telescope and the South Pole Telescope.

79 ASTRONOMY AND ASTROPHYSICS↗

Experimental Realization of the 1D Random Field Ising Model

Here we have measured magnetic-field-induced avalanches in a square artificial spin ice array of interacting nanomagnets. Starting from the ground state ordered configuration, we imaged the individual nanomagnet moments after each successive application of an incrementally increasing field. The statistics of the evolution of the moment configuration show good agreement with the canonical one-dimensional random field Ising model. We extract information about the microscopic structure of the arrays from our macroscopic measurements of their collective behavior, demonstrating a process that could be applied to other systems exhibiting avalanches.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Dealing with Measurement Uncertainties as Nuisance Parameters in Bayesian Model Calibration

In the presence of model discrepancy, the calibration of physics-based models for physical parameter inference is a challenging problem. Lack of identifiability between calibration parameters and model discrepancy requires additional identifiability constraints to be placed on the model discrepancy to obtain unique physical parameter estimates. If these assumptions are violated, the inference for the calibration parameters can be systematically biased. In many applications, such as in dynamic material property experiments, many of the calibration inputs refer to measurement uncertainties. Here, we develop a metric for identifying overfitting of these measurement uncertainties, propose a prior capable of reducing this overfitting, and show how this leads to a diagnostic tool for validation of physical parameter inference. The approach is demonstrated for a benchmark example and applied for a material property application to perform inference on the equation of state parameters of tantalum.

97 MATHEMATICS AND COMPUTING↗

An Advanced Microscopic Energy Consumption Model for Automated Vehicle:Development, Calibration, Verification

The automated vehicle (AV) equipped with the Adaptive Cruise Control (ACC) system is expected to reduce the fuel consumption for the intelligent transportation system. This paper presents the Advanced ACC-Micro (AA-Micro) model, a new energy consumption model based on micro trajectory data, calibrated and verified by empirical data. Utilizing a commercial AV equipped with the ACC system as the test platform, experiments were conducted at the Columbus 151 Speedway, capturing data from multiple ACC and Human-Driven (HV) test runs. The calibrated AA-Micro model integrates features from traditional energy consumption models and demonstrates superior goodness of fit, achieving an impressive 90% accuracy in predicting ACC system energy consumption without overfitting. A comprehensive statistical evaluation of the AA-Micro model's applicability and adaptability in predicting energy consumption and vehicle trajectories indicated strong model consistency and reliability for ACC vehicles, evidenced by minimal variance in RMSE values and uniform RSS distributions. Conversely, significant discrepancies were observed when applying the model to HV data, underscoring the necessity for specialized models to accurately predict energy consumption for HV and ACC systems, potentially due to their distinct energy consumption characteristics.

Ma, Ke↗

An Improved Method for Coupling Hydrodynamics with Astrophysical Reaction Networks

Reacting astrophysical flows can be challenging to model, because of the difficulty in accurately coupling hydrodynamics and reactions. This can be particularly acute during explosive burning or at high temperatures where nuclear statistical equilibrium is established. We develop a new approach, based on the ideas of spectral deferred corrections (SDC) coupling of explicit hydrodynamics and stiff reaction sources as an alternative to operator splitting, that is simpler than the more comprehensive SDC approach we demonstrated previously. We apply the new method to a double-detonation problem with a moderately sized astrophysical nuclear reaction network and explore the time step size and reaction network tolerances, to show that the simplified-SDC approach provides improved coupling with decreased computational expense compared to traditional Strang operator splitting. This is all done in the framework of the Castro hydrodynamics code, and all algorithm implementations are freely available.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

QED radiative corrections to neutrino-nucleon elastic scattering

Neutrino oscillation experiments at accelerator energies aim to establish CP violation in the neutrino sector by measuring the energy-dependent rate of $\nu_e$ appearance and $\nu_\mu$ disappearance in a $\nu_\mu$ beam. Extracting the correct oscillation rate demands control over QED radiative corrections at the percent level. Focusing on the critical charged-current neutrino-nucleon scattering process, we show that the cross section factorizes into two pieces. The first piece depends on hadron structure but is universal for $\nu_e$ and $\nu_\mu$, and hence constrained by high-statistics $\nu_\mu$ data. The second piece is nonuniversal and suffers large logarithm enhancements, but is computed to high precision using renormalization group improved perturbation theory. Our results provide a missing ingredient for the robust interpretation of current NOvA and T2K experiments, and can be applied to future experiments such as DUNE and HyperK.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Improving seasonal precipitation forecasts in the Western United States through statistical downscaling

Abstract Seasonal precipitation forecasts in the western United States are critical resources for water resource management, especially during winter. While current seasonal forecasting systems provide monthly precipitation forecasts operationally, their coarse resolution limits their effectiveness in capturing the localized precipitation patterns and snowpack conditions essential for water resource managers in the mountainous regions. Here, analog statistical downscaling is demonstrated as an effective approach to enhance the spatial resolution of operational seasonal forecasts provided by the North American Multi-Model Ensemble. Downscaling was performed by building an analog ‘library’, in which corresponding model forecasts and observed values during the training period were stored. In the testing period, unseen model forecasts referenced the closest historical forecast from the analog library and applied the corresponding observational value for each point. This analysis indicates that downscaled products can capture localized features more accurately than the original coarse resolution forecasts, reducing forecast error across the western United States. Moreover, downscaling individual ensemble members—rather than downscaling the ensemble mean—further reduces forecasting error for their multi-model ensemble mean products. The greatest error reductions in the downscaled product, measured by root mean squared error (RMSE), were observed at low to mid-elevations (500–2000 meters), with 50%–70% improvement relative to the original forecasts. In the higher elevations (2000 meters and above), changes in RMSE relative to the original forecast were limited to 10%–30% improvements. The improvement is more substantial for forecast systems with 10 ensemble members compared to that with 4 members, but this relationship does not hold for the system with 24 ensemble members. These findings show that analog statistical downscaling can effectively address the spatial limitations of seasonal precipitation forecasts with minimal computational cost, providing a valuable framework for enhancing coarse resolution forecasting products while providing insights into the timing of ensemble mean calculations during the downscaling process.

Vernon, B. (ORCID:0009000891670689)↗

Efficient computation of N -point correlation functions in D dimensions

We present efficient algorithms for computing the N-point correlation functions (NPCFs) of random fields in arbitrary D-dimensional homogeneous and isotropic spaces. Such statistics appear throughout the physical sciences and provide a natural tool to describe stochastic processes. Typically, algorithms for computing the NPCF components have $\mathscr O$(n N ) complexity (for a dataset containing n particles); their application is thus computationally infeasible unless N is small. By projecting the statistic onto a suitably defined angular basis, we show that the estimators can be written in a separable form, with complexity $\mathscr O$(n 2 ) or $\mathscr O$(n g log n g ) if evaluated using a Fast Fourier Transform on a grid of size n g . Our decomposition is built upon the D-dimensional hyperspherical harmonics; these form a complete basis on the (D – 1) sphere and are intrinsically related to angular momentum operators. Concatenation of (N – 1) such harmonics gives states of definite combined angular momentum, forming a natural separable basis for the NPCF. As N and D grow, the number of basis components quickly becomes large, providing a practical limitation to this (and all other) approaches: However, the dimensionality is greatly reduced in the presence of symmetries; for example, isotropic correlation functions require only states of zero combined angular momentum. We provide a Julia package implementing our estimators and show how they can be applied to a variety of scenarios within cosmology and fluid dynamics. The efficiency of such estimators will allow higher-order correlators to become a standard tool in the analysis of random fields.

97 MATHEMATICS AND COMPUTING↗

Selective Antisite Defect Formation in WS 2 Monolayers via Reactive Growth on Dilute W-Au Alloy Substrates

Defects are ubiquitous in 2D materials and can affect the structure and properties of the materials and also introduce new functionalities. Methods to adjust the structure and density of defects during bottom-up synthesis are required to control the growth of 2D materials with tailored optical and electronic properties. In this study, the authors present an Au-assisted chemical vapor deposition approach to selectively form S W and S2 W antisite defects, whereby one or two sulfur atoms substitute for a tungsten atom in WS 2 monolayers. Guided by first-principles calculations, they describe a new method that can maintain tungsten-poor growth conditions relative to sulfur via the low solubility of W atoms in a gold/W alloy, thereby significantly reducing the formation energy of the antisite defects during the growth of WS 2 . The atomic structure and composition of the antisite defects are unambiguously identified by Z-contrast scanning transmission electron microscopy and electron energy-loss spectroscopy, and their total concentration is statistically determined, with levels up to ≈5.0%. Furthermore, scanning tunneling microscopy/spectroscopy measurements and first-principles calculations also verified these antisite defects and revealed the localized defect states in the bandgap of WS 2 monolayers. This bottom-up synthesis method to form antisite defects should apply in the synthesis of other 2D materials.

2D materials↗

Evaluation of Amorphous Oxide Coatings for High-Voltage Li-Ion Battery Applications Using a First-Principles Framework

Cathode surface coatings are widely used industrially as a means to suppress degradation and improve electrochemical performance of lithium-ion batteries. However, developing an optimal coating is challenging, as different coating materials may enhance one aspect of performance while hindering another. Furthermore, to elucidate the fundamental thermodynamic and transport properties of amorphous cathode coating materials, here, we present a framework for calculating and analyzing the Li + and O 2- transport and the stability against delithiation in such materials. Our framework includes systematic workflows of ab-initio molecular dynamics calculations to obtain amorphous structures and diffusion trajectories coupled with an analysis of critical changes of the active-ion local environment during diffusion. Based on these data, we provide an estimate of room-temperature diffusivities, including statistical error bars, and the evaluation of the coating suitability in terms of its ability to facilitate Li + transport while blocking O 2- transport. Finally, we add the thermodynamic stability analysis of the coating chemistry within the operating voltage of common Li-ion cathodes. We apply this framework to two commonly used amorphous coating materials, Al 2 O 3 and ZnO. We find that (1) in general, a higher Li + content increases both Li + and O 2- diffusivities in both Al 2 O 3 and ZnO. Also, Li + and O 2- diffuse much faster in ZnO than in Al 2 O 3 . (2) However, neither Al 2 O 3 nor ZnO is expected to retain a significant concentration of Li + at high charge. (3) ZnO performs much more poorly in terms of O 2- blocking, and hence, Al 2 O 3 is preferred for high-voltage cathode applications. These results will help to quantitatively evaluate amorphous materials, such as metal oxides and fluorides, for different performance metrics and facilitate the development of optimal cathode coatings.

25 ENERGY STORAGE↗