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At least 469 records · Page 26

F γ : A new observable for photon-hadron discrimination in hybrid air shower events

To search for ultra-high-energy photons in primary cosmic rays, air shower observables are needed that allow a good separation between primary photons and primary hadrons. In this paper, we present a new observable, F γ , which can be extracted from ground-array data in hybrid events, where simultaneous measurements of the longitudinal and the lateral shower profile are performed. The observable is based on a template fit to the lateral distribution measured by the ground array with the template taking into account the complementary information from the measurement of the longitudinal profile, i.e. the primary energy and the geometry of the shower. F γ shows a very good photon-hadron separation, which is even superior to the separation given by the well-known X max observable (the atmospheric depth of the shower maximum). At energies around 1 EeV (10 EeV), F γ provides a background rejection better than 97.8 % (99.9 %) at a signal efficiency of 50 %. Advantages of the observable F γ are its technical stability with respect to irregularities in the ground array (i.e. missing or temporarily non-operating stations) and that it can be applied over the full energy range accessible to the air shower detector, down to its threshold energy. Finally and furthermore, F γ complements nicely to X max such that both observables can well be combined to achieve an even better discrimination power, exploiting the rich information available in hybrid events.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A phylogenetically novel cyanobacterium most closely related to Gloeobacter

Clues to the evolutionary steps producing innovations in oxygenic photosynthesis may be preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Vampirovibrionia (formerly Melainabacteria) and the thylakoid-containing Cyanobacteria. However, only two species with published genomes are known to occupy this phylogenetic space, both within the genus Gloeobacter. Here, we describe nearly complete, metagenome-assembled genomes (MAGs) of an uncultured organism phylogenetically placed near Gloeobacter, for which we propose the name Candidatus Aurora vandensis {Au’ro.ra. L. fem. n. aurora, the goddess of the dawn in Roman mythology; van.de’nsis. N.L. fem. adj. vandensis of Lake Vanda, Antarctica}. The MAG of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many accessory subunits associated with the photosystems in other species either are missing from the MAG or are poorly conserved. The MAG also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Additional characterization of this organism is expected to inform models of the evolution of oxygenic photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗

A model for the fragmentation kinetics of crumpled thin sheets

As a confined thin sheet crumples, it spontaneously segments into flat facets delimited by a network of ridges. Despite the apparent disorder of this process, statistical properties of crumpled sheets exhibit striking reproducibility. Experiments have shown that the total crease length accrues logarithmically when repeatedly compacting and unfolding a sheet of paper. Here, we offer insight to this unexpected result by exploring the correspondence between crumpling and fragmentation processes. We identify a physical model for the evolution of facet area and ridge length distributions of crumpled sheets, and propose a mechanism for re-fragmentation driven by geometric frustration. This mechanism establishes a feedback loop in which the facet size distribution informs the subsequent rate of fragmentation under repeated confinement, thereby producing a new size distribution. We then demonstrate the capacity of this model to reproduce the characteristic logarithmic scaling of total crease length, thereby supplying a missing physical basis for the observed phenomenon.

42 ENGINEERING↗

Hamiltonian parameter inference from resonant inelastic x-ray scattering with active learning

Identifying model Hamiltonians is a vital step toward creating predictive models of materials. Here, in this study, we combine Bayesian optimization with the EDRIXS numerical package to infer Hamiltonian parameters from resonant inelastic x-ray scattering (RIXS) spectra within the single atom approximation. To evaluate the efficacy of our method, we test it on experimental RIXS spectra of NiPS 3 , NiCl 2 , Ca 3 ⁢LiOsO 6 , and Fe 2⁢ O 3 , and demonstrate that it can reproduce results obtained from hand-fitted parameters to a precision similar to expert human analysis while providing a more systematic mapping of parameter space. Our work provides a key first step toward solving the inverse scattering problem to extract effective multi-orbital models from information-dense RIXS measurements, which can be applied to a host of quantum materials. We also propose atomic model parameter sets for two materials, Ca 3⁢ LiOsO 6 and Fe 2⁢ O 3 , that were previously missing from the literature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Topological cell clustering in the ATLAS calorimeters and its performance in LHC Run 1

The reconstruction of the signal from hadrons and jets emerging from the proton–proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting topological cell clusters have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Lastly, topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS.

43 PARTICLE ACCELERATORS↗

Expectation-maximization algorithms for learning a finite mixture of univariate survival time distributions from partially specified class values

Heterogeneity exists on a data set when samples from di erent classes are merged into the data set. Finite mixture models can be used to represent a survival time distribution on heterogeneous patient group by the proportions of each class and by the survival time distribution within each class as well. The heterogeneous data set cannot be explicitly decomposed to homogeneous subgroups unless all the samples are precisely labeled by their origin classes; such impossibility of decomposition is a barrier to overcome for estimating nite mixture models. The expectation-maximization (EM) algorithm has been used to obtain maximum likelihood estimates of nite mixture models by soft-decomposition of heterogeneous samples without labels for a subset or the entire set of data. In medical surveillance databases we can find partially labeled data, that is, while not completely unlabeled there is only imprecise information about class values. In this study we propose new EM algorithms that take advantages of using such partial labels, and thus incorporate more information than traditional EM algorithms. We particularly propose four variants of the EM algorithm named EM-OCML, EM-PCML, EM-HCML and EM-CPCML, each of which assumes a specific mechanism of missing class values. We conducted a simulation study on exponential survival trees with five classes and showed that the advantages of incorporating substantial amount of partially labeled data can be highly signi cant. We also showed model selection based on AIC values fairly works to select the best proposed algorithm on each specific data set. A case study on a real-world data set of gastric cancer provided by Surveillance, Epidemiology and End Results (SEER) program showed a superiority of EM-CPCML to not only the other proposed EM algorithms but also conventional supervised, unsupervised and semi-supervised learning algorithms.

97 MATHEMATICS AND COMPUTING↗

EMC Test Report Electrodynamic Dust Shield

This report documents the Electromagnetic Interference E M I evaluation performed on the Electrodynamic Dust Shield (EDS) which is part of the MISSE-X System under the Electrostatics and Surface Physics Laboratory at Kennedy Space Center. Measurements are performed to document the emissions environment associated with the EDS units. The purpose of this report is to collect all information needed to reproduce the testing performed on the Electrodynamic Dust Shield units, document data gathered during testing, and present the results. This document presents information unique to the measurements performed on the Bioculture Express Rack payload; using test methods prepared to meet SSP 30238 requirements. It includes the information necessary to satisfy the needs of the customer per work order number 1037104. The information presented herein should only be used to meet the requirements for which it was prepared.

Electrostatics↗

Improving vertical detail in simulated temperature and humidity data using machine learning

Atmospheric models used for weather forecasting and climate predictions discretise the atmosphere onto a vertical grid. There are however atmospheric phenomena that occur on scales smaller than the thickness of those model layers. The formation of low-level clouds due to temperature inversions is an example. This leads to atmospheric models underestimating, or even missing, these clouds and their radiative effects. Using radiosonde observations as training data, a machine learning model is used to improve the vertical detail of modelled profiles of temperature and specific humidity. In addition, a physics-informed machine learning model is developed and compared to the traditional approach; showing improvements in the cloud fraction profiles calculated from its predictions. The vertically enhanced profiles also improve the representation of layers of convective inhibition and anomalous refractivity gradients. This work facilitates targeted improvements to the representation of certain atmospheric processes without the burden of increased memory and computational cost from increasing vertical resolution throughout the whole model.

54 ENVIRONMENTAL SCIENCES↗

Corn Storage Protein - A Molecular Genetic Model

Corn is the highest yielding crop on earth and probably the most valuable agricultural product of the United States. Because it converts sun energy through photosynthesis into starch and proteins, we addressed energy savings by focusing on protein quality. People and animals require essential amino acids derived from the digestion of proteins. If proteins are relatively low in certain essential amino acids, the crop becomes nutritionally defective and has to be supplemented. Such deficiency affects meat and fish production and countries where corn is a staple. Because corn seed proteins have relatively low levels of lysine and methionine, a diet has to be supplemented with soybeans for the missing lysine and with chemically synthesized methionine. We therefore have studied genes expressed during maize seed development and their chromosomal organization. A critical technical requirement for the understanding of the molecular structure of genes and their positional information was DNA sequencing. Because of the length of sequences, DNA sequencing methods themselves were insufficient for this type of analysis. We therefore developed the so-called “DNA shotgun sequencing” strategy, where overlapping DNA fragments were sequenced in parallel and used to reconstruct large DNA molecules via overlaps. Our publications became the most frequently cited ones during the decade of 1981-1990 and former Associate Director of Science for the Office of Basic Energy Sciences Patricia M. Dehmer presented our work as one of the great successes of this program. A major component of the sequencing strategy was the development of bacterial strains and vectors, which were also used to develop the first biotechnology crops. These crops possessed new traits thanks to the expression of foreign genes in plants. To enable such expression, chimeric genes had to be constructed using our materials and methods by the industry. Because we made our materials and methods freely available to academia and industry, progress in plant research and new crop development could accelerate and benefit the public.

60 APPLIED LIFE SCIENCES↗

Final Report Scalable Analysis Methods and In Situ Infrastructure for Extreme Scale Knowledge Discovery

The primary challenge motivating this project is the widening gap between the ability to compute information and to store it for subsequent analysis. This gap adversely impacts science code teams, who can perform analysis only on a small fraction of the data they calculate, resulting in the substantial likelihood of lost or missed science, when results are computed but not analyzed. Our approach is to perform as much analysis or visualization processing on data while it is still resident in memory, which is known as in situ processing. The idea in situ processing was not new at the time of the start of this effort in 2014, but efforts in that space were largely ad hoc, and there was no concerted effort within the research community that aimed to foster production-quality software tools suitable for use by Department of Energy (DOE) science projects. Our objective was to produce and enable the use of production-quality in situ methods and infrastructure, at scale, on DOE high-performance computing (HPC) facilities, though we expected to have an impact beyond DOE due to the widespread nature of the challenges, which affect virtually all large-scale computational science efforts. To achieve this objective, we engaged in software technology research and development (R&D), in close partnerships with DOE science code teams, to produce software technologies that were shown to run efficiently at scale on DOE HPC platforms.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Exclusive Backward-Angle Omega Meson Electroproduction

Exclusive meson electroproduction at different squared four-momenta of the exchanged virtual photon, Q 2 , and at different four-momentum transfers, t and u, can be used to probe QCD's transition from hadronic degrees of freedom at the long distance scale to quark-gluon degrees of freedom at the short distance scale. Backward-angle meson electroproduction was previously ignored, but is anticipated to offer complimentary information to conventional forward-angle meson electroproduction studies on nucleon structure. This work is a pioneering study of backward-angle ω cross sections through the exclusive 1 H(e, e'p)ω reaction using the missing mass reconstruction technique. The extracted cross sections are separated into the transverse (T), longitudinal (L), and LT, TT interference terms. The analyzed data were part of experiment E01-004 (Fπ-2), which used 2.6-5.2 GeV electron beams and HMS+SOS spectrometers in Jefferson Lab Hall C. The primary objective was to detect coincidence π in the forward-angle, where the backward-angle omega events were fortuitously detected. The experiment has central Q 2 values of 1.60 and 2.45 GeV 2 , at W = 2.21 GeV. There was significant coverage in phi and epsilon, which allowed separation of σ T,L,LT,TT . The data set has a unique u coverage of -u ~ 0, which corresponds to -t > 4 GeV 2 . The separated σ T result suggest a flat ~ 1/Q 1.33±1.21 dependence, whereas sigma_L seems to hold a stronger 1/Q 9.43±6.28 dependence. The σL/σ T ratio indicate σ T dominance at Q 2 = 2.45 GeV 2 at the ~90% confidence level. After translating the results into the -t space of the published CLAS data, our data show evidence of a backward-angle omega electroproduction peak at both Q 2 settings. Previously, this phenomenon showing both forward and backward-angle peaks was only observed in the meson photoproduction data. Through comparison of our σ T data with the prediction of the Transition Distribution Amplitude (TDA) model, and signs of σ T dominance, promising indications of the applicability of the TDA factorization are demonstrated at a much lower Q 2 value than its preferred range of Q 2 > 10 GeV 2 . These studies have opened a new means to study the transition of the nucleon wavefunction through backward-angle experimental observables.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Hypothetical Scenario Generator for Fault-Tolerant Diagnosis

The Hypothetical Scenario Generator for Fault-tolerant Diagnostics (HSG) is an algorithm being developed in conjunction with other components of artificial- intelligence systems for automated diagnosis and prognosis of faults in spacecraft, aircraft, and other complex engineering systems. By incorporating prognostic capabilities along with advanced diagnostic capabilities, these developments hold promise to increase the safety and affordability of the affected engineering systems by making it possible to obtain timely and accurate information on the statuses of the systems and predicting impending failures well in advance. The HSG is a specific instance of a hypothetical- scenario generator that implements an innovative approach for performing diagnostic reasoning when data are missing. The special purpose served by the HSG is to (1) look for all possible ways in which the present state of the engineering system can be mapped with respect to a given model and (2) generate a prioritized set of future possible states and the scenarios of which they are parts.

James, Mark↗

Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.

59 BASIC BIOLOGICAL SCIENCES↗

Videos, photos, and AI-derived grain size data associated with “High-throughput AI Video Surveys Enable Reproducible Multiscale Sediment Size Mapping, with Implications for Hydrobiogeochemical Parameterization”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the manuscript “High-throughput AI Video Surveys Enable Reproducible Multiscale Sediment Size Mapping, with Implications for Hydrobiogeochemical Parameterization” under review. This data package includes five data types: 1) raw photos and videos from drone survey and walking smartphone surveys; 2) images derived from raw videos; 3) manual labeling of reference scales; 4) metadata for all images and photo resolution derived from artificial intelligence (AI) models or manual labels, 5) grain size data obtained from AI models for all photos, 6) metadata and grain size data after quality control, 7) summaries of sample efficiency for all data, and 8) computational fluid dynamics (CFD) data used to support hydro-biogeochemical (HBGC) parameter estimation. Such data is used to 1) demonstrate significant improvements in accuracy, efficiency, and quality control for grain size data collection with the help of AI models, 2) study the spatial heterogeneity of grain size and observation reproducibility based on tens of thousands of data points generated by the AI models, and 3) evaluate the impacts of grain size heterogeneity on key HBGC parameters across sediment-to-reach and hourly-to-yearly scales. In particular, the data package contains 116 folders and 179696 files. The files include 41 videos in .mov format, 64047 photos in .jpg format, 13541 video-derived photos in .png format, 12747 segmentation mask data in .tif format, 12747 segmentation data in .json format, 24771 .csv files that with metadata and grain size for each individual photo as well as water depth and velocity data from CFD and observation, 51791 .txt files of raw AI predicted labels, and 11 flight record data in .srt format. The summary for all metadata and grain size statistics information is included in “Scales_V3_NG.csv” and “Statistics_V3_NG.csv”. The summary for data that pass data quality control (QC) level 0-2 is included in “QCStatistics_V3_NG.csv”. The QC level 0 represents photos whose photo resolution is positive, excluding photos that miss reference scale. The QC level 1 means reference scale circularity uncertainty is less than 5% for smartphone images while representing photo resolution is larger than 0.44 mm/pixel for drone images. The QC level 2 means excluding photos whose grain number is less than 100, a minimum number of grains recommended by classic literature. The summary for each video’s name, length, frame rates, survey area, grain number, survey efficiency, etc. can be found in “QCSummary_V3_NG.csv”. The summary for site name, GPS coordinates, and number of images at each site can be found in “SitesSummary_V3_*.csv” files. Overall computational efficiency summary is reported in Table 4 of accompanying manuscript. Additionally, the nitrate concentration data used in this work was downloaded from an existing dataset published on ESS-DIVE (Boat-Dragged Sensor Hanford Reach.csv; Conner A. et al., 2020). We thank the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, Cowiche Canyon Conservatory, Port of Benton, and the Confederated Tribes and Bands of the Yakama Nation for access to field locations where the data were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate data collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

Evaluation of Transport-Equations-Based Transition Models for High-Speed Boundary Layers Using OVERFLOW

Accurate modeling of laminar-turbulent transition is crucial for the design of hypersonic flight systems. However, the current transition models used in production CFD codes are insufficient for high-speed flows. Many extensions to low-speed models have been suggested; however, a thorough verification and validation effort is needed before these models can be used in design settings. Challenges include potentially missing details of the model implementation requirements and/or a complete specification of the input parameters needed to replicate the test findings. A meaningful assessment of the generalization capability of these models is also hindered by a lack of information regarding the specific flow configurations and associated grids employed for model calibration. As a key first step toward model verification, we present an independent assessment of two recently proposed models for high-speed transition, namely, a model within the SST-𝛾 framework and a model based on the SST-𝛾 – 𝜈 𝐿 equations. These models are implemented in the NASA OVERFLOW 2.3e solver and their performance in predicting first mode, second mode, and crossflow transition has been evaluated for several test cases in the supersonic and hypersonic regimes. Besides the test cases employed by the model developers, which could have also been used for model calibration, the present assessment includes supplementary configurations that contribute to an unbiased assessment of the models. The outcomes presented in this study indicate the potential for the models to be applied to high-speed flight configurations. Key steps toward future improvements to these models are also outlined.

CFD↗

Evaluation of Transport-Equation-Based Transition Models for High-Speed Boundary Layers Using OVERFLOW

Accurate modeling of laminar-turbulent transition is crucial for the design of hypersonic flight systems. However, the current transition models used in production CFD codes are insufficient for high-speed flows. Many extensions to low-speed models have been suggested; however, a thorough verification and validation effort is needed before these models can be used in design settings. Challenges include potentially missing details of the model implementation requirements and/or a complete specification of the input parameters needed to replicate the test findings. A meaningful assessment of the generalization capability of these models is also hindered by a lack of information regarding the specific flow configurations and associated grids employed for model calibration. As a key first step toward model verification, we present an independent assessment of two recently proposed models for high-speed transition, namely, a model within the SST-$\gamma$ framework and a model based on the SST-$\gamma-\nu_L$ equations. These models are implemented in the NASA OVERFLOW 2.3e solver and their performance in predicting first mode, second mode, and crossflow transition has been evaluated for several test cases in the supersonic and hypersonic regimes. Besides the test cases employed by the model developers, which could have also been used for model calibration, the present assessment includes supplementary configurations that contribute to an unbiased assessment of the models. The outcomes presented in this study indicate the potential for the models to be applied to high-speed flight configurations. Key steps toward future improvements to these models are also outlined.

High-speed flow↗

The Next Generation Marshall Grazing Incidence X-Ray Spectrometer (MaGIXS) Sounding Rocket Experiments

The Marshall Grazing Incidence X-ray Spectrometer (MaGIXS) is a sounding rocket experiment that carries an X-ray slitless imaging spectrograph to observe spectrally dispersed soft X-ray (SXR) images of the solar corona over a wide field-of-view. The first flight of MaGIXS occurred on 30 July 2021, during which several emission lines from coronal structures including X-ray bright points were observed. Analysis of MaGIXS-1 data demonstrated the application of new inversion techniques and opened a new arena of inverting complex spectroheliogram data, which has spatial-spectral information overlapped. The second flight of MaGIXS, with a simplified optical design, is scheduled for 2024. The goal of MaGIXS-2 is to observe high temperature diagnostic emission lines within an active region core. MaGIXS-1 discovered dominant missing emission lines near 15Å wavelength region, which hosts several closely spaced satellite lines of Fe XVII, Fe XVI, and Fe XV ions, arising from relatively cool plasma that peaks near 2MK. These lines are expected to be enhanced at lower temperatures and offers one of the most unique diagnostics to measure electron temperature, as well as signatures of equilibrium state of the plasma in active regions, which has not been studied so far. The science goal of the third sounding rocket flight of MaGIXS is to determine coronal heating parameters, such as the spatial and temporal properties of coronal heating events, by measuring discriminating observations, such as electron temperature, effective temperature, density, abundance, and departures from thermal equilibrium of the plasma, by observing the Sun in the SXR wavelength range. For this, the MaGIXS instrument will be upgraded with a new X-ray telescope mirror that will provide higher spatial and spectral resolution and throughput, allowing for spectral lines to be observed at the relevant spatial and temporal scales. In addition, MaGIXS-3 will also carry The Resolving Inversion Context X-ray Spectrometer (TRICXS), a high dispersion Bragg crystal spectrometer to spectrally resolve the lines near 15Å, critical to unlock the full diagnostic potential of this wavelength range. Here we will present the preliminary concept design of MaGIXS-3 and discuss the potential observations.

X-ray Imaging↗

Electronic landscape of the f -electron intermetallics with the ThCr 2 Si 2 structure

Although strongly correlated f -electron systems are well known as reservoirs for quantum phenomena, a persistent challenge is to design specific states. What is often missing are simple ways to determine whether a given compound can be expected to exhibit certain behaviors and what tuning vector(s) would be useful to select the ground state. In this review, we address this question by aggregating information about Ce, Eu, Yb, and U compounds with the ThCr 2 Si 2 structure. We construct electronic/magnetic state maps that are parameterized in terms of unit cell volumes and d -shell filling, which reveals useful trends including that (i) the magnetic and nonmagnetic examples are well separated, and (ii) the crossover regions harbor the examples with exotic states. These insights are used to propose structural/chemical regions of interest in these and related materials, with the goal of accelerating discovery of the next generation of f -electron quantum materials.

42 ENGINEERING↗