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At least 415 records · Page 23

WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

59 BASIC BIOLOGICAL SCIENCES↗

Dark energy survey year 1 results: Constraining baryonic physics in the Universe

ABSTRACT Measurements of large-scale structure are interpreted using theoretical predictions for the matter distribution, including potential impacts of baryonic physics. We constrain the feedback strength of baryons jointly with cosmology using weak lensing and galaxy clustering observables (3 × 2pt) of Dark Energy Survey (DES) Year 1 data in combination with external information from baryon acoustic oscillations (BAO) and Planck cosmic microwave background polarization. Our baryon modelling is informed by a set of hydrodynamical simulations that span a variety of baryon scenarios; we span this space via a Principal Component (PC) analysis of the summary statistics extracted from these simulations. We show that at the level of DES Y1 constraining power, one PC is sufficient to describe the variation of baryonic effects in the observables, and the first PC amplitude (Q1) generally reflects the strength of baryon feedback. With the upper limit of Q1 prior being bound by the Illustris feedback scenarios, we reach $\sim 20{{\ \rm per\ cent}}$ improvement in the constraint of $S_8=\sigma _8(\Omega _{\rm m}/0.3)^{0.5}=0.788^{+0.018}_{-0.021}$ compared to the original DES 3 × 2pt analysis. This gain is driven by the inclusion of small-scale cosmic shear information down to 2.5 arcmin, which was excluded in previous DES analyses that did not model baryonic physics. We obtain $S_8=0.781^{+0.014}_{-0.015}$ for the combined DES Y1+Planck EE+BAO analysis with a non-informative Q1 prior. In terms of the baryon constraints, we measure $Q_1=1.14^{+2.20}_{-2.80}$ for DES Y1 only and $Q_1=1.42^{+1.63}_{-1.48}$ for DESY1+Planck EE+BAO, allowing us to exclude one of the most extreme AGN feedback hydrodynamical scenario at more than 2σ.

79 ASTRONOMY AND ASTROPHYSICS↗

Enhancing strontium clock atom interferometry using quantum optimal control

Strontium clock atom interferometry is a promising new technology, with multiple experiments under development around the world to explore its potential for dark matter and gravitational wave detection. In these detectors, large momentum transfer using sequences of many laser pulses is necessary, and thus high-fidelity pulses are important since small errors become magnified. Quantum optimal control (QOC) is a framework for developing control pulse waveforms that achieve high fidelity and are robust against experimental imperfections. Resonant single-photon transitions using the narrow clock transition of strontium involve significantly different quantum dynamics than more established atom interferometry methods based on far-detuned two-photon Raman or Bragg transitions, which leads to new opportunities and challenges when applying QOC. Here, we study in simulation QOC pulses for strontium clock interferometry and demonstrate their advantage over basic square pulses (primitive pulses) and composite pulses in terms of robustness against multiple noise channels. In conclusion, this could improve the scale of large momentum transfer in Sr clock interferometers, paving the way to achieving these scientific goals.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

System Validation Platform Working Directories

A suite of software tools used to interface with power electronic equipment for laboratory testing and device certification. They are typically used as equipment drivers with using the System Validation Platform (SVP) graphical user interface (GUI). Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-1185 O

Johnson, JayT↗

Global Climate

The 2019 global lower tropospheric temperature (LTT), which encompasses the atmosphere from the surface to ~10 km, ranked second warmest in seven datasets and first or third in the remaining two (Fig. 2.7). These records extend back to 1958 using radiosonde (balloon-borne instrumentation) data and one reanalysis dataset (JRA55), which demonstrate reasonable agreement with the 40+ year satellite record (since late 1978) and two other reanalysis datasets (since 1979 and 1980, ERA5 and MERRA2, respectively). Aweak El Niño contributed to increased global temperatures as 2019 values were +0.44° to +0.68°C higher than the 1981–2010 average (depending on the dataset), being just slightly cooler (~0.07°C on average) than the record warm year of 2016. At least fourof the five globally complete datasets (ERA5, MERRA2, JRA55, RSS, UAH) recorded each of the four months—June, September, November, and December—as experiencing their warmest monthly global LTT.

58 GEOSCIENCES↗

Scalability of high-performance PDE solvers

Performance tests and analyses are critical to effective high-performance computing software development and are central components in the design and implementation of computational algorithms for achieving faster simulations on existing and future computing architectures for large-scale application problems. In this article, we explore performance and space-time trade-offs for important compute-intensive kernels of large-scale numerical solvers for partial differential equations (PDEs) that govern a wide range of physical applications. We consider a sequence of PDE-motivated bake-off problems designed to establish best practices for efficient high-order simulations across a variety of codes and platforms. We measure peak performance (degrees of freedom per second) on a fixed number of nodes and identify effective code optimization strategies for each architecture. In addition to peak performance, we identify the minimum time to solution at 80% parallel efficiency. The performance analysis is based on spectral and p-type finite elements but is equally applicable to a broad spectrum of numerical PDE discretizations, including finite difference, finite volume, and h-type finite elements.

97 MATHEMATICS AND COMPUTING↗

Frontier Job-Centric Telemetry Dataset

Comprehensive analysis of high-performance computing (HPC) systems requires linking workload execution to system behavior. This kind of analysis is vital for diagnosing performance issues, managing capacity, detecting anomalous workloads, and understanding how applications interact with system hardware. This job-centric telemetry dataset unifies scheduler job records with node-level measurements, enabling direct association between workloads and their corresponding power, thermal, and performance characteristics. It contains sanitized, scheduler related metadata for 152,400 individual jobs that ran on the Frontier supercomputer and ended on selected days throughout 2024 and 2025, a subpopulation of ~6.8% of the total number of allocated jobs with non-zero run time on the system over that same period. Each is linked with files that contain telemetry time series records of the power utilization and temperature behavior of its allocated nodes and their processors during the run time of the job. Where available, a portion of the job files also contain network performance time series. Jobs are sampled from select days that reflect normal levels of user activity and possess job size distributions with large numbers of leadership class jobs (>20% of Frontier nodes). Jobs in this dataset attempt to best represent successful user workflows.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

High-resolution ptychographic imaging enabled by high-speed multi-pass scanning

As a coherent diffraction imaging technique, ptychography provides high-spatial resolution beyond Rayleigh’s criterion of the focusing optics, but it is also sensitively affected by the decoherence coming from the spatial and temporal variations in the experiment. Here we show that high-speed ptychographic data acquisition with short exposure can effectively reduce the impact from experimental variations. To reach a cumulative dose required for a given resolution, we further demonstrate that a continuous multi-pass scan via high-speed ptychography can achieve high-resolution imaging. This low-dose scan strategy is shown to be more dose-efficient, and has potential for radiation-sensitive sample studies and time-resolved imaging.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

EGS Collab: Modeling and Simulation Working Group Teleconference Series (99-128)

This submission contains the presentation slides and recordings from EGS Collab Modeling and Simulation Working Group (MSWG) teleconferences number 99 through 128. These teleconferences served three objectives for the project: 1) share simulation results, 2) communicate field activities and results to the simulation teams, and 3) hold open scientific discussions on EGS topics.

15 GEOTHERMAL ENERGY↗

APS upgrade: Commissioning the world’s first light source based on swap-out injection

The Advanced Photon Source (APS) has recently completed a major upgrade, replacing its 25-year-old storage ring with a cutting-edge hybrid seven-bend achromat lattice enhanced by six additional reverse bends. The new design achieves a natural emittance of 42 pm-rad, enabling the production of X-rays up to 500 times brighter than those generated by the original APS. A key innovation of the upgrade is the implementation of a swap-out injection scheme, which replaces entire depleted bunches instead of performing traditional top-up injection. This approach enables on-axis injection to accommodate for the reduced dynamic aperture resulting from strong focusing. This paper outlines the commissioning process, shares initial operating experience with swap-out injection, and presents performance data for new systems such as the bunch-lengthening cavity.

Sajaev, Vadim [Argonne, PHY]↗

NSUF BOILER Pre-Irradiation Characterization and High Flux Isotope Reactor Experiment Design

Alumina-forming austenitic (AFA) stainless steels have emerged as a candidate alloy because of their high-temperature strength, formability, cost, and compatibility with primary coolants for lead-cooled fast reactors (LFRs). This class of steels has exceptional high-temperature oxidation performance; however, a high concentration of Ni is required to stabilize the austenite phase and to provide sufficient creep strength. AFA stainless steels are also susceptible to liquid metal embrittlement (LME). Additionally, under neutron irradiation, Ni will enrich at grain boundaries due to radiation-induced segregation (RIS). Nickel RIS can increase the LME under these coupled effects. Oak Ridge National Laboratory (ORNL) and the NSUF program have leveraged its High Flux Isotope Reactor (HFIR) and experience with complex irradiation experiments to design experiment capsules that test the aforementioned coupled effects. These capsules are designed for insertion in the central flux trap, the highest flux region, of HFIR. The experiment capsules will be filled with Pb, designed to passively melt from the gamma heating in HFIR. The specimens were fabricated into miniature tensile specimens from two different alloys, GA05-25Ni and GA05-20Ni, varying Ni concentrations. The experiment capsules are designed to achieve target temperatures of 400 °C and 650 °C with accumulated dosage of 3 dpa. This report documents the specimen alloy characterization, experimental design, and expected performance of the capsules.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

The pNab experiment and the quest for ever better neutron beam polarization

The Nab and pNAB collaborations are conducting a program of studies of free neutron beta decay, with the primary goal of testing the unitarity of the Cabbibo-Kobayashi-Maskawa matrix that describes quark mixing due to the weak interaction. For this purpose, a large, novel electromagnetic spectrometer, the Nab spectrometer, has been designed, built, and placed in use to determine the correlation coefficients in unpolarized neutron beta decay: "a", the neutrino-electron correlation coefficient; and "b", the Fierz term. The subject of this paper is pNAB, the second phase of the program, that will deploy the same spectrometer with a polarized neutron beam to determine "A", the beta asymmetry; and "B", the neutrino asymmetry coefficients. A focus of this paper will be on the strategies to provide a high and precisely known neutron beam polarization.

Baessler, Stefan↗