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At least 685 records · Page 38

Design and Performance of Kokkos Staging Space toward Scalable Resilient Application Couplings

With the growing number of applications designed for heterogeneous HPC devices, application programmers and users are finding it challenging to compose scalable workflows as ensembles of these applications, that are portable, performant and resilient. The Kokkos C++ library has been designed to simplify this cumbersome procedure by providing an intra-application uniform programming model and portable performance. However, assembling multiple Kokkos-enabled applications into a complex workflow is still a challenge. Although Kokkos enables a uniform programming model, the inter-application data exchange still remains a challenge from both performance and software development cost perspectives. In order to address this issue, we propose Kokkos data staging memory space, an extension of Kokkos' data abstraction (memory space) for heterogeneous computing systems. This new abstraction allows to express data on a virtual shared-space for multiple Kokkos applications, thus extending Kokkos to support inter-application data exchange to build an efficient application workflow. Additionally, we study the effectiveness of asynchronous data layout conversions for applications requiring different memory access patterns for the shared data. Our preliminary evaluation with a synthetic benchmark indicate the effectiveness of this conversion adapted to three different scenarios representing access frequency and use patterns of the shared data.

97 MATHEMATICS AND COMPUTING↗

Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications

X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0 , which is available to download from https://12idb.xray.aps.anl.gov/solx.html.

Zuo, Xiaobing (ORCID:0000000201344804)↗

In-Line Membrane Thickness Mapping with Real-Time Data Processing

The goal of this project is commercialization of a novel, patented by NREL, non-contact, in-line quality control thickness mapping tool that will enable 100% area inspection of multilayer polymer film assemblies, such as a PEM on a casting substrate, during continuous high-volume R2R manufacturing.

ENGINEERING,HYDROGEN↗

Search for New Bosons in Gluon-Gluon and Vector Boson Fusion Processes at the LHC and Development of Silicon Module Assembly Techniques for the CMS High Granularity Calorimeter

A search for heavy resonances decaying to a pair of vectors bosons is presented which utilizes events in which a hadronically decaying Z or W boson is identified using jet substructure techniques and large missing transverse momentum is found. Data analyzed were recorded by the Compact Muon Solenoid experiment at the CERN Large Hadron Collider in 2016, 2017, and 2018, and correspond to 137 fb$^{-1}$ . The events are categorized as having arisen from Vector Boson Fusion process or not, and are characterized by their transverse mass distribution. The standard model backgrounds are estimated based on observed yields in control regions. No excess of events above the expected SM background are observed and limits are placed on the production cross section of Radion (spin-0), Wprime (spin-1) and Bulk graviton (spin2) particles. In adiditon, the high luminosity LHC and the CMS HGCAL upgrade are also presented. The assembly techniques and various tests for the Silicon module and the cassette are discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Assembly of MiniFuel Targets for Irradiation of U-Mo Fuel Specimens in the High Flux Isotope Reactor

To support the development of advanced low-enriched uranium for use in nuclear reactors, irradiation testing of U-Mo disk specimens was performed at the Oak Ridge National Laboratory (ORNL) High Flux Isotope Reactor (HFIR) to collect experimental irradiation data on this type of fuel at pressurized water reactor–relevant temperatures. U-Mo is a uranium alloy that has superior dimensional stability relative to alpha-phase uranium metal and has a substantially higher uranium density compared to UO 2 . U-Mo disks specimens were fabricated at Idaho National Laboratory and inserted into MiniFuel targets for HFIR irradiation. Three MiniFuel targets were successfully assembled, welded, tested, and delivered to HFIR, along with their quality assurance documentation. The targets were inserted into HFIR’s inner vertical experiment facility within the permanent beryllium reflector. Each target contains six disk specimens and will be irradiated in HFIR for three, four, and eight cycles, with target temperatures between 250 and 500°C. This report summarizes the experiment design, test matrix, pre-characterization of specimens, and experiment assembly.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A differentiable, physics-informed ecosystem modeling and learning framework for large-scale inverse problems: demonstration with photosynthesis simulations

Photosynthesis plays an important role in carbon, nitrogen, and water cycles. Ecosystem models for photosynthesis are characterized by many parameters that are obtained from limited in situ measurements and applied to the same plant types. Previous site-by-site calibration approaches could not leverage big data and faced issues like overfitting or parameter non-uniqueness. Here we developed an end-to-end programmatically differentiable (meaning gradients of outputs to variables used in the model can be obtained efficiently and accurately) version of the photosynthesis process representation within the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) model. As a genre of physics-informed machine learning (ML), differentiable models couple physics-based formulations to neural networks (NNs) that learn parameterizations (and potentially processes) from observations, here photosynthesis rates. We first demonstrated that the framework was able to correctly recover multiple assumed parameter values concurrently using synthetic training data. Then, using a real-world dataset consisting of many different plant functional types (PFTs), we learned parameters that performed substantially better and greatly reduced biases compared to literature values. Further, the framework allowed us to gain insights at a large scale. Our results showed that the carboxylation rate at 25 °C (V c,max25 ) was more impactful than a factor representing water limitation, although tuning both was helpful in addressing biases with the default values. This framework could potentially enable substantial improvement in our capability to learn parameters and reduce biases for ecosystem modeling at large scales.

54 ENVIRONMENTAL SCIENCES↗

Metagenome-assembled genomes from topsoils along a hillslope water gradient across early snowmelt to late summer in East River, CO

Drought is changing the American Mountain West at unprecedented rates with unknown consequences to soil microbiome composition and function. As a part of LBNL Watershed Science Focus Area (SFA), we investigated shifts in microbial community and transcriptional activity on a subalpine conifer-meadow transition zone throughout the summer of 2023 as soil dried down. This work took place in Crested Butte, CO on Snodgrass mountain, using a proxy for drought conditions.Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal community at 0-10cm from three sites along a hillslope water gradient across five timepoints from early snowmelt to late summer. 42 metagenomes were sequenced at Joint Genome Institute (JGI) and can be found under the JGI GOLD (Genomes Online Database) sequencing project Gs0166660. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>70%) and contamination (<10%), and dereplicated at 95% ANI using drep. This dataset (1) a zip file of 157 MAGs (as fasta files, Gs0166660_bins_tar.gz), (2) sample metadata file with sample IGSNs (International Generic Sample Numbers) (samples.csv), (3) bounding box coordinates for the sampled locations (Gs0166660.kml), (4) metagenome assembly and coassembly metadata file listing IMG/M (Integrated Microbial Genomes/Metagenomes) metagenome accessions linking samples to metagenomes (EastRiver_Drought_ESSDive_Metadata.csv), (5) location metadata file (locations.csv), (6) file-level metadata file (flmd.csv) and (7) data dictionary (dd.csv) file.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

Development of a test system for data links of the ATLAS Inner Tracker (ITk) upgrade silicon pixel detector

This contribution introduces a novel test system developed to evaluate the signal transmission quality in high-speed data links for the 2026 Inner Tracker (ITk) upgrade of the ATLAS experiment. Using an FPGA-based data acquisition (DAQ) framework, the setup can run simultaneous Bit Error Rate (BER) tests for up to 64 channels and generate virtual eye diagrams, for qualifying the ∼26k electrical links at the ATLAS ITk data rate of 1.28 Gb/s. The paper includes results from system calibration, yielding its contribution to the measured losses, and preliminary results from tests of prototype and pre-production assemblies of on-detector links of the three ATLAS ITk Pixel subsystems.

47 OTHER INSTRUMENTATION↗

Verifying MCNP Models of the TEX High 240 Plutonium Benchmark

Computational modeling programs are invaluable tools that allow us to understand systems, safely develop new processes, and make reliable predictions about future designs. However, the effectiveness of these codes is limited by the degree to which their parameters match the real world. In the field of nuclear engineering, cross section data is one of these vital parameters. Accurate cross section data on important fissile and fissionable isotopes promotes the design of safer and more efficient fabrication, transportation, storage, and stockpiling of nuclear fuel. Unfortunately, there are knowledge gaps in data on key isotopes. In 2011, a multinational meeting hosted by the US Department of Energy Nuclear Criticality Safety Program ranked the priority of certain cross section data needs. In response, Lawrence Livermore National Lab (LLNL) designed the Thermal and Epithermal eXperiment (TEX) series of benchmark experiments. Benchmark experiments are used to validate current cross section data. They validate data by comparing the results of an actual experiment to the predicted results from a computational model. The data a benchmark applies to depends on the isotope and energy range the experiment’s neutron multiplication factor ( k eff ) is most sensitive to. The development and testing of the TEX High 240 Plutonium Benchmark will help validate 240 Pu cross section data. The configuration and materials of this benchmark are designed to be most sensitive to 240 Pu's intermediate energy range (from 0.625 ev to 100 keV ). MCNP® models of the assembly have been developed by LLNL and the results have been written in the final design report. In order for the discrepancies between benchmark models and experiments to be attributed to cross section inaccuracies, the accuracy of the models needs to be verified. The goal of this project is to verify of the results of LLNL's modeling by creating a new set of MCNP models and comparing the results.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Searches for New Long-Lived Particles and Upgrade to the ATLAS Inner Detector (Final Technical Report)

The search for new fundamental particles is one of the defining goals of the Large Hadron Collider (LHC). The discovery of the Higgs Boson by the ATLAS and CMS collaborations provided the capstone of the Standard Model of particle physics, but outstanding questions remain. Why does the Higgs boson have a mass of 125 GeV when its natural mass would be many orders of magnitude larger? Is there a universal symmetry which unites all three forces described by the Standard Model? Can that symmetry be extended to include gravity? Is dark matter, evidenced by astronomical observations, made of a particle that interacts via Standard Model forces with the rest of matter? Together, these motivations provide compelling arguments that new physical processes await discovery. This project addressed some outstanding questions about the fundamental particles and their interactions with the ATLAS experiment at the Large Hadron Collider. In particular, the project improved the discovery potential for new, long- lived particles produced via electroweak processes in proton-proton collisions and set world-leading limits on their existence for certain values of their potential mass and lifetime. To achieve this, the project developed new data analysis methods, developed new triggers to select events with new long-lived particles during data-taking of the ATLAS experiment, and analyzed the largest proton–proton collision dataset ever produced. The project also supported significant development of the data acquisition software for the upgrade to the ATLAS inner detector, the Inner TracKer (ITk). The upgrade of the ATLAS inner detector is essential to the success of the entire Phase II physics program on ATLAS. Personnel supported by the project provided support for integration, assembly, and testing of the inner two layers of the ITk pixel system during its prototype and pre-production phase. Four PhD students and two post-doctoral scholars were supported by the grant and received invaluable scientific training as part of the research endeavor. The students and postdocs gained essential professional skills in the areas of advanced data analysis techniques, statistical analysis of data and simulation, programming in C++ and Python, hardware and instrumentation development, and presentation and collaboration skills. Additionally, approximately ten undergraduate students supported through other funding sources participated in research activities synergistic with the goals of this project, receiving essential mentorship from the personnel supported by this project.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

General Biology 2 Sugar Beet Lab - SU2025 - Final

This module uses the Department of Energy Systems Biology Knowledgebase (KBase) platform to explore topics such as genome assembly, metagenomics, and phylogenomics. Here students will use sequences from DNA that they collected to compare the metagenomes of microbial communities from the rhizosphere of plants grown in fertilized vs. unfertilized soils. Using these data students will evaluate the impact of fertilizer on these communities and how these microbial communities influence soil health and plant growth.

59 BASIC BIOLOGICAL SCIENCES↗

Seasonal dynamics of core fungi in the switchgrass phyllosphere, and co-occurrence with leaf bacteria

Plant leaves harbor complex microbial communities that influence plant health and productivity. Nevertheless, a detailed understanding of phyllosphere community assembly and drivers is needed, particularly for phyllosphere fungi. Here, we investigated seasonal dynamics of epiphytic phyllosphere fungal communities in switchgrass ( Panicum virgatum L.), a focal bioenergy crop. We also leverage previously published data on switchgrass phyllosphere bacterial communities from the same experimental plants, allowing us to compare fungal and bacterial dynamics and explore inter-Domain network associations in the switchgrass phyllosphere. Overall, we found a strong impact of sampling date on fungal community composition, with multiple taxonomic levels exhibiting clear temporal patterns in relative abundance. In addition, leaf nitrogen concentration, leaf dry matter content, plant height, and minimum daily air temperature explained significant variation in phyllosphere fungal communities, likely due to their correlation with sampling date. Finally, among the core taxa, fungal-bacterial network associations were much more common than bacteria-bacteria associations, suggesting the importance of inter-Domain phylogenetic diversity in microbiome assembly. Although our findings highlight the complexity of phyllosphere microbiome assembly, the clear temporal patterns in lineage-specific fungal abundances give promise to the potential for accurately predicting shifts in fungal phyllosphere communities throughout the growing season, a key research priority for sustainable agriculture.

16S rRNA↗

Reaction Rate Ratios for Recent Fast Metal Experiments with Large Plutonium Masses

Reaction rate ratios are integral responses that are used within the criticality experiments field because they contain spectral information. While these types of measurements have been utilized for nuclear data validation with historic experiments, few experiments of this type have been utilized for recent experiments, as few exist. This work focuses on measured reaction rate ratios for two nearly bare plutonium critical assemblies with different geometries: one that is cube like (with a Pu mass of 40 kg) and one that is slab like (with a Pu mass of 109 kg). Irradiations were performed with both configurations in which foils were placed near the center of the assembly. Plutonium, highly enriched uranium, depleted uranium, and Au foils were included in the irradiation and counted via high-purity germanium detectors. From these measurements, reaction rate ratios were calculated. Measured and simulated values and uncertainties are presented for the reaction rate ratios. Ratios utilizing the following reactions are given in this work: 197 Au(n, γ), 197 Au(n,2n), 235 U(n,fission), 238 U(n, fission), 238 U(n,2n), 238 U(n,γ), and 239 Pu(n,fission). Uncertainties for the measured reaction rate ratios ranged from 4% to 7%, and the contribution of various parameters to this uncertainty was investigated. The results are compared to historical experiments and should be used for nuclear data validation for future nuclear data library releases. These measurements are part of the EUCLID (Experiments Underpinned by Computational Learning for Improvements in Nuclear Data) project, which utilizes measurement responses in addition to k eff (such as these reaction rate ratios) to help reduce uncertainties in 239 Pu nuclear data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Medium controlled aggregative growth as a key step in mesoporous silica nanoparticle formation

Near monodisperse mesoporous silica nanoparticles (MSN) represent a promising and rapidly developing type of mesoporous silica materials; however, the vast data on their synthesis remains unorganized and ill-understood. We systematically studied the formation of MSN under basic and neutral conditions using various temperatures, CTAB concentrations, hydrolyzing agents (triethanolamine, ammonia, phosphate buffers), and media with different colloidal stabilization properties (with ethanol as a cosolvent and monovalent salts). In the typical conditions for the preparation of stable MSN colloids, the particle size was controlled by colloidal stabilization by the medium (solvent type, ionic strength, and surfactant concentration) in agreement with the “aggregative growth” mechanism, rather than by solely the hydrolysis and condensation rates conventionally used for data interpretation in the classical nucleation theory. Medium properties (pH, ion types and concentration, polarity) also defined the efficiency of silica-surfactant cooperative self-assembly, which directly affected the porosity, mesopore size and pore wall thickness. Interestingly, this traditional silica-surfactant route showed a limited effect on the particle size, emphasizing the dominating role of colloidal stabilization in the studied reaction conditions. In situ pH measurements showed that every reaction medium has unique pH evolution profiles depending on the buffer capacity, hydrolysis and condensation rates. Reaction systems that fail to maintain the working pH can lead to non-porous products or undesired particle morphology and size distribution. The established particle formation mechanism allowed us to formulate comprehensive guidelines for preparing relatively concentrated colloids of near monodisperse (PDI 5–15%) mesoporous 30–700 nm silica spheres with variable porosity and mesopore size. Here, these findings will be particularly useful in designing new mesoporous silica-containing materials for biomedical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydrogen reionization ends by z = 5.3: Lyman-α optical depth measured by the XQR-30 sample

ABSTRACT The presence of excess scatter in the Ly-α forest at z ∼ 5.5, together with the existence of sporadic extended opaque Gunn-Peterson troughs, has started to provide robust evidence for a late end of hydrogen reionization. However, low data quality and systematic uncertainties complicate the use of Ly-α transmission as a precision probe of reionization’s end stages. In this paper, we assemble a sample of 67 quasar sightlines at z > 5.5 with high signal-to-noise ratios of >10 per ≤15 km s−1 spectral pixel, relying largely on the new XQR-30 quasar sample. XQR-30 is a large program on VLT/X-Shooter which obtained deep (SNR > 20 per pixel) spectra of 30 quasars at z > 5.7. We carefully account for systematics in continuum reconstruction, instrumentation, and contamination by damped Ly-α systems. We present improved measurements of the mean Ly-α transmission over 4.9 < z < 6.1. Using all known systematics in a forward modelling analysis, we find excellent agreement between the observed Ly-α transmission distributions and the homogeneous-UVB simulations Sherwood and Nyx up to z ≤ 5.2 (<1σ), and mild tension (∼2.5σ) at z = 5.3. Homogeneous UVB models are ruled out by excess Ly-α transmission scatter at z ≥ 5.4 with high confidence (>3.5σ). Our results indicate that reionization-related fluctuations, whether in the UVB, residual neutral hydrogen fraction, and/or IGM temperature, persist in the intergalactic medium until at least z = 5.3 (t = 1.1 Gyr after the big bang). This is further evidence for a late end to reionization.

79 ASTRONOMY AND ASTROPHYSICS↗

Relating galaxies across different redshift to study galaxy evolution

We propose a general framework leveraging the galaxy–halo connection to link galaxies observed at different redshift in a statistical way, and use the link to infer the redshift evolution of the galaxy population. Our tests based on hydrodynamic simulations show that our method can accurately recover the stellar mass assembly histories up to z ∼ 3 for present star-forming and quiescent galaxies down to 10 10 h −1 M ⊙ . Applying the method to observational data shows that the stellar mass evolution of the main progenitors of galaxies depends strongly on the properties of descendants, such as stellar mass, halo mass, and star formation states. Galaxies hosted by low-mass groups/haloes at the present time have since z ∼ 1.8 grown their stellar mass ∼2.5 times as fast as those hosted by massive clusters. This dependence on host halo mass becomes much weaker for descendant galaxies with similar star formation states. Star-forming galaxies grow about 2–4 times faster than their quiescent counterparts since z ∼ 1.8. Both TNG and EAGLE simulations overpredict the progenitor stellar mass at z > 1, particularly for low-mass descendants.

79 ASTRONOMY AND ASTROPHYSICS↗

Heterologous expression of a fully active Azotobacter vinelandii nitrogenase Fe protein in Escherichia coli

ABSTRACT The functional versatility of the Fe protein, the reductase component of nitrogenase, makes it an appealing target for heterologous expression, which could facilitate future biotechnological adaptations of nitrogenase-based production of valuable chemical commodities. Yet, the heterologous synthesis of a fully active Fe protein of Azotobacter vinelandii ( Av NifH) in Escherichia coli has proven to be a challenging task. Here, we report the successful synthesis of a fully active Av NifH protein upon co-expression of this protein with Av IscS/U and Av NifM in E. coli . Our metal, activity, electron paramagnetic resonance, and X-ray absorption spectroscopy/extended X-ray absorption fine structure (EXAFS) data demonstrate that the heterologously expressed Av NifH protein has a high [Fe 4 S 4 ] cluster content and is fully functional in nitrogenase catalysis and assembly. Moreover, our phylogenetic analyses and structural predictions suggest that Av NifM could serve as a chaperone and assist the maturation of a cluster-replete Av NifH protein. Given the crucial importance of the Fe protein for the functionality of nitrogenase, this work establishes an effective framework for developing a heterologous expression system of the complete, two-component nitrogenase system; additionally, it provides a useful tool for further exploring the intricate biosynthetic mechanism of this structurally unique and functionally important metalloenzyme. IMPORTANCE The heterologous expression of a fully active Azotobacter vinelandii Fe protein (AvNifH) has never been accomplished. Given the functional importance of this protein in nitrogenase catalysis and assembly, the successful expression of AvNifH in Escherichia coli as reported herein supplies a key element for the further development of heterologous expression systems that explore the catalytic versatility of the Fe protein, either on its own or as a key component of nitrogenase, for nitrogenase-based biotechnological applications in the future. Moreover, the “clean” genetic background of the heterologous expression host allows for an unambiguous assessment of the effect of certain nif-encoded protein factors, such as AvNifM described in this work, in the maturation of AvNifH, highlighting the utility of this heterologous expression system in further advancing our understanding of the complex biosynthetic mechanism of nitrogenase.

59 BASIC BIOLOGICAL SCIENCES↗

Downhole Sensing and Event-Driven Sensor Fusion for Depth-of-Cut Based Autonomous Fault Response and Drilling Optimization

Achieving robust and efficient drilling is a critical part of reducing the cost of geothermal energy exploration and extraction. Drilling performance is often evaluated using one or more of three key metrics: depth of cut (DOC), rate of penetration (ROP), and mechanical specific energy (MSE). All three of these quantities are related to each other. DOC refers to the depth a bit penetrates into rock during drilling. This is an important quantity for estimating bit behavior. ROP is the simply the DOC multiplied by the rotational rate, and represents how quickly the drill bit is advancing through the ground. ROP is often the parameter used for drilling control and optimization. Finally, MSE provides insight into drilling efficiency and rock type. MSE calculations rely on ROP, drilling force, and drilling torque. Surface-based sensors at the top of the drill are often used to measure all these quantities. However, top-hole measurements can deviate substantially from the behavior at the bit due to lag, vibrations, and friction. Therefore, relying only on top-hole information can lead to suboptimal drilling control. In this work, we describe recent progress towards estimating ROP, DOC, and MSE using down-hole sensing. We assume down-hole measurements of torque, weight-on-bit (WOB). Our hypothesis is that these measurements can provide more rapid and accurate measures of drilling performance. We show how a multi-layer perceptron (MLP) machine learning algorithm can provide rapid and accurate performance when evaluated on experimental data taken from Sandia’s Hard Rock Drilling Facility. In addition, we implement our algorithms on an embedded system intended to emulate a bottom-hole-assembly for sensing and estimation. Our experimental results show that DOC can be estimated accurately and in real-time. These estimates when combined with measurements for rotary speed, torque, and force can provide improved estimates for ROP and MSE. These results have the potential to enable better drilling assessment, improved control, and extended component lifetimes.

15 GEOTHERMAL ENERGY↗