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At least 775 records · Page 43

Tulane virus protease as a structural surrogate for inhibitor screening of human norovirus proteases

Human norovirus (HuNoV) is a significant cause of gastroenteritis worldwide, affecting people of all age groups. There are currently no vaccines or drugs available, leaving susceptible populations vulnerable to severe or protracted illness. A HuNoV cultivation system is pivotal for screening norovirus antivirals. While the human intestinal enteroid cultivation system allows robust replication of multiple HuNoV strains, it presents technical and cost barriers. Tulane virus (TV), a surrogate for HuNoV, replicates well in monkey kidney cell lines and is closely related to norovirus in cellular biology. Here, we determined the structures of TV protease (TV-Pro) alone and in complex with rupintrivir, a picornavirus inhibitor that also inhibits HuNoV proteases (HuNoV-Pro). Our data validate TV as an efficient surrogate system for rapid screening of HuNoV protease inhibitors. The TV protease structure exhibits significant backbone similarity to the GI.1 HuNoV protease in the substrate-binding domain, with the BII-CII loop in an open conformation stabilized by hydrogen bonds as present in the GI.1 protease. Structural differences in the S2 pocket and two amino acid changes in the S4 pocket result in slightly altered P2 and P4 substrate and inhibitor conformations. Despite these differences, we confirm previous findings that the TV protease can cleave the GI.1 and GII HuNoV polyprotein substrates with high and moderate efficiency, respectively. We found that rupintrivir efficiently inhibits TV protease in vitro and inhibits TV replication in cell culture with similar efficacy in combination with P-glycoprotein efflux pump inhibitors. We conclude that TV is a valuable surrogate for HuNoV protease inhibitor screening and outline strategies to improve its compatibility as such.

crystal structures↗

Exploring life’s hidden majority: microbial dark matter symposium highlights

The Microbial Dark Matter Symposium held on August 28–29, 2025, in Laguna Beach, Orange County, CA, convened a multidisciplinary group of scientists to address the vast unknowns in microbial life—from uncultured taxa and uncharacterized proteins to elusive viruses and spacefaring microbes. Set against a scenic coastal backdrop, the symposium highlighted advances in single-cell genomics, proximity ligation sequencing, and artificial intelligence-ready bioinformatics, while also probing the limits of microbial persistence, metabolism, and ecological distribution. Sessions explored microbial dark matter from multiple dimensions: cultivability, where new strategies are enabling recovery of elusive microbes; functional ambiguity, where metagenomic dark zones are illuminated by computational annotation; and genomic representation, where single-cell methods bridge gaps left by shotgun community sequencing. Researchers shared breakthroughs in identifying atmospheric microbiomes, “dark oxygen” production in groundwater ecosystems, and microbial survival on the International Space Station. The symposium emphasized integration of methods, disciplines, and ecosystems, advancing a collective push to illuminate the microbial dark matter on Earth and beyond. By highlighting emerging tools, pressing questions, and cross-domain insights, the symposium underscored the need for collaborative, open, and adaptive approaches to study the microbial unknown. The meeting marks a pivotal moment in microbiology, where cultivating knowledge of the uncultivated promises transformative understanding of life, everywhere.

Podar, Mircea [ORNL] (ORCID:0000000327760205)↗

Scalable Bayesian Physics-Informed Kolmogorov-Arnold Networks

Uncertainty quantification (UQ) plays a pivotal role in scientific machine learning, especially when surrogate models are used to approximate complex systems. Although multilayer perceptions (MLPs) are commonly employed as surrogates, they often suffer from overfitting due to their large number of parameters. Kolmogorov-Arnold networks (KANs) offer an alternative solution with fewer parameters. However, gradient-based inference methods, such as Hamiltonian Monte Carlo (HMC), may result in computational inefficiency when applied to KANs, especially for large-scale datasets, due to the high cost of back-propagation. To address these challenges, we propose a novel approach, combining the dropout Tikhonov ensemble Kalman inversion (DTEKI) with Chebyshev KANs. This gradient-free method effectively mitigates overfitting and enhances numerical stability. In addition, we incorporate the active subspace method to reduce the parameter-space dimensionality, allowing us to improve the accuracy of predictions and obtain more reliable uncertainty estimates. Extensive experiments demonstrate the efficacy of our approach in various test cases, including scenarios with large datasets and high noise levels. Our results show that the new method achieves comparable or better accuracy, much higher efficiency as well as stability compared to HMC, in addition to scalability. Moreover, by leveraging the low-dimensional parameter subspace, our method preserves prediction accuracy while substantially reducing further the computational cost.

97 MATHEMATICS AND COMPUTING↗

Designing optimal experiments: an application to proton Compton scattering

Interpreting measurements requires a physical theory, but the theory’s accuracy may vary across the experimental domain. To optimize experimental design, and so to ensure that the substantial resources necessary for modern experiments are focused on acquiring the most valuable data, both the theory uncertainty and the expected pattern of experimental errors must be considered. We develop a Bayesian approach to this problem, and apply it to the example of proton Compton scattering. Chiral Effective Field Theory (χEFT) predicts the functional form of the scattering amplitude for this reaction, so that the electromagnetic polarizabilities of the nucleon can be inferred from data. With increasing photon energy, both experimental rates and sensitivities to polarizabilities increase, but the accuracy of χEFT decreases. Our physics-based model of χEFT truncation errors is combined with present knowledge of the polarizabilities and reasonable assumptions about experimental capabilities at HI γ S and MAMI to assess the information gain from measuring specific observables at specific kinematics, i.e. to determine the relative amount by which new data are apt to shrink uncertainties. The strongest gains would likely come from new data on the spin observables Σ 2x and Σ 2x' at ω≃140 to 200 MeV and 40° to 120°. These would tightly constrain γ E1E1 –γ E1M2 . New data on the differential cross section between 100 and 200 MeV and over a wide angle range will substantially improve constraints on α E1 –β M1 , γ π and γ M1M1 –γ M1E2 . Good signals also exist around 160 MeV for Σ 3 and Σ 2z' . As a result, such data will be pivotal in the continuing quest to pin down the scalar polarizabilities and refine understanding of the spin polarizabilities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Operational experience and R&D results using the Google Cloud for High-Energy Physics in the ATLAS experiment

The ATLAS experiment at CERN relies on a Worldwide Distributed Computing Grid infrastructure to support its physics program at the Large Hadron Collider. ATLAS has integrated cloud computing resources to complement its Grid infrastructure and conducted an R&D program on Google Cloud Platform. These initiatives leverage key features of commercial cloud providers: lightweight configuration and operation, elasticity and availability of diverse infrastructures. Here this paper examines the seamless integration of cloud computing services as a conventional Grid site within the ATLAS workflow management and data management systems, while also offering new setups for interactive, parallel analysis. It underscores pivotal results that enhance the on-site computing model and outlines several R&D projects that have benefited from large-scale, elastic resource provisioning models. Furthermore, this study discusses the impact of cloud-enabled R&D projects in three domains: accelerators and AI/ML, ARM CPUs and columnar data analysis techniques.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Elephants Sharing the Highway: Studying TCP Fairness in Large Transfers over High Throughput Links

Escalating bandwidth demand strains high-performance data networks, posing potential performance risks. TCP congestion control algorithms enhance reliability and optimize bandwidth usage. Network performance is influenced by factors such as AQM algorithms and router buffer size. In the context of constrained network resources, understanding how TCP flows share networks and the resulting performance impact is essential. This paper introduces insights into TCP fairness and performance involving a comparison of TCP CUBIC, Reno, Hamilton, and BBR versions 1 and 2 across real-world networks supporting high bandwidths of up to 25 Gbps. The research explores TCP behaviors with AQM algorithms like FIFO, FQ_CODEL, and RED, alongside diverse buffer sizes. Notably, findings reveal that manipulating buffers and queuing methods yields contrasting outcomes based on bandwidth. BBRv2 emerges as a superior fair algorithm, pivotal for swift transfers, particularly in scientific data scenarios. These results provide crucial guidance for future network design, ensuring equitable performance optimization.

Kiran, Mariam↗

Instabilities and Mixing in Inertial Confinement Fusion

By imploding fuel of hydrogen isotopes, inertial confinement fusion (ICF) aims to create conditions that mimic those in the Sun's core. This is fluid dynamics in an extreme regime, with the ultimate goal of making nuclear fusion a viable clean energy source. The fuel must be reliably and symmetrically compressed to temperatures exceeding 100 million degrees Celsius. After the best part of a century of research, the foremost fusion milestone was reached in 2021, when ICF became the first technology to achieve an igniting fusion fuel (thermonuclear instability), and then in 2022 scientific energy breakeven was attained. A key trade-off of the ICF platform is that greater fuel compression leads to higher burn efficiency, but at the expense of amplified Rayleigh–Taylor and Richtmyer–Meshkov instabilities and kinetic-energy-wasting asymmetries. In extreme cases, these three-dimensional instabilities can completely break up the implosion. Even in the highest-yielding 2022 scientific breakeven experiment, high-atomic-number (high-Z) contaminants were unintentionally injected into the fuel. Here we review the pivotal role that fluid dynamics plays in the construction of a stable implosion and the decades of improved understanding and isolated experiments that have contributed to fusion ignition.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Carbon Support Microstructure Impact on High Current Density Transport Resistances in PEMFC Cathode

Cell voltages at high current densities (HCD) of an operating proton-exchange membrane fuel cell (PEMFC) cathode suffer from losses due to the local-O 2 and bulk-H + transport resistances in the catalyst layer. Particularly, the microstructure of high surface area carbon (HSC) support upon which both the platinum catalyst and ionomer are dispersed play a pivotal role in controlling the reactant transport to the active site in the catalyst layer. In this study, we perform a systematic analysis of the underlying microstructure of platinum-cobalt catalyst dispersed on various HSC supports in terms of their surface area and pore-size distribution. The carbon microstructure was found to strongly influence the PtCo nanoparticle dispersion, catalyst layer ionomer distribution and transport losses governing the performance at HCD. Catalyst layer electrochemical diagnostics carried out to quantify local-O 2 transport resistance and bulk-H + transport resistance in the cathode were found to be directly correlated to the micropore (<2 nm) and macropore (>8 nm) surface areas of the carbon support, respectively. Finally, a 1D-performance model has been developed to assimilate our understanding of the catalyst layer microstructure and transport resistances at HCD.

25 ENERGY STORAGE↗

Effect of Engineered Cracks in Catalyst Layers on PEMFC Catalyst Layer Durability

Proton exchange membrane fuel cells (PEMFCs) are expected to play a pivotal role in decarbonizing the transportation sector, and particularly heavy-duty vehicles (HDVs). However, improvements in durability are needed for PEMFCs to compete with state-of-the-art power sources for HDVs. Here, we examine how catalyst layer (CL) cracks that are engineered affect the CL durability by using patterned silicon templates to control the CL crack density at the micrometer scale. Electrochemical analyses show that the initial PEMFC performance is relatively unaffected by crack density, but the performance after durability testing was strongly affected. Specifically, CLs with high crack density showed higher performance relative to CLs without cracks after application of a carbon corrosion accelerated stress test. Electrochemical analyses coupled with X-ray computed tomography and scanning transmission electron microscopy with energy dispersive X-ray spectroscopy showed that the cracks provide shorter oxygen diffusion pathways to reaction sites, leading to decreased oxygen transport resistance. Additionally, we observed that the catalyst durability is unaffected by cracks. Our results provide a mechanistic explanation of the role of cracks in CL durability.

30 DIRECT ENERGY CONVERSION↗

Modeling the Nucleation and Growth of Lead Sulfate Particles on Lead Electrodes

Lead-acid batteries (LABs) play a pivotal role in the energy storage sector with applications spanning from starting-lighting-ignition batteries to grid energy storage. Passivation of lead negative electrodes by PbSO 4 particles is a fundamental mechanism limiting the performance of LAB. In this regard, an electrochemical model is developed that simulates the nucleation and growth (N&G) dynamics of PbSO 4 particles on a flat lead electrode, responsible for its passivation. The model considers the electrochemical reactions between lead electrode and sulfuric acid, N&G of PbSO 4 particles, passivation of the lead surface, and the ternary transport of PbSO 4 (aq), bisulfate, and protons in H 2 SO 4 electrolyte. The model is validated with a dataset of cyclic voltammetry (CV) responses collected at several scan rates and H 2 SO 4 concentrations. The model shows remarkable qualitative and quantitative agreement with the experimental data including CV peak features, discharge capacity, and particle size. The model was employed to explore key N&G quantities, such as supersaturation, nucleation rate, particle count, growth rate, particle size, and surface coverage, and to examine how their interactions influence electrode utilization. Parametric studies were also conducted to evaluate how scan rates and acid concentrations influence the previously mentioned N&G quantities and, subsequently, the utilization of the electrode.

25 ENERGY STORAGE↗

Direct Recycling of End-of-Life Cathode Material Through Redox Chemistry Mediators

Lithium-ion batteries (LIBs) are ideal for electric vehicles and electronic devices because of their high-power density and outstanding cycle life. The need for recycled LIBs material is pivotal for the sustainability of the renewable energy industry. The recycling process needs to be both economically and environmentally conscious. Direct recycling is cheaper and generates the least amount of waste compared to pyrometallurgical and hydrometallurgical processes. Direct recycling explored in this work is useful for reclaiming precious minerals from the End-of-Life (EOL) LIBs material. The EOL material has varying lithium deficiency, hence, redox mediator relithiation restores the lithium content rapidly and at low cost. The redox mechanism relithiate EOL cathode material by shuttling charges very fast between lithium metal and EOL cathode material. The redox mediator is oxidized to create lithium rich solvent and reduced to relithiate EOL cathode material. However, the process is sensitive to pH changes. The redox reaction creates acidic solvent, which may cause lithium leaching. Therefore, use of lithium hydroxide (LiOH) to remove impurities on the surface of the EOL material and as a lithium source creates a basic solution to prevent lithium leaching and relithiate EOL material. This approach will potentially pave way for fast quality cathode material recovery at a low cost.

cathode material↗

eBPF Community ID Calculation

The code titled “eBPF Community ID Calculation” allows easy correlation of monitoring logs with existing network forensics logs on high-performance computing (HPC) systems. This code implements the Community ID Flow Hashing standard to calculate community ID Flow identifiers. These identifiers will be used to correlate host forensics logs with network forensics logs. The correlation provides valuable insight and the ability to easily pivot between disparate data sources. The computer code removes the libpcap dependency from the code base.

Maerz, StefanA↗

Sudoku Online Testing Framework v.0.2

The Sudoku Online Testing Framework provides a configurable basis for testing user interactions to solve visualization-related problems with sudoku puzzles and games. It consists of a server, a client, and test code. The python server implements sudoku puzzle logic and board selection functions. The JavaScript client implements a graphical user interface (GUI) front-end to display the puzzles and facilitate interactions with users. Within the GUI, logical rules may be selected. Cells may be selected to “pivot” on to make a board for each possible value in the cell. 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. SAND2021-6409 O

Leger, Michelle↗

Fox Trails

1. This software utilizes python pandas to pull data from P6 databases or XER files. The software transforms the datasets into multiple main tables by joining, filtering, iteratively flattening hierarchical structured data, and pivoting datasets to give simple flat output tables. The activity table includes all of the information related to an activity including activity codes, global, EPS, and project codes, UDFs, and WBS information as separate columns. This includes the code id, code value and sequence number for all levels in hierarchical codes. The resource table is similar to the activity table and includes all of the information related to resources on activities including UPFs and resource codes. The resource time phased table takes the resource information and time phases it for the budget, forecast, late, and actual dates/units/costs that closely matches P6's user interface's values as it implements the resource curve and calendars. The wbs table contains the WBS structure broken out by levels and includes UDFs, codes, and notebook topics. The final P6 data table is the relationships table which simply contains the relationships. 2. When a user updates the tool with data (via giving it P6 project names with database username/password information or XER files) the system creates the data in #1, then creates a networkx graph with the activity data imbedded in the node data and the relationships added as edges. Each edge also has it's float calculated (working time distance between the predecessor and successor) and attached to the edge. Activities are also tagged as a potential start of a path based on their constraints, constraint dates, remaining start date, and activity status. When a user enters an activity ID into the UI, it runs a shortest path calculation on the network graph between each node tagged as potential start to the entered activity id based on the float tagged on the edge. Each path returned by the algorithm contains all of the nodes on the path in order, as well as the total float of the edges that make the path. This data is then collected and returned to the user in the form of a gantt chart with groupings for each path that includes the total float for each group. 3. Similar to 2, if the user passes through a reference dataset each activity set in the path is checked to see if it had a path in the reference dataset, if that path was the primary path between the start and end activities, and what has changed regarding logic and durations. These changes are color coded and summarized before sent to the user to be displayed by the UI for simple discovery. 4. Utilizing the data from #1, the user can submit desired grouping code(s) and filters to the system. The system will then pull the activities, resources, and relationships and create a gantt chart based on the groupings sent and filtered based on the filters sent. 5. The system will produce a gantt chart in a similar method to #4, but allows interactivity with the data. As the user interacts with the gantt chart, the software captures the changes and stores it with the user making the change so that project controls and implement those changes in P6.

Fox, Ben↗

BioPac

BioPAC is the Biological and other Particles in Aerosols Classifier. It is a software to assist in the accurate measurement and identification of primary biological aerosol particles, which play a pivotal role in mediating the reciprocal relationships between biological systems and atmospheric conditions.

Rahman, Ashfiqur [Pacific Northwest National Labor↗

Self-Supervised Cloud Classification

Abstract Low-level marine clouds play a pivotal role in Earth’s weather and climate through their interactions with radiation, heat and moisture transport, and the hydrological cycle. These interactions depend on a range of dynamical and microphysical processes that result in a broad diversity of cloud types and spatial structures, and a comprehensive understanding of cloud morphology is critical for continued improvement of our atmospheric modeling and prediction capabilities moving forward. Deep learning has recently accelerated our ability to study clouds using satellite remote sensing, and machine learning classifiers have enabled detailed studies of cloud morphology. A major limitation of deep learning approaches to this problem, however, is the large number of hand-labeled samples that are required for training. This work applies a recently developed self-supervised learning scheme to train a deep convolutional neural network (CNN) to map marine cloud imagery to vector embeddings that capture information about mesoscale cloud morphology and can be used for satellite image classification. The model is evaluated against existing cloud classification datasets and several use cases are demonstrated, including training cloud classifiers with very few labeled samples, interrogation of the CNN’s learned internal feature representations, cross-instrument application, and resilience against sensor calibration drift and changing scene brightness. The self-supervised approach learns meaningful internal representations of cloud structures and achieves comparable classification accuracy to supervised deep learning methods without the expense of creating large hand-annotated training datasets. Significance Statement Marine clouds heavily influence Earth’s weather and climate, and improved understanding of marine clouds is required to improve our atmospheric modeling capabilities and physical understanding of the atmosphere. Recently, deep learning has emerged as a powerful research tool that can be used to identify and study specific marine cloud types in the vast number of images collected by Earth-observing satellites. While powerful, these approaches require hand-labeling of training data, which is prohibitively time intensive. This study evaluates a recently developed self-supervised deep learning method that does not require human-labeled training data for processing images of clouds. We show that the trained algorithm performs competitively with algorithms trained on hand-labeled data for image classification tasks. We also discuss potential downstream uses and demonstrate some exciting features of the approach including application to multiple satellite instruments, resilience against changing image brightness, and its learned internal representations of cloud types. The self-supervised technique removes one of the major hurdles for applying deep learning to very large atmospheric datasets.

54 ENVIRONMENTAL SCIENCES↗

PERSIANN Dynamic Infrared–Rain Rate Model (PDIR) for High-Resolution, Real-Time Satellite Precipitation Estimation

Precipitation measurements with high spatiotemporal resolution are a vital input for hydrometeorological and water resources studies; decision-making in disaster management; and weather, climate, and hydrological forecasting. Moreover, real-time precipitation estimation with high precision is pivotal for the monitoring and managing of catastrophic hydroclimate disasters such as flash floods, which frequently transpire after extreme rainfall. While algorithms that exclusively use satellite infrared data as input are attractive owing to their rich spatiotemporal resolution and near-instantaneous availability, their sole reliance on cloud-top brightness temperature (T b ) readings causes underestimates in wet regions and overestimates in dry regions—this is especially evident over the western contiguous United States (CONUS). We introduce an algorithm, the Precipitation Estimations from Remotely Sensed Information Using Artificial Neural Networks (PERSIANN) Dynamic Infrared–Rain rate model (PDIR), which utilizes climatological data to construct a dynamic (i.e., laterally shifting) T b –rain rate relationship that has several notable advantages over other quantitative precipitation-estimation algorithms and noteworthy skill over the western CONUS. Validation of PDIR over the western CONUS shows a promising degree of skill, notably at the annual scale, where it performs well in comparison to other satellite-based products. Analysis of two extreme landfalling atmospheric rivers show that solely IR-based PDIR performs reasonably well compared to other IR- and PMW-based satellite rainfall products, marking its potential to be effective in real-time monitoring of extreme storms. This research suggests that IR-based algorithms that contain the spatiotemporal richness and near-instantaneous availability needed for rapid natural hazards response may soon contain the skill needed for hydrologic and water resource applications.

54 ENVIRONMENTAL SCIENCES↗

The role of equatorial waves in triggering precipitation extremes in the Maritime Continent

This review offers a comprehensive analysis of convectively coupled equatorial waves (CCEWs) and their pivotal role in driving precipitation extremes across the Maritime Continent. It examines the current understanding of CCEWs, evaluates the performance of numerical models and forecasting techniques in predicting these phenomena, and pinpoints critical areas for improvement. The discussion centers on three key types of equatorial waves: equatorial Rossby waves, Kelvin waves, and mixed Rossby–gravity waves. By connecting scientific insights with practical forecasting applications, the review sheds light on the challenges of predicting these waves while identifying opportunities to advance both fundamental knowledge and forecasting accuracy. Designed as an educational resource, it targets operational forecasting centers, meteorologists, and researchers, aiming to enhance the prediction of extreme weather events in the region.

Maritime Continent↗