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At least 235 records · Page 13

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

Absolute calibration of the conical crystal configuration of the zinc spectrometer (ZSPEC) at the OMEGA laser facility

In this study, we present the absolute calibration of the conical crystal for the zinc spectrometer (ZSPEC), an x-ray spectrometer at the OMEGA laser facility at the Laboratory for Laser Energetics. The ZSPEC was originally designed to measure x-ray Thomson scattering using flat or cylindrically curved highly oriented pyrolytic graphite crystals centered around Zn He-alpha emission at 9 keV. To improve the useful spectral range and collection efficiency of the ZSPEC, a conical highly annealed pyrolytic graphite crystal was fabricated for the ZSPEC. The conically bent crystal in the Hall geometry produces a line focus perpendicular to the spectrometer axis, corresponding to the detector plane of electronic detectors at large scale laser facilities such as OMEGA, extending the useful range of the spectrometer to 7–11 keV. Further, using data collected using a microfocus Mo x-ray source, we determine important characteristics of ZSPEC such as the dispersion, spatial resolution, and absolute sensitivity of the instrument. A ray-trace model of ZSPEC provides another point of agreement in calculations of the ZSPEC dispersion and crystal response.

47 OTHER INSTRUMENTATION↗

Demonstration of neutron time-of-flight diffraction with an event-mode imaging detector

Neutron diffraction beamlines have traditionally relied on deploying large detector arrays of 3 He tubes or neutron-sensitive scintillators coupled with photomultipliers to efficiently probe crystallographic and microstructure information of a given material. Given the large upfront cost of custom-made data acquisition systems and the recent scarcity of 3 He, new diffraction beamlines or upgrades to existing ones demand innovative approaches. This paper introduces a novel Timepix3-based event-mode imaging neutron diffraction detector system as well as first results of a silicon powder diffraction measurement made at the HIPPO neutron powder diffractometer at the Los Alamos Neutron Science Center. Notably, these initial measurements were conducted simultaneously with the 3 He array on HIPPO, enabling direct comparison. Data reduction for this type of data was implemented in the MAUD code, enabling Rietveld analysis. Results from the Timepix3-based setup and HIPPO were benchmarked against McStas simulations, showing good agreement for peak resolution. With further development, systems such as the one presented here may substantially reduce the cost of detector systems for new neutron instrumentation as well as for upgrades of existing beamlines.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Inferring small-sample-reactivity worth from oscillation experiment with auto-corrected local flux

To estimate reactivity changes as a function of time from the signal of detectors count rates, one usually uses point kinetic equations. However, when detectors are located inside the core, it is often necessary to compute a correction factor to account for the flux-shape deformation (i.e. the change of detector efficiency that may have been induced by neutron absorbers movements). Various simulation methods have been developed depending on transients observed. They range from the resolution of static equations up to full-time-dependent neutron transport in 3D. However, those methods require high computational-cost calculations of local reaction rates that rely on nuclear data evaluations. Therefore, a 'measured' reactivity is never determined through pure measurements. Taking advantage of the known oscillation movement of a small sample at the center of the MINERVE reactor, the innovative algorithm presented in this paper derives the correction factor needed to get no time drift on reactivity steps. Derived correction factors are in good agreement with those obtained independently with TRIPOLI-4 through sensitivity analysis. Low sensitivity to the sample composition and moderate sensitivity to the detectors position reinforce the reliability of those results. This application paves the way to almost pure nuclear data reactivity measurements. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Defect-mediated metastability and carrier lifetimes in polycrystalline (Ag,Cu)(In,Ga)Se 2 absorber materials

Using a combination of optical and electrical measurements, we develop a model for metastable defects in Ag-alloyed Cu(In,Ga)Se 2 , one of the leading thin film photovoltaic materials. By controlling the pre-selenization conditions of the back contact prior to the growth of polycrystalline (Ag,Cu)(In,Ga)Se 2 absorbers and subsequently exposing them to various stresses (light soaking and dark-heat), we explore in this paper the nature and role of metastable defects on the electro-optical and photovoltaic performance of high-efficiency solar cell materials and devices. Positron annihilation spectroscopy indicates that dark-heat exposure results in an increase in the concentration of the selenium–copper divacancy complex (V Se –V Cu ), attributed to depassivation of donor defects. Deep-level optical spectroscopy finds a corresponding increase of a defect at Ev+0.98 eV, and deep-level transient spectroscopy suggests that this increase is accompanied by a decrease in the concentration of mid-bandgap recombination centers. Time-resolved photoluminescence excitation spectroscopy data are consistent with the presence of the V Se –V Cu divacancy complex, which may act as a shallow trap for the minority carriers. Light-soaking experiments are consistent with the V Se –V Cu optical cycle proposed by Lany and Zunger, resulting in the conversion of shallow traps into recombination states that limit the effective minority carrier recombination time (and the associated carrier diffusion length) and an increase in the doping density that limits carrier extraction in photovoltaic devices.

14 SOLAR ENERGY↗

Active Reservoir Management Engineering and Evaluation Summary – Brine Extraction and Storage Test Phase II Final Report – Volumes 1-3

The Energy & Environmental Research Center (EERC) conducted a multiyear program over two phases to perform a field study of the potential efficacy of formation water extraction during carbon dioxide (CO 2 ) injection for CO 2 storage as a means of improving efficiency and/or effectiveness. Phase I was a 2-year study on potential methodologies for a field study of pressure management, culminating in site selection and experimental and site design. Phase II was a 7-year effort that involved constructing site facilities, conducting experiments, and evaluating collected field data. The experimental portion was split into two collaborative components, one for the active reservoir management (ARM) experiment and a second component to host and demonstrate potential water treatment technologies appropriate for high-saline brine at the project site. The results of the overall project are expected to benefit future saline storage projects through validation of techniques that may reduce stress on sealing formations, increase storage capacity, and reduce area of review. The following report focuses on the Phase II ARM experimental implementation and results. A second companion report summarizes the results of the high-saline brine demonstrations.

54 ENVIRONMENTAL SCIENCES↗

Cric searchable image database as a public platform for conventional pap smear cytology data

Amidst the current health crisis and social distancing, telemedicine has become an important part of mainstream of healthcare, and building and deploying computational tools to support screening more efficiently is an increasing medical priority. The early identification of cervical cancer precursor lesions by Pap smear test can identify candidates for subsequent treatment. However, one of the main challenges is the accuracy of the conventional method, often subject to high rates of false negative. While machine learning has been highlighted to reduce the limitations of the test, the absence of high-quality curated datasets has prevented strategies development to improve cervical cancer screening. The Center for Recognition and Inspection of Cells (CRIC) platform enables the creation of CRIC Cervix collection, currently with 400 images (1,376 × 1,020 pixels) curated from conventional Pap smears, with manual classification of 11,534 cells. This collection has the potential to advance current efforts in training and testing machine learning algorithms for the automation of tasks as part of the cytopathological analysis in the routine work of laboratories.

59 BASIC BIOLOGICAL SCIENCES↗

Attack-resilient algorithms and testbed federation for wide-area protection and control in smart grid

Today’s energy infrastructure is undergoing a massive transformation across all generation, transmission, and distribution systems to provide reliability, efficiency, and sustainability to the power system network. During the past 10 years, there has been a remarkable enhancement in developing close-loop wide-area protection and control (WAPAC) applications, such as automatic generation control (AGC), wide-area protection scheme (WAPS), synchrophasor-based wide-area voltage control system (WAVCS), etc., in the energy management system (EMS) to provide an adequate situational awareness to control center operators during physical disturbances and natural events. The rapid digitalization, unencrypted communication, and numerous data-sharing devices have increased digital access points that have exposed the grid network to countless cyberattacks pertinent to the WAPAC cybersecurity. Given the amount of complex grid network coupled with legacy infrastructures, it is untrustworthy to completely rely on information technology (IT)-based conventional security measures to defend against evolving cyberattacks. Hence, there is a compelling need to go beyond the traditional paradigm of ‘security by obscurity’ and ‘bolt-on’ security measures, and develop a suite of innovative security solutions at multiple layers to transform the current “fault-resilient” grid into “fault and attack-resilient” grid of the future. This dissertation specifically focuses on developing application-specific attack-resilient solutions for critical WAPAC applications in the smart grid. The first part of the study, Attack-Resilient Wide-Area Protection Scheme, presents a cyber-physical attack-resilient system (CPARS) for WAPS, where two anomaly detection methods are proposed to detect multi-level cyberattacks followed by the rules-based intrusion mitigation system (RIMS) to initiate effective mitigation strategies, tailored to these attacks, to restore the normal grid operation after disturbances. The first anomaly detection component, Machine learning-based Anomaly Detection for Centralized WAPS, discusses a novel architecture and methodology for developing a machine-learning-based anomaly detection system (ADS) for the centralized wide-area protection system (CWAPS) by applying the variational mode decomposition (VMD) technique and decision tree (DT) algorithms using cyber logs and synchrophasor measurements. The second component, Multi-Agent-based Anomaly Detection for Decentralized WAPS, presents a two-level hierarchical multi-agent-based decentralized WAPS against the system-aware stealthy cyber-attacks. Finally, for the RIMS, the state transition diagram-based mitigation measures are defined based on the grid operation states and experimental testing and evaluation are presented in a cyber-physical testbed environment. The second part of the study, Attack-Resilient Wide-Area Voltage Control System, addresses the existing vulnerabilities in the wide-area voltage control system (WAVCS), presents the methodology for performing an impact analysis during data integrity attacks, and proposes a data-driven attackresilient system (DARS) by incorporating machine learning-based ADS and rules-based anomaly mitigation system (RAMS) to detect these attacks and provide necessary mitigation actions to maintain the transient voltage stability after disturbances. Finally, the third part, Networked Federation Testbed (NEFTSec) for Smart Grid Cybersecurity, focuses on developing an interconnected federated testbed through a common network like the internet, describes its conceptual architectures, and also presents its design components for experimental testing, validation, and evaluation. Further, it presents the co-simulation interface algorithm (CIA) to facilitate the geographically-dispersed real-time distributed simulation (GD-RTDS) during the cyber-physical federation. In general, this dissertation presents innovative attack-resilient solutions for WAPAC applications that are experimentally tested and evaluated using the PowerCyber testbed and NEFTSec platform to accelerate the transition of state-of-the-art research works to the real-field deployments.

24 POWER TRANSMISSION AND DISTRIBUTION↗

COMPASS-FME Synoptic Sites Level 2 Sensor Data v2-1

This is the version 2-1 Level 2 (L2) data release for COMPASS-FME environmental sensors located at our synoptic field sites. COMPASS-FME is studying sites in two distinct regions, the Chesapeake Bay and the Western Lake Erie Basin. We established the network at seven "synoptic" (observational) sites along the Chesapeake Bay and Lake Erie coastlines, collectively generating over three million observations per month, to track and comprehend environmental changes where land and water intersect. Additionally, the two regions provide an interesting contrast of saltwater and freshwater coasts that allow us to differentiate the impacts of inundation and coastal water chemistries in two nationally important coastal systems. Level 2 (L2) data consist of sensor observations from the COMPASS-FME synoptic sites, TEMPEST, and DELUGE. Compared to the L1 data, these are more consistent (always 15-minute timestamps for the entire year); better QA/QC’d (out of bounds, out of service, and extreme outlier values are removed); and more complete, with a gap-filled time series available alongside the main observations, and additional derived (calculated) variables. L2 data are intended to be rapidly and easily usable in analyses and simulations. However, algorithmic outlier identification always carries the risk of removing valid data, and Level 1 data may be more suitable for analyses that focus on variability or extreme events. This dataset includes: - An overall dataset README file that describes the current version, gives citation and contact information, etc. - Site- and year-specific folders, each holding variable-specific Parquet (a high performance, space efficient format; see https://parquet.apache.org) data files for each site and plot in that year. - Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, detailed flood times, as well as a general description of the site. - Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are reported every 15 minutes. Data files are in Apache Parquet, a high performance, space efficient format for tabular data. These files can be read using R's `arrow` package (https://arrow.apache.org/docs/r/), with similar tools available in other languages. Please see v2-1 L2 Sensor Package QStart.pdf for detailed information on data package structure, temporal coverage, and versioning.

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATU↗

Module Testing Procedures and Results for the CMS Phase-2 Outer Tracker Upgrade at Fermilab

The High-Luminosity LHC (HL-LHC) will operate at significantly increased luminosities and is expected to deliver about 3000 $fb^{-1}$ of proton-proton collision data at $\sqrt{s}=14$ TeV over a decade of operation. To maintain efficient tracking and triggering performance under high pileup and radiation conditions, the CMS experiment is upgrading its tracking detector for Phase-2 operations. The upgraded Outer Tracker (OT) will consist of Pixel-Strip (PS) and Strip-Strip (2S) silicon modules capable of providing tracking information to the Level-1 trigger at 40 MHz. Production and qualification of OT modules have been ongoing for about one year across several assembly and testing centers in the US, Europe, India, and Pakistan, requiring extensive testing to ensure stable operation in the HL-LHC environment. Fermilab is responsible for the production and testing of a significant fraction of the OT modules. The testing activities include IV characterization of silicon sensors, noise and pedestal measurements, verification of communication between module components, and burn-in studies using cold-box systems operated under controlled thermal conditions. Results from module testing and qualification studies performed during production will be presented.

Baradia, Sweta [UC, Davis (main)]↗

Water Metering Best Practices

These best practices provide technical information to select the appropriate water meters on buildings that have been identified and to understand how data can be used and analyzed to improve water management. The guidance focuses on the installation of advanced meters and includes a process that directs agencies on how to prioritize their buildings for water meters. The process centers on metering water-intensive building types.

42 ENGINEERING↗

Real-time structural motif searching in proteins using an inverted index strategy

Biochemical and biological functions of proteins are the product of both the overall fold of the polypeptide chain, and, typically, structural motifs made up of smaller numbers of amino acids constituting a catalytic center or a binding site that may be remote from one another in amino acid sequence. Detection of such structural motifs can provide valuable insights into the function(s) of previously uncharacterized proteins. Technically, this remains an extremely challenging problem because of the size of the Protein Data Bank (PDB) archive. Existing methods depend on a clustering by sequence similarity and can be computationally slow. We have developed a new approach that uses an inverted index strategy capable of analyzing >170,000 PDB structures with unmatched speed. The efficiency of the inverted index method depends critically on identifying the small number of structures containing the query motif and ignoring most of the structures that are irrelevant. Our approach (implemented at motif.rcsb.org ) enables real-time retrieval and superposition of structural motifs, either extracted from a reference structure or uploaded by the user. Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids.

59 BASIC BIOLOGICAL SCIENCES↗

New Architecture to Support Integration and Processing of Seismic Data from Heterogeneous Sources

The Geophysical Monitoring Program (GMP) at Lawrence Livermore National Lab (LLNL) maintains a database and supporting infrastructure for geophysical data used in support of the Nuclear Detonation Detection mission. This database includes data from multiple sources, many of which do not distribute data to the public or for which there is no automated means of access. For example, Figure 1 shows (left) the distribution of waveform data in our database by source. The Incorporated Research Institutions for Seismology Data Management Center (IRISDMC) is our major source of waveform data and those data may be retrieved at will using the Federated Digital Seismograph Networks FDSN web Application Programming Interface (API). However, the next 6 most important sources of waveform data have no or only limited automated access to waveforms. As Figure 1 (right) shows, it is very common for waveform records associate with an event in our database to come from two or more sources, and in some cases data come from 10 sources. This diversity of data sources drives our need for efficient and correct integration of metadata, parametric data, and waveform data.

58 GEOSCIENCES↗

Transfer Factors for the FRMAC Assessment Manual and Turbo FRMAC to Improve Radiological Dose Assessment

The Turbo FRMAC analysis tool is used to perform complex calculations to quickly evaluate radiological consequences and aid in decision making during an emergency response by assessing impacts to the public, workers, and the food supply. Turbo FRMAC calculations are based on methods established by the Federal Radiological Monitoring and Assessment Center (FRMAC). To be able to assess impacts, input data called transfer factors that describe radionuclide uptake by local plants and animals are required. During the code application exercises in late 2016, identifying, finding, and validating nonstandard transfer factors proved to be time consuming and diverted the teams’ activity away from other critical tasks. As a result, a task was undertaken to dramatically expand the list of available transfer factors (food and non-food) and incorporate these factors into Turbo FRMAC. This will ultimately result in improved efficiency of the assessment team to perform calculations during times when the FRMAC is activated and provide more defensible, vetted data from which to calculate results. As a result of these and subsequent exercises, transfer factors were needed for the following items: bell peppers, Christmas tree, deer, flowers, fresh cucumbers, tomatoes, grapefruit, lichens, mushrooms, oranges, snap beans, squash, strawberries, sugarcane for sugar and seed, sweet corn, tea, tobacco, tree bark, and watermelon. To expand the applicability of the information tables, generic transfer data were also provided for common categories and recommendations were made for expanding the list of chemicals based on chemical similarity. The data presented in this report were compiled from recent literature with most of the data encompassing the period from 2000 to 2018. The following radionuclides were targeted during the literature search: elements associated with reactor accidents or nuclear detonations (Sr 89/90, Cs 134/137, Ce 141/144, Ru 103/106, I 129/131/133, Pu 238/239, Am 241, Zr 95, and Nb 95) and elements associated with industrial accidents or dirty bombs (Ir 192 and Co 60). Data from other elements were evaluated if they were identified during the literature search. In addition, reports were evaluated that were recommended by the research consultants. For each plant or animal transfer factor, the goal was to determine the geometric mean, the geometric standard deviation, the minimum, the maximum, and the number of measurements used. If only one measurement was available that was presented as the mean. Concentration ratios with large geometric standard deviations (GSDs) were generally the result of a paucity of measurements or a few disparate measurements. Measurement disparity was observed for data from different soil types. The geometric mean (GM) is a good reference value for planning and responses purposes, but the location-specific concentrations are unlikely to be similar to the model results. Recommendations for further work include: segregating the data to reflect the influence of soil type, developing approaches to incorporate animal data based on aggregated transfer measurements, and including data for foliar deposition on plants.

61 RADIATION PROTECTION AND DOSIMETRY↗

The role of quantum computing in advancing scientific high-performance computing: A perspective from the ADAC institute

Quantum computing (QC) has gained significant attention over the past two decades due to its potential for speeding up classically demanding tasks. This transition from an academic focus to a thriving commercial sector is reflected in substantial global investments. While advancements in qubit counts and functionalities continue at a rapid pace, current quantum systems still lack the scalability for practical applications, facing challenges such as too high error rates and limited coherence times. Here, this perspective paper examines the relationship between QC and high-performance computing (HPC), highlighting their complementary roles in enhancing computational efficiency. It is widely acknowledged that even fully error-corrected QC will not be suited for all computational tasks. Rather, future compute infrastructures are anticipated to employ quantum acceleration within hybrid systems that integrate HPC and QC. While QC can enhance classical computing, traditional HPC remains essential for maximizing quantum acceleration. This integration is a priority for supercomputing centers and companies, sparking innovation to address the challenges of merging these technologies. The novelty of this work lies in its unique perspective, reflecting the collective insights of the Accelerated Data Analytics and Computing (ADAC) Institute, a global consortium of over 20 leading HPC centers. Recognizing the growing importance of QC, ADAC established a Quantum Computing Working Group in 2023 to foster collaboration and knowledge-sharing among its members. This paper synthesizes insights from the group’s collaborative efforts and incorporates findings from a member survey that captures shared experiences, ongoing projects, and strategic directions. By outlining the current landscape and challenges of QC integration into HPC ecosystems, this work offers HPC specialists practical and forward-looking guidance on the opportunities and implications of QC in computationally intensive endeavors.

Accelerated Data Analytics and↗

22 Ne Phase Separation as a Solution to the Ultramassive White Dwarf Cooling Anomaly

The precise astrometric measurements of the Gaia Data Release 2 have opened the door to detailed tests of the predictions of white dwarf cooling models. Significant discrepancies between theory and observations have been identified, the most striking affecting ultramassive white dwarfs. Cheng et al. found that a small fraction of white dwarfs on the so-called Q branch must experience an extra cooling delay of ~8 Gyr not predicted by current models. 22 Ne phase separation in a crystallizing C/O white dwarf can lead to a distillation process that efficiently transports 22 Ne toward its center, thereby releasing a considerable amount of gravitational energy. Here, using state-of-the-art Monte Carlo simulations, we show that this mechanism can largely resolve the ultramassive cooling anomaly if the delayed population consists of white dwarfs with moderately above-average 22 Ne abundances. We also argue that 22 Ne phase separation can account for the smaller cooling delay currently missing for models of white dwarfs with more standard compositions.

79 ASTRONOMY AND ASTROPHYSICS↗

Condensed Phase Water Molecular Multipole Moments from Deep Neural Network Models Trained on Ab Initio Simulation Data

Ionic solvation phenomena in liquids involve intense interactions in the inner solvation shell. For interactions beyond the first shell, the ion–solvent interaction energies result from the sum of many smaller-magnitude contributions that can still include polarization effects. Deep neural network (DNN) methods have recently found wide application in developing efficient molecular models that maintain near-quantum accuracy. In this work, we extend the DeePMD-kit code to produce accurate molecular multipole moments in the bulk and near interfaces. The new method is validated by comparing the DNN moments with those generated by ab initio simulations. The moments are used to compute the electrostatic potential at the center of a molecular-sized hydrophobic cavity in water. The results show that the fields produced by the DNN models are in quantitative agreement with the AIMD-derived values. These efficient methods will open the door to more accurate solvation models for large solutes such as proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluating HPC Scheduling Strategies for Urgent Workloads

Scientific computing centers increasingly face workloads with diverse urgency requirements, driven by applications that demand rapid or even immediate execution. Appropriately configured scheduling policies can significantly improve both user satisfaction and overall cluster utilization. In this work, we present a systematic analysis of scheduler configurations under scenarios where a fraction of jobs have urgent computing needs. We evaluate multiple job scheduling simulators, develop a lightweight job-submission emulation framework, and create tools to analyze and visualize the resulting scheduling data. Our study identifies key trade-offs between responsiveness, fairness, and efficiency, and offers a set of practical scheduling configurations (particularly for Slurm) that can be tailored to HPC environments supporting mixed-urgency workloads.

Maheshwari, Ketan [ORNL] (ORCID:000000033800662X)↗