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At least 1,261 records · Page 70

Atlas of putative minima and low-lying energy networks of water clusters n = 3 - 25

We report a database consisting of the putative minima and ~3.2 million local minima lying within 5 kcal/mol from the putative minima for water clusters of sizes n = 3 – 25 using an improved version of the Monte Carlo Temperature Basin Paving (MCTBP) global optimization procedure in conjunction with the ab-initio based, flexible, polarizable Thole-Type Model (TTM2.1-F, version 2.1) interaction potential for water. Several of the low-lying structures, as well as lowlying penta-coordinated water networks obtained with the TTM2.1-F potential, were further refined at the Møller-Plesset second order perturbation MP2/aug-cc-pVTZ level of theory. In total, we have identified 3,138,303 networks corresponding to local minima of the clusters n = 3 – 25, whose Cartesian coordinates and relative energies can be obtained from the webpage https://sites.uw.edu/wdbase/. Networks containing penta-coordinated water molecules start to appear at n = 11 and, quite surprisingly, are energetically close (within 1 – 3 kcal/mol) to the putative minima, a fact that has been confirmed from the MP2 calculations. This large database of water cluster minima spanning quite dissimilar hydrogen bonding networks is expected to influence the development and assessment of the accuracy of interaction potentials for water as well as lower scaling electronic structure methods (such as different density functionals). Furthermore, it can also be used in conjunction with data science approaches (including but no limited to neural networks, machine and deep learning) to understand the properties of water, nature’s most important substance.

Rakshit, Avijit↗

Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

We introduce a database (HAB11) of electronic coupling matrix elements (H{sub ab}) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute H{sub ab} values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

74 ATOMIC AND MOLECULAR PHYSICS↗

Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes

ABSTRACT Mucoromycota fungi and their Mollicutes-related endobacteria (MRE) are an ideal system for studying bacterial–fungal interactions and evolution due to the long-term and intimate nature of their interactions. However, methods for detecting MRE face specific challenges due to the poor representation of MRE in sequencing databases coupled with the high sequence divergence of their genomes, making traditional similarity searches unreliable. This has precluded estimations on the diversity of MRE associated with Mucoromycota. To determine the prevalence of previously undetected MRE in fungal genome sequences, we scanned 389 Mucoromycota genome assemblies available from the National Center for Biotechnology Information for the presence of MRE sequences using publicly available tools to map contigs from fungal assemblies to publicly available MRE genomes. We demonstrate a higher diversity of MRE genomes than previously described in Mucoromycota and a lack of cophylogeny between MRE and the majority of their fungal hosts. This supports the late invasion hypothesis regarding MRE acquisition across most of the examined fungal families. In contrast with other Mucoromycota lineages, MRE from the Gigasporaceae displayed some degree of cophylogeny with their hosts, which may indicate that horizontal transmission is restricted between members of this family or that transmission is strictly vertical. These results underscore the need for a refined process to capture sequencing data from potential fungal endosymbionts to discern their evolution and transmission. Screens of fungal genomes for MRE can help improve the quality of fungal genome assemblies while identifying new MRE lineages to further test hypotheses on their origin and evolution. IMPORTANCE Mollicutes-related endobacteria (MRE) are obligate intracellular bacteria found within Mucoromycota fungi. Despite their frequent detection, MRE roles in host functioning are still unknown. Comparative genomic investigations can improve our understanding of the impact of MRE on their fungal hosts by identifying similarities and differences in MRE genome evolution. However, MRE genomes have only been assembled from a small fraction of Mucoromycota hosts. Here, we demonstrate that MRE can be present yet undetected in publicly available Mucoromycota genome assemblies. We use these newfound sequences to assess the broader diversity of MRE and their phylogenetic relationships with respect to their hosts. We demonstrate that publicly available tools can be used to extract novel MRE sequences from assembled fungal genomes leading to insights on MRE evolution. This work contributes to a greater understanding of the fungal microbiome, which is crucial to improving knowledge on the dynamics and impacts of fungi in microbial ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

Database to Enable Facial Analysis for Driving Studies (DEFADS)

Naturalistic Driving Studies (NDS) collect and utilize data on drivers in real-world environments in instrumented vehicles. A common problem with such studies is driver privacy. In this work we collected a dataset of 77 human subjects performing scripted driving-related activities. We used three camera systems for the collection, including two high-resolution webcam devices as well as a third system from an actual NDS (the Second Strategic Highway Research Project, or SHRP2). This report covers the data collection process and summarizes the dataset, which will be made publicly available to researchers under a data usage license.

97 MATHEMATICS AND COMPUTING↗

Functional traits driving species role in the structure of terrestrial vertebrate scavenger networks

Abstract Species assemblages often have a non‐random nested organization, which in vertebrate scavenger (carrion‐consuming) assemblages is thought to be driven by facilitation in competitive environments. However, not all scavenger species play the same role in maintaining assemblage structure, as some species are obligate scavengers (i.e., vultures) and others are facultative, scavenging opportunistically. We used a database with 177 vertebrate scavenger species from 53 assemblages in 22 countries across five continents to identify which functional traits of scavenger species are key to maintaining the scavenging network structure. We used network analyses to relate ten traits hypothesized to affect assemblage structure with the “role” of each species in the scavenging assemblage in which it appeared. We characterized the role of a species in terms of both the proportion of monitored carcasses on which that species scavenged, or scavenging breadth (i.e., the species “normalized degree”), and the role of that species in the nested structure of the assemblage (i.e., the species “paired nested degree”), therefore identifying possible facilitative interactions among species. We found that species with high olfactory acuity, social foragers, and obligate scavengers had the widest scavenging breadth. We also found that social foragers had a large paired nested degree in scavenger assemblages, probably because their presence is easier to detect by other species to signal carcass occurrence. Our study highlights differences in the functional roles of scavenger species and can be used to identify key species for targeted conservation to maintain the ecological function of scavenger assemblages.

54 ENVIRONMENTAL SCIENCES↗

Emissions implications of downscaled electricity generation scenarios for the western United States

This study explores how emissions from electricity generation in the Western Interconnection region of the U.S. might respond in circa 2030 to contrasting scenarios for fuel prices and greenhouse gas (GHG) emissions fees. We examine spatial and temporal variations in generation mix across the region and year using the PLEXOS unit commitment and dispatch model with a production cost model database adapted from the Western Electricity Coordinating Council. Emissions estimates are computed by combining the dispatch model results with unit-specific, emissions-load relationships. Wind energy displaces natural gas and coal in scenarios with relatively expensive natural gas or with GHG fees. Correspondingly, annual emissions of NOx, SO2, and CO2 are reduced by 20-40% in these cases. NOx emissions, which are a concern as a precursor of ground-level ozone, are relatively high and consistent across scenarios during summer, when peak electricity loads occur and wind resources in the region are comparatively weak. Accounting for the difference in start-up versus stabilized NOx emissions rates for natural gas plants had little impact on region-wide emissions estimates due to the dominant contribution from coal-fired plants, but would be more important in the vicinity of the natural gas units.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Post-landing major element quantification using SuperCam laser induced breakdown spectroscopy

The SuperCam instrument on the Perseverance Mars 2020 rover uses a pulsed 1064 nm laser to ablate targets at a distance and conduct laser induced breakdown spectroscopy (LIBS) by analyzing the light from the resulting plasma. SuperCam LIBS spectra are preprocessed to remove ambient light, noise, and the continuum signal present in LIBS observations. Prior to quantification, spectra are masked to remove noisier spectrometer regions and spectra are normalized to minimize signal fluctuations and effects of target distance. In some cases, the spectra are also standardized or binned prior to quantification. To determine quantitative elemental compositions of diverse geologic materials at Jezero crater, Mars, we use a suite of 1198 laboratory spectra of 334 well-characterized reference samples. The samples were selected to span a wide range of compositions and include typical silicate rocks, pure minerals (e.g., silicates, sulfates, carbonates, oxides), more unusual compositions (e.g., Mn ore and sodalite), and replicates of the sintered SuperCam calibration targets (SCCTs) onboard the rover. For each major element (SiO 2 , TiO 2 , Al 2 O 3 , FeO T , MgO, CaO, Na 2 O, K 2 O), the database was subdivided into five “folds” with similar distributions of the element of interest. One fold was held out as an independent test set, and the remaining four folds were used to optimize multivariate regression models relating the spectrum to the composition. We considered a variety of models, and selected several for further investigation for each element, based primarily on the root mean squared error of prediction (RMSEP) on the test set, when analyzed at 3 m. In cases with several models of comparable performance at 3 m, we incorporated the SCCT performance at different distances to choose the preferred model. Shortly after landing on Mars and collecting initial spectra of geologic targets, we selected one model per element. Subsequently, with additional data from geologic targets, some models were revised to ensure results that are more consistent with geochemical constraints. The calibration discussed here is a snapshot of an ongoing effort to deliver the most accurate chemical compositions with SuperCam LIBS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Constructing a Tandem Mass Spectral Library for Forensic Ricin Identification

Ricin, a protein found in castor seeds, is a lethal toxin that is designated as a category 2 select agent. Because castor seeds are easy to obtain and the toxin can be easily extracted, cases of attempted ricin poisoning are relatively common. A shotgun proteomics method for ricin identification has recently been developed (manuscript in preparation), in which ricin peptides are identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by proteomics database search, and peptide-spectrum matches are verified and compared to standard spectra by a human expert. To make this process more reproducible, objective, and high-throughput, we have created a ricin spectral library for peptide identification to supplement the human review step. To construct these spectral libraries, two pure ricin samples (from a proposed standard reference material) and crude castor seed extracts were digested with trypsin and analyzed using a standard shotgun LC-MS/MS protocol. Spectral libraries were created from the filtered search results from four database search tools. The library was then used in a search using SpectraST on samples from castor seeds. Analysis showed that the spectral library search resulted in more peptides identified from crude castor seed samples compared to MS-GF+ and Sequest plus Percolator. These results suggest that computational comparison of putative ricin peptide spectra to library spectra can be an effective method of confirming the presence of ricin, and that spectral library search may be suitable to augment the more manual and subjective aspects of the currently recommended human expert review.

Spectral Library, Ricin, forensic, proteomic↗

Drivers of Future Physical Water Scarcity and Its Economic Impacts in Latin America and the Caribbean

Future water scarcity is a global concern with significant impacts on the energy, water, and land (EWL) sectors. Countries in Latin America and the Caribbean (LAC) are significant producers of agricultural goods consumed around the world, so disruptions resulting from land and water scarcity in LAC are a source of global supply chain risk. Understanding where water scarcity in LAC could occur and what could drive that scarcity to emerge is critical for strategic resource management and planning, both regionally and globally. Assessing future water scarcity impacts in LAC is challenging given the multisector dynamic interactions among the EWL sectors and the multiple uncertainties acting across different spatial scales. We use scenario discovery to explore the drivers of future water scarcity, considering assumptions related to climate, socioeconomics, and the EWL sectors. Understanding what factors drive uncertainty across outcomes can help stakeholders in targeting long-term solutions and future data collection efforts. To illuminate these dynamics, we use a database consisting of a large ensemble of scenarios representing diverse worlds simulated using the Global Change Analysis Model. We quantify future water scarcity and its economic impacts across the scenarios using three metrics: (1) physical water scarcity, (2) water price, and (3) crop profit. We find that physical water scarcity and water price are driven primarily by reservoir storage capacity assumptions, highlighting the importance of strategic water infrastructure development in maintaining future water availability and accessibility. Crop profit is driven by a combination of water supply and demand assumptions, which emphasizes the complex nature of EWL multisector dynamics. While most of LAC is poised to have abundant land and water resources available for development, water basins in Mexico and along the Pacific coast of South America experience high levels of severity and uncertainty across the future scenarios for at least one of the metrics. We find that the drivers of extreme scarcity vary spatially and across the metrics, further highlighting the heterogeneity of the region and the importance of considering multiple metrics to assess water scarcity vulnerability.

54 ENVIRONMENTAL SCIENCES↗

ExpoKids: An R-based tool for characterizing aggregate chemical exposure during childhood

Background: Aggregate exposure, the combined exposures to a single chemical from all pathways, is a critical children’s health issue. Objective: The primary objective is to develop a tool to illustrate potential differences in aggregate exposure at various childhood lifestages and the adult lifestage. Methods: We developed ExpoKids (an R-based tool) using oral exposure estimates across lifestages generated by US EPA’s Exposure Factors Interactive Resource for Scenarios Tool (ExpoFIRST). Results: ExpoKids is applied to illustrate aggregate oral exposure, for ten media, as average daily doses (ADD) and lifetime average daily doses (LADD) in five graphs organized across seven postnatal childhood lifestages and the adult lifestage. This data visualization tool conveys ExpoFIRST findings, from available exposure data, to highlight the relative contributions of media and lifestages to chemical exposure. To evaluate the effectiveness of ExpoKids, three chemical case examples (di[2-ethylhexyl] phthalate [DEHP], manganese, and endosulfan) were explored. Data available from the published literature and databases for each case example were used to explore research questions regarding media and lifestage contributions to aggregate exposure. Significance: These illustrative case examples demonstrate ExpoKids’ versatile application to explore a diverse set of children’s health risk assessment and management questions by visually depicting specific media and lifestage contributions to aggregate exposure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Meta-analyses of studies of the human microbiota

Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the microbiota are based on the same bacterial 16S ribosomal RNA (rRNA) gene target, they can, in principle, be compared to determine the relative importance of different disease/physiologic/developmental states. However, differences in experimental protocols used may produce variation that outweighs biological differences. By comparing 16S rRNA gene sequences generated from diverse studies of the human microbiota using the QIIME database, we found that variation in composition of the microbiota across different body sites was consistently larger than technical variability across studies. However, samples from different studies of the Western adult fecal microbiota generally clustered by study, and the 16S rRNA target region, DNA extraction technique, and sequencing platform produced systematic biases in observed diversity that could obscure biologically meaningful compositional differences. In contrast, systematic compositional differences in the fecal microbiota that occurred with age and between Western and more agrarian cultures were great enough to outweigh technical variation. Furthermore, individuals with ileal Crohn’s disease and in their third trimester of pregnancy often resembled infants from different studies more than controls from the same study, indicating parallel compositional attributes of these distinct developmental/physiological/disease states. Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.

59 BASIC BIOLOGICAL SCIENCES↗

Computational investigation of inverse Heusler compounds for spintronics applications

In this work, first-principles calculations of the electronic structure, magnetism, and structural stability of inverse Heusler compounds with the chemical formula X 2 YZ are presented and discussed with a goal of identifying compounds of interest for spintronics. Compounds for which the number of electrons per atom for Y exceed that for X and for which X and Y are each one of the 3d elements, Sc-Zn, and Z is one of the group IIIA-VA elements: Al, Ga, In, Si, Ge, Sn, P, As, or Sb were considered. The formation energy per atom of each compound was calculated. By comparing our calculated formation energies to those calculated for phases in the inorganic crystal structure database of observed phases, we estimate that inverse Heuslers with formation energies within 0.052 eV/atom of the calculated convex hull are reasonably likely to be synthesizable in equilibrium. The observed trends in the formation energy and relative structural stability as the X, Y, and Z elements vary are described. In addition to the Slater-Pauling gap after 12 states per formula unit in one of the spin channels, inverse Heusler phases often have gaps after 9 states or 14 states. We describe the origin and occurrence of these gaps. We identify 14 inverse Heusler semiconductors, 51 half-metals, and 50 near-half-metals with negative formation energy. Additonally, our calculations predict 4 half-metals and 6 near-half-metals to lie close to the respective convex hull of stable phases, and thus may be experimentally realized under suitable synthesis conditions, resulting in potential candidates for future spintronics applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Strategic Plan for Nuclear Energy -- Knowledge Base for Advanced Modeling and Simulation (NE-KAMS)

The Nuclear Energy Computational Fluid Dynamics Advanced Modeling and Simulation (NE-CAMS) system is being developed at the Idaho National Laboratory (INL) in collaboration with Bettis Laboratory, Sandia National Laboratory (SNL), Argonne National Laboratory (ANL), Utah State University (USU), and other interested parties with the objective of developing and implementing a comprehensive and readily accessible data and information management system for computational fluid dynamics (CFD) verification and validation (V&V) in support of nuclear energy systems design and safety analysis. The two key objectives of the NE-CAMS effort are to identify, collect, assess, store and maintain high resolution and high quality experimental data and related expert knowledge (metadata) for use in CFD V&V assessments specific to the nuclear energy field and to establish a working relationship with the U.S. Nuclear Regulatory Commission (NRC) to develop a CFD V&V database, including benchmark cases, that addresses and supports the associated NRC regulations and policies on the use of CFD analysis. In particular, the NE-CAMS system will support the Department of Energy Office of Nuclear Energy Advanced Modeling and Simulation (NEAMS) Program, which aims to develop and deploy advanced modeling and simulation methods and computational tools for reliable numerical simulation of nuclear reactor systems for design and safety analysis. Primary NE-CAMS Elements There are four primary elements of the NE-CAMS knowledge base designed to support computer modeling and simulation in the nuclear energy arena as listed below. Element 1. The database will contain experimental data that can be used for CFD validation that is relevant to nuclear reactor and plant processes, particularly those important to the nuclear industry and the NRC. Element 2. Qualification standards for data evaluation and classification will be incorporated and applied such that validation data sets will result in well-defined, well-characterized data. Element 3. Standards will be established for the design and operation of experiments for the generation of new validation data sets that are to be submitted to NE-CAMS that addresses the completeness and characterization of the dataset. Element 4. Standards will be developed for performing verification and validation (V&V) to establish confidence levels in CFD analyses of nuclear reactor processes; such processes will be acceptable and recognized by both CFD experts and the NRC.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Air Leakage of US Homes: Regression Analysis and Improvements from Retrofit

LBNL Residential Diagnostics Database (ResDB) contains blower door measurements and other diagnostic test results of homes in United States. Of these, approximately 134,000 single-family detached homes have sufficient information for the analysis of air leakage in relation to a number of housing characteristics. We performed regression analysis to consider the correlation between normalized leakage and a number of explanatory variables: IECC climate zone, floor area, height, year built, foundation type, duct location, and other characteristics. The regression model explains 68% of the observed variability in normalized leakage. ResDB also contains the before and after retrofit air leakage measurements of approximately 23,000 homes that participated in weatherization assistant programs (WAPs) or residential energy efficiency programs. The two types of programs achieve rather similar reductions in normalized leakage: 30% for WAPs and 20% for other energy programs.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

AGC-2 Irradiation Report

The Next Generation Nuclear Plant (NGNP) will be a helium-cooled, very high temperature reactor (VHTR) with a large graphite core. In past applications, graphite has been used effectively as a structural and moderator material in both research and commercial high temperature gas cooled reactor (HTGR) designs.[ , ] Nuclear graphite H 451, used previously in the United States for nuclear reactor graphite components, is no longer available. New nuclear graphites have been developed and are considered suitable candidates for the new NGNP reactor design. To support the design and licensing of NGNP core components within a commercial reactor, a complete properties database must be developed for these current grades of graphite. Quantitative data on in service material performance are required for the physical, mechanical, and thermal properties of each graphite grade with a specific emphasis on data related to the life limiting effects of irradiation creep on key physical properties of the NGNP candidate graphites. Based on experience with previous graphite core components, the phenomenon of irradiation induced creep within the graphite has been shown to be critical to the total useful lifetime of graphite components. Irradiation induced creep occurs under the simultaneous application of high temperatures, neutron irradiation, and applied stresses within the graphite components. Significant internal stresses within the graphite components can result from a second phenomenon—irradiation induced dimensional change. In this case, the graphite physically changes i.e., first shrinking and then expanding with increasing neutron dose. This disparity in material volume change can induce significant internal stresses within graphite components. Irradiation induced creep relaxes these large internal stresses, thus reducing the risk of crack formation and component failure. Obviously, higher irradiation creep levels tend to relieve more internal stress, thus allowing the components longer useful lifetimes within the core. Determining the irradiation creep rates of nuclear grade graphites is critical for determining the useful lifetime of graphite components and is a major component of the Advanced Graphite Creep (AGC) experiment.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Geant4 Material Definition

In Geant4, materials are defined using elements (G4Element) and isotopes (G4Isotope), supporting both single-element compositions and multi-element molecules or mixtures (by mass fraction). Each material is characterized by a mandatory density condition and optional parameters, such as state, temperature, and pressure. To simplify material definition and ensure accuracy, the G4NistManager is recommended for retrieving elements and materials from the NIST Material Database. These features make material specification in Geant4 flexible, efficient and consistent for describing complex detector geometry descriptions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

FY 2026 Midyear Report: Seismic Monitoring of Underground Vibration Sources Using Distributed Acoustic Sensing and Seismometers

Safeguards-relevant temporal changes in underground facilities can be observed using geophysical monitoring techniques. Seismic waves, in particular, provide valuable insights into subsurface activities and can serve as an important tool for detecting anomalous events that may indicate containment breaches at geological repositories. This midyear report summarizes ongoing efforts to automatically and rapidly detect and locate anomalous vibration signals that could be indicative of potential containment breaches. Previous work during FY25 focused on compiling continuous seismic datasets from two underground sites and developing a database of continuous waveforms and ground-truth event data derived from multiple sensing modalities. Building on this foundation, we are adapting anomaly detection and geolocation algorithms to explore methods for monitoring underground activities using two relatively low-maintenance sensing technologies: a dense surface geophone array deployed at the Pleasant Gap mine in Pennsylvania, and a three-dimensional fiber-optic cable array for distributed acoustic sensing (DAS) installed in the subsurface at the Sanford Underground Research Facility (SURF) in South Dakota. This report summarizes work conducted during the first two quarters of FY26, during which we refined a dynamic power spectral density (PSD)-based detector, applied it independently to each geophone station, and then combined the per‑station detections with density-based spatial clustering of applications with noise (DBSCAN) to cluster events and produce spatial maps over a nine‑day interval. In addition, we outline plans for a field trial at the Waste Isolation Pilot Plant (WIPP) in New Mexico to compare traditional seismic monitoring approaches with DAS techniques and to evaluate the benefits of combined data analysis. Activities during the past two quarters have included the preparation and submission of a Field Test Plan to WIPP for approval, as well as submission to headquarters for review and feedback.

58 GEOSCIENCES↗