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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Anomalous Behavior in the Atomic Structure of Nb$^{3}$Sn under High Pressure

In the present study, the local atomic structure of a Nb3Sn superconductor sample has been probed by X-ray absorption fine structure (XAFS) as a function of hydrostatic pressure (from ambient up to 26 GPa) using a diamond anvil cell set-up. The analysis of the Nb-K edge extended X-ray absorption fine structure (EXAFS) data was carried out combining standard multi shell structural refinement and reverse Monte Carlo method to provide detailed in situ characterization of the pressure-induced evolution of the Nb local structure in Nb3Sn. The results highlight a complex evolution of Nb chains at the local atomic scale, with a peculiar correlated displacement of Nb–Nb and Nb–Nb–Nb configurations. Such a local effect appears related to anomalies evidenced by X-ray diffraction in other superconductors belonging to the same A15 crystallographic structure.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Fantastic Fits with fantasy of Active Galactic Nuclei Spectra: Exploring the Fe II Emission near the Hα Line

In this study, a refined approach for multicomponent fitting of active galactic nuclei (AGNs) spectra is presented utilizing the newly developed Python code Fully Automated pythoN Tool for AGN Spectra analYsis (fantasy). AGN spectra are modeled by simultaneously considering the underlying broken power-law continuum, predefined emission line lists, and an Fe II model, which is here extended to cover the wavelength range 3700–11000 Å. The Fe II model, founded solely on atomic data, effectively describes the extensive emission of the complex iron ion in the vicinity of the Hγ and Hβ lines, as well as near the Hα line, which was previously rarely studied. The proposed spectral fitting approach is tested on a sample of high-quality AGN spectra from the Sloan Digital Sky Survey Data Release 17. The results indicate that when Fe II emission is present near Hβ, it is also detected redward from Hα, potentially contaminating the broad Hα line wings and thus affecting the measurements of its flux and width. The production of Fe II emission is found to be strongly correlated with Eddington luminosity and appears to be controlled by a similar mechanism as the hydrogen Balmer lines. The study highlights the benefits of fitting type 1 AGN spectra with the fantasy code, pointing that it may be used as a robust tool for analyzing a large number of AGN spectra in the coming spectral surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

ℤ2 × ℤ2 Equivariant Quantum Neural Networks: Benchmarking against Classical Neural Networks

This paper presents a comparative analysis of the performance of Equivariant Quantum Neural Networks (EQNNs) and Quantum Neural Networks (QNNs), juxtaposed against their classical counterparts: Equivariant Neural Networks (ENNs) and Deep Neural Networks (DNNs). We evaluate the performance of each network with three two-dimensional toy examples for a binary classification task, focusing on model complexity (measured by the number of parameters) and the size of the training dataset. Our results show that the Z2×Z2 EQNN and the QNN provide superior performance for smaller parameter sets and modest training data samples.

Dong, Zhongtian (ORCID:0000000210003454)↗
DOE OSTI2025

Development of an ERT‐Based Framework for Bentonite Buffers Monitoring From Laboratory Tests: 1. Characterizing Thermal–Hydrological–Mechanical Processes

Abstract Bentonite clay is widely used in engineered barrier systems for the permanent disposal of high‐level radioactive waste due to its low permeability, high swelling capacity, and thermal stability. However, the complex thermal‐hydrological‐mechanical (THM) processes induced by heating from decaying radioactive waste and hydration from surrounding rock can lead to heterogeneous changes that are difficult to measure and predict. This study develops an Electrical Resistivity Tomography (ERT)‐based framework for monitoring THM processes, progressing from sample‐scale to bench‐scale tests, to inform field‐scale applications. Sample‐scale tests analyzed small bentonite samples under controlled variations in water content, temperature, and porosity to establish fundamental resistivity relationships. Bench‐scale tests involved larger bentonite columns subjected to heating (up to 200°C) and hydration under controlled pressure, simulating repository conditions. ERT measurements, complemented by X‐ray CT imaging, temperature monitoring, and tracing sensors, revealed coupled THM processes, such as hydration‐induced compression, swelling, and thermal gradients, leading to complex resistivity patterns. The results demonstrate the potential of ERT for capturing THM‐induced resistivity changes, though challenges remain in upscaling and quantitative analysis. This study evaluates laboratory test capabilities and proposes future improvements for understanding THM‐induced resistivity responses. A conceptual framework for ERT implementation in field‐scale monitoring is presented, synthesizing findings from both scales and exploring how ERT data can inform long‐term modeling and reduce prediction uncertainties. Overall, this ERT‐based framework offers a robust method for monitoring bentonite buffers, aiding in early issue detection and supporting the safe long‐term disposal of radioactive waste in geological repositories, while highlighting the need for future development. Plain Language Summary Bentonite clay is crucial in engineered barrier systems (EBS) for containing high‐level radioactive waste due to its ability to absorb water, swell, seal and remain stable under high temperatures. When bentonite absorbs water and heats up from radioactive decay, it experiences complex changes in its physical and mechanical properties. Understanding these changes is important for ensuring the long‐term safety and effectiveness of EBS. This study used Electrical Resistivity Tomography (ERT), a non‐invasive method that measures electrical conductivity to monitor these changes during laboratory experiments. The ERT data revealed significant variations in resistivity corresponding to changes in water content, temperature, and density, providing detailed spatial and temporal insights into the behavior of bentonite. These findings enhance our ability to predict the long‐term performance of bentonite barriers, ensuring the safe containment of radioactive waste. By improving our understanding of bentonite's behavior, this research supports the development of more reliable and effective barrier systems for radioactive waste disposal, protecting the environment and public health. Key Points ERT monitoring was employed to capture resistivity changes in bentonite during controlled heating and hydration experiments, providing insights into THM processes ERT data reveal significant resistivity changes correlated with water content, temperature, and mechanical effects, enhancing the understanding of THM dynamics in bentonite This study explores the potential of the framework for application in field‐scale EBS monitoring, emphasizing the need for integrating additional geophysical methods for comprehensive subsurface imaging

Chen, Hang↗
DOE OSTI2024

Realization of two-sublattice exchange physics in the triangular lattice compound Ba 3 Er(BO 3 ) 3

Geometric frustration commonly occurs in materials where magnetic rare-earth ions are arranged on a two-dimensional triangular lattice. These compounds have been gaining significant attention lately, as they hold the promise of revealing unique quantum states of matter. However, little attention has been devoted to cases where spin-$\frac{1}{2}$ rare-earth ions are substituted with ions exhibiting higher spin multiplicities. Here, we successfully synthesize high-quality single crystal samples of Ba 3 Er(BO 3 ) 3 , which is part of the family of triangular lattice compounds. In our experiments, conducted at extremely low temperatures (around 100 millikelvin), we observe two sublattice exchange interactions in Ba 3 Er(BO 3 ) 3 , resulting in the hexagonal lattice spins exhibiting a mixture of ferromagnetic and antiferromagnetic tendencies. Our theoretical analysis suggest that this behavior may be attributed to the distinct positions of magnetic ions within the crystal lattice. However, the presence of quantum effects adds an extra layer of complexity to our findings, calling for further exploration.

36 MATERIALS SCIENCE↗
DOE OSTI2021

The H I absorption zoo: JVLA extension to z ~ 0.4

Here, we present an H I 21 cm absorption study of a sample of 26 radio-loud active galactic nuclei (AGN) at 0.25 < z < 0.4 carried out with the Karl G. Jansky Very Large Array. Our aim was to study the rate of incidence of H I in different classes of radio AGN, the morphology and kinematics of the detected H I, and the nature of the interaction between the H I and the radio source at these redshifts. Our sample consists of 14 sources with sizes of up to tens of kpc and 12 compact sources (< a few kpc) in the radio-power range 10 25.7 W Hz –1 –10 26.5 W Hz –1 . We detect H I in five sources, corresponding to a detection rate of ~19%. Within the error bars, this agrees with the detection rate found at lower redshifts. We find that the rest-frame UV luminosities of most of the sources in the sample, including all the detections, are below the proposed threshold above which the H I is supposed to have been ionised. An analysis of the optical emission-line spectra of the sources shows that despite their high radio powers, about one-third of the sample, including two detections, are low-ionisation sources. The radio continuum emission from the sources detected in H I is unresolved at ~5 to 10 kpc scales in our observations, but shows extended structure on parsec scales. We analysed the H I 21 cm absorption spectra of the detections to understand the morphology and kinematics of H I. The absorption profiles are mostly complex with widths between the nulls ranging from ~60 km s –1 to 700 km s –1 . These detections also exhibit remarkably high H I column densities in the range ~10 21 cm –2 –10 22 cm –2 for T spin = 100 K and unit covering factor. Our modelling of the H I 21 cm absorption profiles suggests that in two sources the gas appears to be disturbed, and in three cases, including one with disturbed H I, the majority of the absorption is consistent with it arising from an H I disc. Despite the high radio power of our sources, we do not detect fast outflows. However, the optical emission lines in these detections show the presence of significantly disturbed gas in the nuclear regions in the form of very wide and highly blueshifted emission-line components. Since some of our detections are also low-ionisation AGN, it is quite possible that this disturbance is caused by the radio jets. Overall, our findings point towards a continuation of the low-z trends in the H I detection rate and the incidence of H I in radio AGN up to z ~ 0.4.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Towards resolving protein structures at the atomic scale using atom probe tomography

In the field of Structural Biology, Atom Probe Tomography (APT) is in the nascent stages of development wherein coarse-grained visuals of proteins have been captured. The characterization of organic samples or biomolecules through the technique is currently limited to the detection of a few dominant signatures. The problem of indecipherable characterization can inherently be traced back to multiple forms of technique-specific responses to organic samples and consequent triggers leading to organic-sample and sample-medium interactions. While it is possible for captured manifestations of protein reconstructions to seemingly appear intact from a basic visual purview, the parameter-protein associative responses throughout the structure as a direct consequence of the inherent workings of the technique (until harmonized with organic sample complexity and behavior) and field evaporation-based factors make non-aberrative atomic associations infeasible. The work focused on identifying and theorizing the (above stated and other) fundamental mechanisms that stronghold the study of intricate atomic to higher order associations in proteins through APT. Attempts at structure elucidation of the cryogenic sample under study, through indirect associations (and methods) based on other imaging techniques, further revealed the distinct and highly distortive nature at the atomic scale deterring structural tunability and thus characterization of APT based cryogenic samples under analysis. As a direct counter to the atomic scale characterization problem, by taking the experiment-specific uncertainties, and probable APT-centric organic sample-based variabilities into account, a basic result is extracted and presented. Through mass-spectrometric and computational analysis, specific individual amino acids (Sulfur-containing protein-bound amino acids) in proteins and aspects of protein structure (probable backbone fragments, partial sequence - partial backbone portions) have been identified and characterized. Under analysis considerations, a few of the simplest known and easily inferable segments that favor structural deteriorations in the reconstructions are stated. Additionally, to overcome technique-specific deterrents to the characterization of biomolecules in cryogenic sample medium, the development of a protein-labeling strategy tailored to APT is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Respirator Cartridge Performance on Mixed Vapors from Hanford Tank Headspaces and Exhausters - 20427

Between 2016 and 2018, the Hanford Tank Operations Contractor - Washington River Protection Solutions (WRPS) - conducted a series of tests of air-purifying respirator (APR) chemical cartridges commonly used at Hanford tank farms to determine the period of time for which the cartridges would provide adequate performance when used in APRs and powered-air-purifying respirators (PAPRs) to protect workers when exposed to a mixture of vapors exiting tank headspaces. Although cartridge manufacturers provide service life estimating tools for individual chemical compounds, the projected performance of these cartridges on complex vapor mixtures is not available, and the adequacy of APRs for tank farm applications represents an important workforce concern. The Occupational Safety and Health Administration identifies cartridge testing as a valid approach for establishing cartridge service life. The primary function of the WRPS Cartridge Test Program was to obtain objective data to determine service lives for the APR and PAPR cartridges used at Hanford tank farms. WRPS contracted with Pacific Northwest National Laboratory to analyze the test data and offer an independent analysis of and recommendations based on respirator cartridge performance. A total of 28 APR and 10 PAPR cartridge tests were conducted between 2016 and 2018 on 12 different tank headspaces and tank farm exhauster slipstreams. Two APR cartridges from SCOTT (now 3M) and two PAPR cartridges from MSA Safety, Inc. and 3M were evaluated using a cartridge testing system specifically designed to measure and monitor test conditions and sample cartridge inlet and outlet vapor streams for important chemical compounds. Testing focused on analysis of approximately 61 tank vapor chemicals of potential concern (COPCs) that have been previously detected in tank vapors at levels above 10% of their occupational exposure limits (OELs). Each test was conducted over 16 hours of run time. Evidence of chemical breakthrough was assessed by comparing inlet and outlet COPC concentrations over the duration of each test. The breakthrough threshold was normally defined as exceeding 10% of the compounds OEL at the cartridge outlet. Ammonia breakthrough was observed in a majority of the cartridge tests and occurred earlier than breakthrough of any other chemical compound. Several other COPCs did exhibit breakthrough behavior, including mercury, 1,3-butadiene, furan, 2,5 dihydrofuran, and N-nitrosodimethylamine (NDMA), but only in a very limited number of cartridge tests and only after ammonia breakthrough had occurred. In addition, tests results suggest that breakthrough of some of these COPCs may have been affected by competition with and breakthrough of other non-COPC organics, such as ethanol and acetone, with substantially lower toxicological hazard. Comparison of cartridge manufacturers' service life estimates with the experimentally derived breakthrough times indicates that manufacturers' estimates are generally conservative, even in the presence of the complex mixed vapor streams experienced in these tests. With consideration of appropriate safety margins, these results provide valuable insights on cartridge performance to inform industrial hygiene professionals in establishing appropriate cartridge change-out schedules for APR and PAPR use in the Hanford tank farms. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

A structured framework for predicting sustainable aviation fuel properties using liquid-phase FTIR and machine learning

Sustainable aviation fuels have the potential to improve efficiency, reduce emissions, and enhance energy security. To help identify viable sustainable aviation fuels and accelerate research, machine learning models have been developed to predict relevant physicochemical properties. However, many models have limited applicability, leverage data from complex analytical techniques with confined spectral ranges, or use feature decomposition methods that offer limited interpretability. Using liquid-phase Fourier Transform Infrared (FTIR) spectra, this study presents a structured method for creating accurate and interpretable property prediction models for neat molecules, aviation fuels, and blends. Liquid FTIR spectra can be collected quickly and consistently, offering high reliability, sensitivity, and component specificity using less than 2 ml of sample. The method first decomposes FTIR spectra into fundamental building blocks using non-negative matrix factorization (NMF) to enable scientific analysis of FTIR spectra attributes and fuel properties. The NMF features are then used to create five ensemble models for predicting final boiling point, flash point, freezing point, density at 15°C, and kinematic viscosity at -20°C. All models were trained using experimental property data from neat molecules, aviation fuels, and blends. The models accurately predict key properties across a broad range of neat molecules and representative fuels and blends, while enabling interpretation of relationships between compositional elements, such as functional groups or chemical classes, and their resulting properties. This demonstrates strong potential to support sustainable aviation fuel research and development. The models and data are available on an interactive web tool.

Fourier transform infrared spectroscopy↗
DOE OSTI2026

Dark Energy Survey year 6 results: Magnification modeling and its impact on galaxy clustering and galaxy-galaxy lensing cosmology

Gravitational lensing magnification alters the observed spatial distribution of galaxies and must be accounted for to prevent biases in cosmological probes of the large-scale structure. We investigate its effects on the Dark Energy Survey Year 6 galaxy clustering and galaxy-galaxy lensing analyses using the fiducial lens (position tracer) sample M ag L im++. Magnification bias is parameterized by a coefficient that describes the response of the number of selected objects per unlensed area element to a change in the lensing convergence. We quantify this coefficient using the BALROG synthetic source injection catalog to account for the complexity of the selection function, and compare these results with simplified estimates. The resulting values of the magnification coefficients for each redshift bin are [3.16 ± 0.08, 2.76 ± 0.21, 4.09 ± 0.15, 4.42 ± 0.16, 4.90 ± 0.29, 4.83 ± 0.25]. Relative to Year 3, this analysis provides more precise and accurate magnification bias estimates through a larger BALROG area and reweighting to better match the data properties. Here, the cosmological results are robust when tested against various magnification parameter prior choices and also when adding cross-clustering between lens redshift bins. Neglecting magnification, however, introduces significant systematic shifts: relative to the fiducial analysis with Gaussian priors centered on the BALROG -derived estimates, we observe shifts of 1.37σ in S 8 and -0.84σ in Ω m (with cosmic shear included: -0.61σ in S 8 and -0.71σ in Ω m ), in agreement with findings from simulated data, demonstrating that magnification must be modeled to avoid biases. Freeing the magnification bias in lens bin 2 leads to unphysical negative values, further justifying its exclusion from the fiducial Year 6 analysis.

Cosmological parameters↗
DOE OSTI2019

High-throughput quantitative analysis of phytohormones in sorghum leaf and root tissue by ultra-performance liquid chromatography-mass spectrometry

Plant development, growth, and adaptation to stress are regulated by phytohormones, which can influence physiology even at low concentrations. Phytohormones are chemically grouped according to both structure and function as auxins, cytokinins, abscisic acid, jasmonates, salicylates, gibberellins, and brassinosteroids, among others. This chemical diversity and requirement for highly sensitive detection in complex matrices create unique challenges for comprehensive phytohormone analysis. Here, we present a robust and efficient quantitative UPLC-MS/MS assay for 17 phytohormones, including jasmonates, salicylates, abscisic acid, gibberellins, cytokinins, and auxins. Using this assay, 12 phytohormones were detected and quantified in sorghum plant tissue without the need for solid phase extraction (SPE) or liquid-liquid extraction. Variation of phytohormone profiles was explored in both root and leaf tissues between three genotypes, harvested at two different developmental time points. The results highlight the importance of tissue type, sampling time, and genetic factors when designing experiments that involve phytohormone analysis of sorghum. This research lays the groundwork for future studies, which can combine phytohormone profiling with other datasets such as transcriptome, soil microbiome, genome, and metabolome data, to provide important functional information about adaptation to stress and other environmental variables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Automated Hybrid Variance Reduction on Advanced Architectures in the Shift Monte Carlo Code

Monte Carlo transport methods are the most accurate schemes for solving problems with complex energy and spatial features, but they come with a high computational cost. Although hybrid methods have enabled the use of Monte Carlo transport for a large class of problems, they still require significant computing resources. Modern multicore CPUs with large numbers of compute cores and graphical processing units (GPUs) provide opportunities to optimize the memory and run-time costs of hybrid Monte Carlo methods. This paper documents the development and analysis of three Monte Carlo transport algorithms that support hybrid transport using the consistent adjoint-driven importance sampling (CADIS) and forward-weighted CADIS methods in the Shift Monte Carlo code: history-based transport using static and dynamic threading on multicore CPUs and event-based transport enabling weight window tracking on GPUs. The results are shown for two challenging hybrid problems on the Frontier supercomputer at the Oak Ridge Leadership Computing Facility. The results show that all three methods yield good performance and enable solutions of difficult fixed-source transport problems in less than 2 min on 20 nodes of Frontier. Dynamic threading was observed to give up to 20% better scaling behavior than static threading. Moreover, the AMD Instinct 250X GPU was found to give 9 to 11 times greater throughput per graphics compute die than the best CPU performance. In conclusion, additional opportunities for optimization of hybrid transport on GPUs are discussed.

Denovo↗
DOE OSTI2023

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, can reveal the co-occurrence of microbes, providing a glimpse into the network of associations in these communities. However, the inference of networks from 16S data involves numerous steps, each requiring specific tools and parameter choices. Moreover, the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and identify the steps that contribute substantially to the variance. We further determine the tools and parameters that generate robust co-occurrence networks and develop consensus network algorithms based on benchmarks with mock and synthetic data sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows these default tools and parameters and can help explore the outcome of these combinations of choices on the inferred networks. We envisage that this pipeline could be used for integrating multiple data sets and generating comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes.

16S rRNA↗
DOE OSTI2026

Optimizing Cryo-Focused Pyrolysis GC/MS for Tracing Soil Organic Matter Across Diverse Ecosystems

The cycling of organic matter in terrestrial soils and sediments is central to a range of biogeochemical processes that regulate nutrient cycling, crop productivity, trace gas emissions, and contaminant transport. Pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) is a powerful tool for characterizing bulk soil organic matter (SOM) at the molecular level. In this study, we used a cryo-focused py-GC/MS system to analyze soil samples from seven diverse ecosystems: vernal pool, prairie pothole, temperate forest, tropical forest, tundra, wildfire-affected boreal forest, and grassland. We addressed a key bottleneck in molecular-level SOM characterization by developing an automated data analysis pipeline to optimize py-GC/MS and complementary evolved gas analysis/mass spectrometry (EGA/MS) methods, incorporating advanced tools for peak deconvolution, developing a custom compound class library, and implementing fragmentation spectrum-based molecular networking for the first time. This improved workflow was applied to soil samples from all seven ecosystems, including multiple depths and density fractions. Our findings demonstrate that ecosystem type plays a dominant role in shaping compositional differences in SOM. We also identified trends in the source of SOM compounds (e.g., microbial vs plantderived) across soil depth and density fractions, which are critical for understanding persistence and turnover of SOM. Our molecular networking analysis indicated that although many compounds are widespread across ecosystems, others are restricted to specific environments, such as wetlands. This underscores the utility of molecular-level data in elucidating the complexity of SOM composition and the environmental drivers that shape it. Such molecular-level insights can deepen our knowledge of biogeochemical SOM cycles.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Projected U.S. drought extremes through the twenty-first century with vapor pressure deficit

Global warming is expected to enhance drought extremes in the United States throughout the twenty-first century. Projecting these changes can be complex in regions with large variability in atmospheric and soil moisture on small spatial scales. Vapor Pressure Deficit (VPD) is a valuable measure of evaporative demand as moisture moves from the surface into the atmosphere and a dynamic measure of drought. Here, VPD is used to identify short-term drought with the Standardized VPD Drought Index (SVDI); and used to characterize future extreme droughts using grid dependent stationary and non-stationary generalized extreme value (GEV) models, and a random sampling technique is developed to quantify multimodel uncertainties. The GEV analysis was performed with projections using the Weather Research and Forecasting model, downscaled from three Global Climate Models based on the Representative Concentration Pathway 8.5 for present, mid-century and late-century. Results show the VPD based index (SVDI) accurately identifies the timing and magnitude short-term droughts, and extreme VPD is increasing across the United States and by the end of the twenty-first century. The number of days VPD is above 9 kPa increases by 10 days along California’s coastline, 30–40 days in the northwest and Midwest, and 100 days in California’s Central Valley.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources

The ever-increasing metagenomic data necessitate appropriate cataloguing in a way that facilitates the comparison and better contextualization of the underlying investigations. To this extent, information associated with the sequencing data as well as the original sample and the environment where it was obtained from is crucial. To date, there are not any publicly available repositories able to capture environmental metadata pertaining to hydrocarbon-rich environments. As such, contextualization and comparative analysis among sequencing datasets derived from these environments is to a certain degree hindered or cannot be fully evaluated. The metagenomics data management system for hydrocarbon resources (MetaHCRs) enables the capturing of marker gene and whole metagenome sequencing data as well as over 300 contextual attributes associated with samples, organisms, environments and geological properties, among others. Moreover, MetaHCR implements the Minimum Information about any Sequence–hydrocarbon resource specification from the Genomic Standards Consortium; it integrates a user-friendly web interface and relational database model, and it enables the generation of complex custom search. MetaHCR has been tested with 36 publicly available metagenomic studies, and its modular architecture can be easily customized for other types of environmental and metagenomics studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Background optimization of powder electron diffraction for implementation of the e-PDF technique and study of the local structure of iron oxide nanocrystals

The local structural characterization of iron oxide nanoparticles is explored using a total scattering analysis method known as pair distribution function (PDF) (also known as reduced density function) analysis. The PDF profiles are derived from background-corrected powder electron diffraction patterns (the e-PDF technique). Due to the strong Coulombic interaction between the electron beam and the sample, electron diffraction generally leads to multiple scattering, causing redistribution of intensities towards higher scattering angles and an increased background in the diffraction profile. In addition to this, the electron–specimen interaction gives rise to an undesirable inelastic scattering signal that contributes primarily to the background. The present work demonstrates the efficacy of a pre-treatment of the underlying complex background function, which is a combination of both incoherent multiple and inelastic scatterings that cannot be identical for different electron beam energies. Therefore, two different background subtraction approaches are proposed for the electron diffraction patterns acquired at 80 kV and 300 kV beam energies. From the least-square refinement (small-box modelling), both approaches are found to be very promising, leading to a successful implementation of the e-PDF technique to study the local structure of the considered nanomaterial.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular phylogenetic analysis of the Paguristes tortugae Schmitt, 1933 complex and selected other Paguroidea (Crustacea: Decapoda: Anomura)

Morphological characters, as presently applied to describe members of the Paguristes tortugae Schmitt, 1933 species complex, appear to be of limited value in inferring phylogenetic relationships within the genus, and may have similarly misinformed understanding of relationships between members of this complex and those presently assigned to the related genera Areopaguristes Rahayu & McLaughlin, 2010 and Pseudopaguristes McLaughlin, 2002. Previously undocumented observations of similarities and differences in color patterns among populations additionally suggest genetic divergences within some species, or alternatively seem to support phylogenetic groupings of some species. In the present study, a Maximum Likelihood (ML) phylogenetic analysis was undertaken based on the H3, 12S mtDNA, and 16S mtDNA sequences of 148 individuals, primarily representatives of paguroid species from the western Atlantic. This molecular analysis supported a polyphyletic Diogenidae Ortmann, 1892, although incomplete taxonomic sampling among the genera of Diogenidae limits the utility of this finding for resolving family level relationships. Several hypotheses regarding the evolutionary relationships among hermit crab genera were refuted by the Kishino-Hasegawa (KH). ShimodairaHasegawa (SH) and Approximately Unbiased (AU) tree topology tests, among them the hypothesis that Areopaguristes is monophyletic. A lack of support for the monophyly of Areopaguristes calls into question the phylogenetic validity of gill number for the differentiation of Paguristes, Areopaguristes, and Pseudopaguristes. The study was inconclusive with regard to the relationships among these three genera, but previously unknown diversity within both Paguristes and Areopaguristes was demonstrated. Existence of an undescribed species confounded under the name Paguristes tortugae Schmitt, 1933 was supported by genetics, morphology, and coloration. A second undescribed species with remarkable similarity to Areopaguristes hummi Wass, 1955 was discovered based on genetics and coloration.

12S↗