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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

NRC Multiphysics Analysis Capability Deployment FY2020 - Part 4

This report details progress and activities of Idaho National Laboratory (INL) on the Nuclear Regulatory Commission (NRC) project “Development and Modeling Sup- port for Advanced Non-Light Water Reactors.” The tasks completed for this report are: • Task 3a: This task demonstrates the effectiveness of Griffin’s methods for interpolating cross sections and SPH correction factors as a function of control drum rotation. The Monte Carlo code Serpent is used to generate reference results. The accuracy of Griffin-calculated eigenvalues and reaction rates are studied as a function of control drum rotation for cross section and SPH factor libraries of varying fidelity. Higher-fidelity libraries require less interpolation and are therefore inherently more accurate; however, they require more computational resources to create. Overall, Griffin is able to accurately model eigenvalue and reaction rates over the full range of drum rotation using a library generated from three to five discrete drum rotations for a particular microreactor design. • Task 3c: This preliminary task successfully demonstrates the performance of a coupled neutron-photon transport calculation with Griffin using the spherical harmonics approximation. The Griffin solutions are compared to reference solutions from the continuous energy Monte Carlo codes MCNP and Serpent. Furthermore, this work also demonstrates how to prepare the neutron and photon libraries using NJOY, MCNP, and Serpent with the latest ENDF/B-VIII data for 235 U and graphite. The Griffin total energy deposition in the active core region is calculated within 0.3% of the reference, but it degrades in the reflector regions with a maximum difference of -1.5%. Overall, the results look promising and future analysis should use an improved data stream and focus on determining the potential cancellation of error within each energy group.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Search for vector-like leptons with long-lived particle decays in the CMS muon system in proton-proton collisions at $$\sqrt{\text{s}}$$ = 13 TeV

Abstract A first search is presented for vector-like leptons (VLLs) exclusively decaying into a light long-lived pseudoscalar boson and a standard model τ lepton. The pseudoscalar boson is assumed to have a mass below the τ + τ − threshold, so that it decays exclusively into two photons. It is identified using the CMS muon system. The analysis is carried out using a data set of proton-proton collisions at a center-of-mass energy of 13 TeV collected by the CMS experiment in 2016–2018, corresponding to an integrated luminosity of 138 fb −1. Selected events contain at least one pseudoscalar boson decaying electromagnetically in the muon system and at least one hadronically decaying τ lepton. No significant excess of data events is observed compared to the background expectation. Upper limits are set at 95% confidence level on the vector-like lepton production cross section as a function of the VLL mass and the pseudoscalar boson mean proper decay length. The observed and expected exclusion ranges of the VLL mass extend up to 700 and 670 GeV, respectively, depending on the pseudoscalar boson lifetime.

Chekhovsky, V. [Yerevan Physics Institute]↗
DOE OSTI2025

Search for vector-like leptons with long-lived particle decays in the CMS muon system in proton-proton collisions at $\sqrt{s}$ = 13 TeV

A first search is presented for vector-like leptons (VLLs) exclusively decaying into a light long-lived pseudoscalar boson and a standard model τ lepton. The pseudoscalar boson is assumed to have a mass below the τ + τ − threshold, so that it decays exclusively into two photons. It is identified using the CMS muon system. The analysis is carried out using a data set of proton-proton collisions at a center-of-mass energy of 13 TeV collected by the CMS experiment in 2016–2018, corresponding to an integrated luminosity of 138 fb −1 . Selected events contain at least one pseudoscalar boson decaying electromagnetically in the muon system and at least one hadronically decaying τ lepton. No significant excess of data events is observed compared to the background expectation. Upper limits are set at 95% confidence level on the vector-like lepton production cross section as a function of the VLL mass and the pseudoscalar boson mean proper decay length. The observed and expected exclusion ranges of the VLL mass extend up to 700 and 670 GeV, respectively, depending on the pseudoscalar boson lifetime.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Monitoring Seasonal Shear Wave Velocity Changes in the Top 6 m at Garner Valley in Southern California With Borehole Data

Abstract Subsurface structures play important roles in seismic ground motion, crustal hydrology, stability of the built environment, and more. Constraining temporal changes of subsurface shear wave velocity ( V S ) can provide useful information to all these topics and the growing field of hydrological monitoring with seismic velocity. Using borehole records at Garner Valley, CA, we estimate seasonal subsurface V S variations from impulse response functions (IRFs) of earthquake data (2005–2018) along with IRFs and cross‐correlation of cross‐hole experiment data (2015–2018). The inferred V S variations are up to ∼25% in the top 6 m and ∼10% at 2–5 m in depth. The V S variations correlate strongly with the water table depth changes, suggesting that the changes are mostly due to fluctuations of pore pressure in the shallow material. The shallow velocity changes alter the near‐surface conditions, can affect seismic hazard estimation, and may be improperly attributed to deeper processes without careful analysis.

58 GEOSCIENCES↗
DOE OSTI2020

First-principles equations of state and structures of liquid metals in multi-megabar conditions

Liquid metals at extreme pressures and temperatures are widely interested in the high-pressure community. Based on density functional theory molecular dynamics, we conduct first-principles investigations on the equation of state ( EOS) and structures of four metals (Cu, Fe, Pb, and Sn) at 1.5–5 megabar conditions and 5 × 10 3 –4 × 10 4 K. Our first-principles EOS data enable evaluating the performance of four EOS models in predicting Hugoniot densities and temperatures of the four systems. We find the melting temperature of Cu is 1000–2000 K higher and shows a similar Clapeyron slope, in comparison to those of Fe. Our structure, coordination number, and diffusivity analysis indicates all the four liquid metals form similar simple close-packed structures. Our results set theoretical benchmarks for EOS development and structures of metals in their liquid states and under dynamic compression.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Impact of survey spatial variability on galaxy redshift distributions and the cosmological 3 × 2-point statistics for the Rubin Legacy Survey of Space and Time (LSST)

We investigate the impact of spatial survey non-uniformity on the galaxy redshift distributions for forthcoming data releases of the Rubin Observatory Legacy Survey of Space and Time (LSST). Specifically, we construct a mock photometry data set degraded by the Rubin OpSim observing conditions, and estimate photometric redshifts of the sample using a template-fitting photo-z estimator, BPZ, and a machine learning method, FlexZBoost. We select the Gold sample, defined as $i\lt 25.3$ for 10 yr LSST data, with an adjusted magnitude cut for each year and divide it into five tomographic redshift bins for the weak lensing lens and source samples. We quantify the change in the number of objects, mean redshift, and width of each tomographic bin as a function of the coadd i-band depth for 1-yr (Y1), 3-yr (Y3), and 5-yr (Y5) data. In particular, Y3 and Y5 have large non-uniformity due to the rolling cadence of LSST, hence provide a worst-case scenario of the impact from non-uniformity. We find that these quantities typically increase with depth, and the variation can be $10\!-\!40~{{\rm per\ cent}}$ at extreme depth values. Using Y3 as an example, we propagate the variable depth effect to the weak lensing $3\times 2$ pt analysis, and assess the impact on cosmological parameters via a Fisher forecast. We find that galaxy clustering is most susceptible to variable depth, and non-uniformity needs to be mitigated below 3 per cent to recover unbiased cosmological constraints. There is little impact on galaxy–shear and shear–shear power spectra, given the expected LSST Y3 noise.

cosmology↗
DOE OSTI2024

Unbiased particle conformation extraction from scattering spectra using orthonormal basis expansions

A strategy is outlined for quantitatively evaluating the particle density profiles from small-angle scattering spectra of dilute solutions. The approach employs an orthonormal basis function expansion method, enabling the determination of characteristic mass distributions in self-assembled structures without the need for a specific structural model. Through computational benchmarking, the efficacy of this approach is validated by effectively reconstructing the density profile of soft-ball systems with varying fuzziness from their scattering signatures. Further, the feasibility of the method is demonstrated by fitting small-angle neutron scattering data obtained from Pluronic L64 micelles at different temperatures. This proposed approach is both simple and analytical, eliminating the requirement for a presumptive structural model in scattering analysis. The new method could therefore facilitate quantitative descriptions of complex nanoscopic structures inherent to numerous soft-matter systems using small-angle scattering techniques.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Measurement of the production cross section for a W boson in association with a charm quark in proton–proton collisions at $\sqrt{s} = 13\,\hbox {TeV}$

The strange quark content of the proton is probed through the measurement of the production cross section for a W boson and a charm (c) quark in proton–proton collisions at a center-of-mass energy of 13$\,\text {Te}\hspace{-.08em}\text {V}$. The analysis uses a data sample corresponding to a total integrated luminosity of 138$\,\text {fb}^{-1}$ collected with the CMS detector at the LHC. The W bosons are identified through their leptonic decays to an electron or a muon, and a neutrino. Charm jets are tagged using the presence of a muon or a secondary vertex inside the jet. The $\hbox {W}+\hbox {c}$ production cross section and the cross section ratio $R_\textrm{c}^{\pm }= \sigma ({\hbox {W}}^{+}+\bar{\text {c}})/\sigma (\hbox {W}^{-}+{\textrm{c}})$ are measured inclusively and differentially as functions of the transverse momentum and the pseudorapidity of the lepton originating from the W boson decay. The precision of the measurements is improved with respect to previous studies, reaching 1% in $R_\textrm{c}^{\pm }= 0.950 \pm 0.005\,\text {(stat)} \pm 0.010 \,\text {(syst)} $. The measurements are compared with theoretical predictions up to next-to-next-to-leading order in perturbative quantum chromodynamics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Characterization and Valuation of the Uncertainty of Calibrated Parameters in Microsimulation Decision Models

We evaluated the implications of different approaches to characterize the uncertainty of calibrated parameters of microsimulation decision models (DMs) and quantified the value of such uncertainty in decision making. We calibrated the natural history model of CRC to simulated epidemiological data with different degrees of uncertainty and obtained the joint posterior distribution of the parameters using a Bayesian approach. We conducted a probabilistic sensitivity analysis (PSA) on all the model parameters with different characterizations of the uncertainty of the calibrated parameters. We estimated the value of uncertainty of the various characterizations with a value of information analysis. We conducted all analyses using high-performance computing resources running the Extreme-scale Model Exploration with Swift (EMEWS) framework. The posterior distribution had a high correlation among some parameters. The parameters of the Weibull hazard function for the age of onset of adenomas had the highest posterior correlation of -0.958. When comparing full posterior distributions and the maximum-a-posteriori estimate of the calibrated parameters, there is little difference in the spread of the distribution of the CEA outcomes with a similar expected value of perfect information (EVPI) of $\$$653 and $\$$685, respectively, at a willingness-to-pay (WTP) threshold of $\$$66,000 per quality-adjusted life year (QALY). Ignoring correlation on the calibrated parameters’ posterior distribution produced the broadest distribution of CEA outcomes and the highest EVPI of $\$$809 at the same WTP threshold. Different characterizations of the uncertainty of calibrated parameters affect the expected value of eliminating parametric uncertainty on the CEA. Ignoring inherent correlation among calibrated parameters on a PSA overestimates the value of uncertainty.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Metals and methylotrophy: Via global gene expression studies

A number of minerals, such as copper, cobalt, and rare earth elements (REE), are essential modulators of microbial one carbon metabolism. This chapter provides an overview of the gene expression study design and analysis protocols for uncovering REE-induced changes in methylotrophic bacteria. By interrogating relationships and differences in total gene expression induced by mineral micronutrients, a deeper understanding of gene regulation at a systems scale can be gained. With careful design and execution of RNA-sequencing experiments, thorough processing and assessment of read quality can be utilized to assess and adjust for possible biases. By ensuring only quality data are utilized in downstream processes, differential gene expression, overrepresented analyses, and gene-set enrichment analyses provide reliable and reproducible representation of pathways and functions which are being affected by changes in environmental conditions.

Johnson, Zachary J.↗
DOE OSTI2021

Introducing PRIMRE’s MRE Software Knowledge Hub

This paper focuses on the role of the Marine Renewable Energy (MRE) Software Knowledge Hub on the Portal and Repository for Information on Marine Renewable Energy (PRIMRE). The MRE Software Knowledge Hub provides online services for MRE software users and developers, and seeks to develop assessments and recommendations for improving MRE software in the future. Online software discovery platforms, known as the Code Hub and the Code Catalog, are provided. The Code Hub is a collection of open-source MRE software that includes a landing page with search functionality, linked to files hosted on the MRE Code Hub GitHub organization. The Code Catalog is a searchable online platform for discovery of useful (open-source or commercial) software packages, tools, codes, and other software products. To gather information about the existing MRE software landscape, a software survey is being performed, the preliminary results of which are presented herein. Initially, the data collected in the MRE software survey will be used to populate the MRE Software knowledge hub on PRIMRE, and future work will use data from the survey to perform a gap analysis and develop a vision for future software development. Additionally, as one of PRIMRE’s roles is to support development of MRE software within project partners, a silo of knowledge relating to best practices has been gathered.

marine, energy, open source software, MHKiT, MRE C↗
DOE OSTI2021

Introducing PRIMRE's MRE Software Knowledge Hub (February 2021)

This paper focuses on the role of the Marine Renewable Energy (MRE) Software Knowledge Hub on the Portal and Repository for Information on Marine Renewable Energy (PRIMRE). The MRE Software Knowledge Hub provides online services for MRE software users and developers, and seeks to develop assessments and recommendations for improving MRE software in the future. Online software discovery platforms, known as the Code Hub and the Code Catalog, are provided. The Code Hub is a collection of open-source MRE software that includes a landing page with search functionality, linked to files hosted on the MRE Code Hub GitHub organization. The Code Catalog is a searchable online platform for discovery of useful (open-source or commercial) software packages, tools, codes, and other software products. To gather information about the existing MRE software landscape, a software survey is being performed, the preliminary results of which are presented herein. Initially, the data collected in the MRE software survey will be used to populate the MRE Software knowledge hub on PRIMRE, and future work will use data from the survey to perform a gap analysis and develop a vision for future software development. Additionally, as one of PRIMRE's roles is to support development of MRE software within project partners, a silo of knowledge relating to best practices has been gathered. An early draft of new guidance developed from this knowledge is presented.

gap analysis↗
DOE OSTI2022

Comparing and contrasting In-Vial and full-scale systems for sparging volatile analytes

Here, in-vial sparging was demonstrated as an effective, practical alternative to a full-scale sparging system for supporting the analysis of volatile constituents. Using elemental mercury (Hg 0 ) and toluene as representative purgeable analytes, the mass removal for various sparge configurations was measured and a reduced order model was developed and validated. In the primary experiments, Hg 0 in the sparge gas was trapped on activated carbon or gold, thermally desorbed, and quantified using atomic absorption or atomic fluorescence spectroscopy. Toluene experiments using the same in-vial sparge apparatus and sparge parameters were performed to demonstrate the applicability of the reduced order model to a broad range of compounds. Toluene removal was tracked by measuring the remaining toluene in sparged aliquots using Ultraviolet-visible (UV–Vis) spectroscopy. For the sparging, flow rates varied from 25 to 75 mL/min for periods from 0 to 30 min. Sparge performance, mass removal as a function of time, and sparge gas volume were measured for both in-vial and full-scale systems. A model based on dimensionless Henry's Law coefficient, normalized sparge gas volume, and fractional extent of equilibrium matched the experimental data for both compounds and provides a practical tool for future applications. For the conditions tested in this study, the calibrated model indicated that the sparge gas in the in-vial system reached approximately 33% of its equilibrium value before exiting the water surface, while a full-scale system reached approximately 100%. The tests validated the quality, reproducibility, and predictability of sparging performance for both full scale and in-vial sparge systems. Related factors such as waste generation, worker risk, and labor were also assessed. Full scale sparge systems provide the advantage of lower detection levels due to larger sample volume, while the in-vial sparge systems provide advantages for most other factors; including automatability, reducing secondary wastes, lessening the need to clean and check the sparge apparatus, and lowering labor and costs. The data and associated reduced order model support continued development and deployment of in-vial sparge platforms as a practical option for analysis of purgeable analytes such as volatile organic compounds and volatile metals/organometallics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms

Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft 3 (1.27 m 3 ), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO 2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Statistical White-Line Analysis in High-Throughput TXM-XANES for Chemical State Quantification

The transmission X-ray microscopy (TXM) based X-ray absorption near-edge structure (XANES) technique provides three-dimensional mapping of element-specific chemical states at nanometer-scale spatial resolution and micrometer-scale fields of view. However, compared to conventional volume-averaged XANES (VA-XANES) measurements, the inherently small voxel size in TXM-XANES leads to a lower signal-to-noise ratio, making full-spectrum analysis computationally demanding and less robust. Here, we present the structural and compositional conditions for a statistical white-line analysis framework under which chemical state information can be directly extracted from the white-line peak position in voxel spectra without the need for voxel-wise background subtraction or normalization, under well-defined structural and compositional conditions. The method is validated on layered oxide cathode materials, where low-order polynomial fitting accurately reproduces white-line features, and the extracted energy distributions correlate strongly with VA-XANES results. This statistical approach enables high-throughput, dose-efficient, and noise-robust chemical state quantification in TXM-XANES, offering broad applicability to functional materials requiring nanoscale oxidation-state mapping.

TXM↗
DOE OSTI2025

Metagenome-assembled genomes from topsoils collected during NEON campaign in East River, CO (06/14/2018-06/28/2018)

The Watershed Function Science Focus Area (WF SFA) at Lawrence Berkeley National Lab is working to build a mechanistic understanding of the distribution and dynamics of biogeochemical processes in mountainous watersheds and their response to perturbation. In June 2018, the NEON (National Ecological Observatory Network) Airborne Observatory Platform (AOP) performed a taskable airborne imaging campaign to collect visible to shortwave infrared (VSWIR) imaging spectroscopy and LiDAR data across 330 km2 in the Upper East River at Crested Butte, CO. We conducted a parallel ground sampling campaign to sample vegetation traits, as well as soil physical, chemical, and microbiological characteristics. We collected these samples from 438 sites across 12 locations spanning much of the elevation, topographic, and geologic variability across the study area. A subset of 250 samples were used for soil metagenomics which is presented here. In addition, at each site, vegetation samples were collected to measure species-specific leaf water content and leaf mass area, foliar elemental composition and foliar CN stable isotope ratios. Soil samples were collected to measure soil physical properties which include bulk density and soil texture analysis. A suite of soil chemical properties was measured from the samples collected at each site, including pH, organic matter, concentrations exchangeable cations, total elemental composition, and the concentrations of extractable N pools (e.g. total free amino acids, ammonium, nitrate, dissolved organic N, and total dissolved N). Additionally, we have measured soil microbial biomass CN stoichiometry. Here, we present 1982 metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from topsoil collected from during NEON 2018 campaign. All metagenomes were sequenced at JGI (Joint Genome Institute) (GOLD Study ID: Gs0149986). Metagenomes were assembled using JGI Metagenome Workflow (10.1128/mSystems.00804-20). The dataset includes (1) zip files for 1982 MAG fasta files (neon_genomes1-5.tar.gz, split into 5 tarballs to keep tarballs under 0.5 GB), (2) neon_Gs0149986_samples_soilproperties_metagenomes.csv: the sample information together with the accession numbers for the underlying metagenomes and the associated soil physical and chemical measurements in NMDC (National Microbiome Data Collaborative) compliant format, (3) neon_Gs0149986.kml: location bounding box file for the sampled locations, (4) samples.csv: sample metadata file used to register Internationall Generic Sample Numbers (IGSNs), (5) flmd.csv: file level metadata file, and (6) dd.csv: data dictionary file. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2025

Mapping Hsp104 interactions using cross‐linking mass spectrometry

Molecular machines from the AAA+ (ATPases Associated with diverse cellular Activity) superfamily of protein disaggregases play important roles in protein folding, disaggregation and DNA processing. Recent cryo-EM structures of AAA+ molecular machines have uncovered nuanced changes in their conformation that underlie their specialized functions. Structural knowledge of these molecular machines in complex with substrates begins to explain their mechanism of activity. Here, we explore how cross-linking mass spectrometry (XL-MS) can be used to interpret changes in conformation induced by ATP in Hsp104 and how a substrate may interact with Hsp104. We applied a panel of cross-linking reagents to produce cross-linking maps of Hsp104 and interpret our data on previously determined X-ray and cryo-EM structures of Hsp104 from a thermophilic yeast, Calcarisporiella thermophila. We developed an analysis pipeline to differentiate between intra-subunit and inter-subunit contacts within the hexameric homo-oligomer. We identify cross-links that break the asymmetry that is present in Hsp104 in an ATP-hydrolysis competent conformation but is absent in an ATP-hydrolysis-defective mutant. Finally, we identify contacts between Hsp104 and a selected protein (proprotein convertase subtilisin/kexin type 9 PCSK9) to reveal contacts on the central channel of Hsp104 across the length of this protein indicating that we might have trapped interactions consistent with its translocation. Our simple and robust XL-MS-based experiments and methods help interpret how these molecular machines change conformation and bind to other proteins even in the context of homo-oligomeric assemblies enabling coupling state-of-the-art modeling approaches with XL-MS.

60 APPLIED LIFE SCIENCES↗