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DOE OSTI2024

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Performance simulation of the soft gamma-ray concentrator

The soft gamma-ray concentrator is a telescope mission concept utilizing a suitable arrangement of bent multilayer structures of alternating low- and high-density materials. This lens is able to channel gamma-ray photons via total external reflection and concentrate the incident radiation to a point. The channeling technique offers the potential for concentrating gamma rays with focal lengths <10 m and energies >100 keV, beyond the reach of current grazing-incidence hard x-ray mirrors. For the performance estimation of such an instrument, we have developed a flexible set of computer modeling tools to compute the optical properties of multilayer structures, predict the channeling efficiency for a given multilayer configuration, and aid in the optimization of potential gamma-ray concentrator-based telescope designs. This modeling includes the multilayer optical properties calculated by the IMD software, the ray tracing using an IDL code, and the focal plane detector simulation by MEGAlib. We illustrate the potential of this approach by presenting simulated astronomical observations from a balloon-borne platform. The final result, including simulated effective area, instrument sensitivity, and polarization performance, shows that the gamma-ray concentrator will provide greatly increased sensitivity for next-generation soft gamma-ray missions with modest cost and complexity.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Sierra/SolidMechanics 5.0 Theory Manual

Presented in this document are the theoretical aspects of capabilities contained in the Sierra/SM code. This manuscript serves as an ideal starting point for understanding the theoretical foundations of the code. For a comprehensive study of these capabilities, the reader is encouraged to explore the many references to scientific articles and textbooks contained in this manual. It is important to point out that some capabilities are still in development and may not be presented in this document. Further updates to this manuscript will be made as these capabilities come closer to production level.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Validation of a Pressure Dependent PBX 9501 Cookoff Model

A pressure dependent cookoff model for PBX 9501 was developed. This cookoff model was implemented in the finite element (FE) heat transfer code Aria and was used to simulate a set of cookoff experiments. This set is called the Large Scale Annular Cookoff (LSAC) experiments. Three dimensional and axisymmetric heat conduction FE models were implemented to simulate these experiments. The predictive ability of the PBX 9501 pressure dependent cookoff model was evaluated using Latin Hypercube sampling (LHS). Predictions of the thermal times to ignition and temperatures are compared with the experiments.

42 ENGINEERING↗

DOE OSTI2021

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes

One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with a database of known genes. This method presents many pitfalls, most notably the catch that you only find genes that you have seen before. The four most popular prokaryotic gene-prediction programs (GeneMark, Glimmer, Prodigal, Phanotate) all use a protein-coding training model to predict protein-coding genes, with the latter three allowing for the training model to be created ab initio from the input genome. Different methods are available for creating the training model, and to increase the accuracy of such tools, we present here GOODORFS, a method for identifying protein-coding genes within a set of all possible open reading frames (ORFS). Our workflow begins with taking the amino acid frequencies of each ORF, calculating an entropy density profile (EDP), using KMeans to cluster the EDPs, and then selecting the cluster with the lowest variation as the coding ORFs. To test the efficacy of our method, we ran GOODORFS on 14,179 annotated phage genomes, and compared our results to the initial training-set creation step of four other similar methods (Glimmer, MED2, PHANOTATE, Prodigal). We found that GOODORFS was the most accurate (0.94) and had the best F1-score (0.85), while Glimmer had the highest precision (0.92) and PHANOTATE had the highest recall (0.96).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Evaluating an Earth system model from a water manager perspective

Abstract. The large spatial scale of global Earth system models (ESMs) is often cited as an obstacle to using the output by water resource managers in localized decisions. Recent advances in computing have improved the fidelity of hydrological responses in ESMs through increased connectivity between model components. However, the models are seldom evaluated for their ability to reproduce metrics that are important for and resonate with practitioners or that allow practitioners to situate higher-resolution model outputs within a cascade of uncertainty stemming from different models and scenarios. We draw on the combined experience of the author team and water manager workshop participants to identify salient water management metrics and evaluate whether they are credibly reproduced over the conterminous USA by the Community Earth System Model v2 (CESM2) Large Ensemble. We find that, while the exact values may not match the observations, aspects such as interannual variability can be reproduced by CESM2 for the mean wet day precipitation and length of dry spells. CESM2 also captures the proportion of total annual precipitation that derives from the heaviest rain days in watersheds that are not snow-dominated. Aggregating the 7 d mean daily runoff to two-digit Hydrological Unit Code (HUC2) watersheds also shows that rain-dominated regions capture the timing and interannual variability of annual maximum and minimum flows. We conclude that there is potential for far greater use of large-ensemble ESMs, such as CESM2, in long-range water management decisions to supplement high-resolution regional projections.

Tye, Mari R. (ORCID:0000000324911020)↗

DOE OSTI2021

ExaWind: Exascale Predictive Wind Plant Flow Physics Modeling

The scientific goal of the ExaWind project is to advance our fundamental understanding of the flow physics governing whole wind plant performance, including wake formation, complex terrain impacts, and turbine-turbine-interaction effects. The primary application codes in the ExaWind environment are Nalu-Wind, an unstructured-grid computational fluid dynamics (CFD) code, AMR-Wind, a structured-grid CFD code, and OpenFAST, a whole-turbine simulation code. In this poster we present our progress towards simulating the ExaWind challenge problem, which is a predictive simulation of a wind farm with tens of megawatt-scale wind turbines dispersed over an area of 50 square kilometers.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

DOE OSTI2021

Reduced-model scrape-off layer turbulence (nSOLT) simulations comparing three fueling scenarios

The 2D scrape-off-layer turbulence code (nSOLT) includes 1D Boltzmann neutral–plasma interactions, a model of divertor recycling (introduced here), and a fixed source of plasma concentrated at the core-side boundary. Three fueling methods are considered herein: (1) neutral injection in the far-SOL is accomplished by specifying the density of Franck–Condon distributed neutrals streaming in from the boundary. (2) Divertor recycling is modeled by injecting a fraction of the particle parallel flux in the scrape-off layer (SOL) back into the edge region as a source of plasma. (3) A constant source fuels the edge plasma from the core-side boundary to model pellet injection. For machine parameters (B, R m , and L // ) illustrative of the MAST-U device, and for a deuterium plasma, turbulent equilibria are obtained that share the same plasma fueling rate for each of the three fueling methods, with only one of the sources on in each case. In the presence of self-consistent turbulence, quasi-steady plasma and neutral (deuterium) profiles, fueling efficiencies, SOL transparencies, and heat flux widths are compared. Characteristics of the turbulent fluctuations, including skewness, cross-phases, and power spectra, are described. The calculated fueling efficiencies, SOL transparencies to neutral penetration, and many of the turbulent properties are remarkably similar for all three fueling methods despite significant differences in the plasma profiles. The nonlinear states of the three cases are dominated by separatrix-spanning vortex cells that control particle and heat losses into the SOL.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

The LSU-Argonne conversion electron spectrometer: A new detector for the X-Array and SATURN decay station

In this study, a new conversion electron detector has been commissioned at the ATLAS/ CARIBU facility at Argonne National Laboratory. The LSU-Argonne Conversion Electron Spectrometer (LACES) is a LN 2 -cooled Si(Li) detector system designed to be incorporated into a decay station that comprises the dedicated HPGe clover array with a box geometry (X -Array) and the Scintillator and Tape Using Radioactive Nuclei (SATURN) device. This integration enables simultaneous measurements of conversion electrons and gamma-rays in decay experiments, yielding novel information on transition multipolarities, electric monopole transitions, and isomeric states that decay mostly via conversion electrons. A measurement of the energy resolution of LACES yielded 2.3-keV FWHM at 975 keV for electrons and 1.3-keV FWHM at 75 keV for X-rays. A detailed study of the absolute detection efficiency (at 5 mm from the source) was performed, where this quantity was determined experimentally in the range of electron transition energies between 25.5 keV and 1047.8 keV and subsequently simulated using the GEANT4 code. Measurement and simulations are found to be in excellent agreement. A precise characterization, for this type of detector system, of the absolute detection efficiency for such a wide energy range is reported for the first time.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Computation of linear MHD instabilities with the multi-region relaxed MHD energy principle

Over the last decade, a variational principle based on a generalisation of Taylor's relaxation, referred to as multi-region relaxed magnetohydrodynamics (MRxMHDs) has been developed. The numerical solutions of the MRxMHD equilibria have been constructed using the Stepped Pressure Equilibrium Code (SPEC) (Hudson et al 2012 Phys. Plasmas 19 112502). In principle, SPEC could also be established to describe the MRxMHD stability of an equilibrium. In this work, a theoretical framework is developed to relate the second variation of the energy functional to the so-called Hessian matrix, enabling the prediction of MHD linear instabilities of cylindrical plasmas, and is implemented in SPEC. The negative and positive eigenvalues of the Hessian matrix predict the stability of an equilibrium. Verification studies of SPEC stability results with the M3D-C 1 code and the tearing mode $\Delta^{^{\prime}}$ criterion have been conducted for ideal and resistive MHD instabilities, respectively, in a pressureless cylindrical tokamak, and have shown good agreement. Overall, our stability analysis is a critical step towards understanding the MHD stability of three-dimensional MHDs where nested flux surfaces, magnetic islands and stochastic regions co-exist.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Quantification of the effect of uncertainty on impurity migration in PISCES-A simulated with GITR

A Bayesian inference strategy has been used to estimate uncertain inputs to global impurity transport code (GITR) modeling predictions of tungsten erosion and migration in the linear plasma device, PISCES-A. This allows quantification of GITR output uncertainty based on the uncertainties in measured PISCES-A plasma electron density and temperature profiles (n e , T e ) used as inputs to GITR. The technique has been applied for comparison to dedicated experiments performed for high (4 × 10 22 m –2 s –1 ) and low (5 × 10 21 m –2 s –1 ) flux 250 eV He–plasma exposed tungsten (W) targets designed to assess the net and gross erosion of tungsten, and corresponding W impurity transport. The W target design and orientation, impurity collector, and diagnostics, have been designed to eliminate complexities associated with tokamak divertor plasma exposures (inclined target, mixed plasma species, re-erosion, etc) to benchmark results against the trace impurity transport model simulated by GITR. The simulated results of the erosion, migration, and re-deposition of W during the experiment from the GITR code coupled to materials response models are presented. Specifically, the modeled and experimental W I emission spectroscopy data for a 429.4 nm line and net erosion through the target and collector mass difference measurements are compared. Furthermore, the methodology provides predictions of observable quantities of interest with quantified uncertainty, allowing estimation of moments, together with the sensitivities to plasma temperature and density.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Abstract Background Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the Na V 1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations in SCN1A are associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency; however, putative causal non-coding promoter mutations have been identified. Methods To determine the functional role of one of these potentially redundant Scn1a promoters, we focused on the non-coding Scn1a 1b regulatory region, previously described as a non-canonical alternative transcriptional start site. We generated a transgenic mouse line with deletion of the extended evolutionarily conserved 1b non-coding interval and characterized changes in gene and protein expression, and assessed seizure activity and alterations in behavior. Results Mice harboring a deletion of the 1b non-coding interval exhibited surprisingly severe reductions of Scn1a and Na V 1.1 expression throughout the brain. This was accompanied by electroencephalographic and thermal-evoked seizures, and behavioral deficits. Conclusions This work contributes to functional dissection of the regulatory wiring of a major epilepsy risk gene, SCN1A . We identified the 1b region as a critical disease-relevant regulatory element and provide evidence that non-canonical and seemingly redundant promoters can have essential function.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Sierra/SolidMechanics 4.58 Theory Manual

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Graphite for Advanced Nuclear Reactors: Deployment Readiness Review

Historically, graphite has been used in numerous reactor technologies, including research/test reactors and, commercially, in advanced gas reactors. These non-metallic materials can play a key role as internal core structures, reflectors, or neutron moderators, making them important for deployment of certain advanced reactor technologies. This report explores the industry readiness for graphite material deployment, documenting Codes and Standards applicable to their design, qualification, and manufacturing. Discussions also examine the manufacturing processes, aging/degradation, inspection techniques, and disposal options. The report covers the current status, documents gaps, and proposes some conclusions about approaches to managing some of the current gaps.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

THERMAL MODELING OF HANFORD LEAD CANISTER’S HEATER BENCH TESTS

A computational fluid dynamics (CFD) model was built to simulate planned testing of heater assemblies for the Hanford Lead Canister (HLC) project. The HLC is a canister storage system that will contain heaters to simulate the decay heat of nuclear material and provide the canister storage system with environmental conditions equivalent to the operating conditions on a dry storage pad. The HLC will be equipped with long-term data collection and monitoring systems to provide an early warning of corrosion, pitting, cracking, or other signs of canister degradation that might threaten the integrity of the containment boundary over the potentially long term of dry storage. An important part of the HLC development is to confirm the function and ability of the electric heater assemblies that were specially designed to provide heating similar to the decay heat of nuclear material contained within the canister storage system. Heater bench testing is planned for early 2022 in a test configuration that does not include the canister. The goal of the bench testing is to verify that the heaters can replicate the decay heat of a canister with nuclear material and to validate the thermal models, which are critical to understanding the HLC’s thermal environment, including the local air flow within the canister storage system. Testing of the heater assemblies inside the canister system are planned in the future to validate canister level thermal models, and rigorous pre-deployment testing of the complete HLC cask and canister system is intended to be completed before the HLC is deployed in the 2025-2026 timeframe. This study presents the pre-test temperature predictions of the bench testing. A description of the heater assemblies and planned bench testing is presented. The model was developed with the commercial CFD code STAR-CCM+. An uncertainty analysis was run with the CFD model to determine the uncertainty in the temperature predictions and provide a range over which the predicted temperatures are expected to vary. The uncertainty analysis was performed by coupling STAR-CCM+ with the software Dakota, which provides advanced parametric analyses, including quantification of margins and uncertainty with computational models. This work is expected to provide insight into SNF canister behavior.

Suffield, Sarah R.↗

DOE OSTI2023

Machine Learning-Enabled Quantitative Analysis of Optically Obscure Scratches on Nickel-Plated Additively Manufactured (AM) Samples

Additively manufactured metal components often have rough and uneven surfaces, necessitating post-processing and surface polishing. Hardness is a critical characteristic that affects overall component properties, including wear. This study employed K-means unsupervised machine learning to explore the relationship between the relative surface hardness and scratch width of electroless nickel plating on additively manufactured composite components. The Taguchi design of experiment (TDOE) L9 orthogonal array facilitated experimentation with various factors and levels. Initially, a digital light microscope was used for 3D surface mapping and scratch width quantification. However, the microscope struggled with the reflections from the shiny Ni-plating and scatter from small scratches. To overcome this, a scanning electron microscope (SEM) generated grayscale images and 3D height maps of the scratched Ni-plating, thus enabling the precise characterization of scratch widths. Optical identification of the scratch regions and quantification were accomplished using Python code with a K-means machine-learning clustering algorithm. The TDOE yielded distinct Ni-plating hardness levels for the nine samples, while an increased scratch force showed a non-linear impact on scratch widths. The enhanced surface quality resulting from Ni coatings will have significant implications in various industrial applications, and it will play a pivotal role in future metal and alloy surface engineering.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Ground-based Transmission Spectroscopy with VLT FORS2: Evidence for Faculae and Clouds in the Optical Spectrum of the Warm Saturn WASP-110b

We present a ground-based optical transmission spectrum for the warm Saturn-mass exoplanet WASP-110b from two transit observations made with the FOcal Reducer and Spectrograph on the Very Large Telescope. The spectrum covers the wavelength range from 4000–8333 Å, which is binned in 46 transit depths measured to an averaged precision of 220 parts per million (ppm) over an averaged 80 Å bin for a Vmag = 12.8 star. The measured transit depths are unaffected by a dilution from a close A-type field dwarf, which was fully resolved. The overall main characteristic of the transmission spectrum is an increasing radius with wavelength and a lack of the theoretically predicted pressure-broadened sodium and potassium absorption features for a cloud-free atmosphere. We analyze archival high-resolution optical spectroscopy and find evidence for low to moderate activity of the host star, which we take into account in the atmospheric retrieval analysis. Using the AURA retrieval code, we find that the observed transmission spectrum can be best explained by a combination of unocculted stellar faculae and a cloud deck. Transmission spectra of cloud-free and hazy atmospheres are rejected at a high confidence. With a possible cloud deck at its terminator, WASP-110b joins the increasing population of irradiated hot-Jupiter exoplanets with cloudy atmospheres observed in transmission.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Field–potential finite-difference time-domain (FiPo FDTD) technique for computational electromagnetics

Modeling light–matter interactions at the nanoscale requires accurate handling of coupled quantum and electromagnetic systems. This coupling requires information about the electric scalar potential Φ and the magnetic vector potential A, which are not typically calculated in standard computational electromagnetics implementations. To that end, we have developed a field–potential finite-difference time-domain (FiPo FDTD) algorithm, which solves a set of first-order equations for Φ and A alongside equations for the electric and magnetic fields E and H. The FiPo Basic code is essentially conventional FDTD, but with an added module that calculates the potentials. The FiPo Hybrid code self-consistently calculates both fields and potentials and is particularly suitable for coupling with quantum electronic transport solvers because it can be sourced by the potentials themselves. To terminate the domain and mimic infinite space, we have derived and implemented a convolutional perfectly matched layer (CPML) absorbing boundary condition for FiPo FDTD whose performance is on par with state-of-the-art CPMLs for standard FDTD. We present FiPo simulation results on several example systems.

Avazpour, L. [University of Wisconsin-Madison, WI ↗