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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

SuperNu Version 4.x

We seek to release SuperNu, Version 4.x, as a continuation of development for the open source SuperNu software. The SuperNu, Version 3.x Monte Carlo radiative transfer code for astrophysical transients was released with GPLv3 copyright, asserted by LANL in 2015. For the next release we have features planned for development , including: opacity implementation (including non-local thermodynamic equilibrium effects), generalized source implementation (e.g. for emulating shock heating in Type II supernovae), 3T (electron, ion, radiation) internal energy update, special relativity corrections through O(v^2/c^2), light polarization (e.g. for comparison to spectroplarimetry observations of supernovae and kilonovae), and infrastructure features (checkpoint and restart of simulations, and tools including setup and Slurm batch scripts and simulation post-processing/analysis scripts). These features are intended to improve the fidelity and/or better understand uncertainty in supernova and kilonova light curve calculations.

Wollaeger, Ryan↗
DOE OSTI2021

Integrating PGAS and MPI-based Graph Analysis

This project demonstrates that Chapel programs can interface with MPI-based libraries written in C++ without storing multiple copies of shared data. Chapel is a language for productive parallel computing using global address spaces (PGAS). We identified two approaches to interface Chapel code with the MPI-based Grafiki and Trilinos libraries. The first uses a single Chapel executable to call a C function that interacts with the C++ libraries. The second uses the mmap function to allow separate executables to read and write to the same block of memory on a node. We also encapsulated the second approach in Docker/Singularity containers to maximize ease of use. Comparisons of the two approaches using shared and distributed memory installations of Chapel show that both approaches provide similar scalability and performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Plasma Wall Interaction with 3-D Plasma Boundaries

The interaction of the edge plasma and the material surfaces is one of the most critical challenges on the path to harness fusion power as new, fundamental energy source. This challenge typically combines the thrust to reach high density, low temperature (detached) plasmas in front of the divertor target plates as well as understanding the plasma material interaction (PMI) in particular in this regime. The combination of both research thrusts represents an extraordinarily challenging subject encompassing spatial scales spanning nanometers to meters in all states of matter and across a broad energy range. Modeling capabilities, which help to interpret data from nowadays experiments and enable extrapolation to future devices are urgently required. This is in particular true for toroidal magnetic confinement devices with three-dimensional (3D) plasma boundaries. Such plasma boundary geometries occur in tokamaks, when small amplitude magnetic perturbations are used to stabilize the unruly edge plasma or in stellarators, that are inherently 3D plasma confinement devices. In this project, the impact of 3D plasma boundaries on the plasma material interaction (PMI) was assessed. This work focused on plasma boundary conditions, in which high-density conditions at the material surfaces yield mitigation of the otherwise immense heat and particle loads that these materials would see. These so-called high recycling and eventually detached plasma regimes are of great interest for future reactor operation. In the project, key features that are unique to 3D boundaries were explored in comparison to canonically assumed axisymmetric plasma edge situations in tokamaks. In particular, the relevance of the 3D boundary situation in the extrapolation to the plasma boundary solution at ITER, the next step fusion energy experiment under construction as a multi-national, world-wide large-science experiment in southern France, has been explored. The EMC3-EIRENE plasma edge fluid and kinetic neutral transport code has been advanced to cope with the challenging and unprecedented conditions in the ITER boundary plasma including 3D fields that are planned to be used to suppress harmful edge instabilities, the so-called edge localized modes. This is a vital integration challenge for ITER and the results from this grant have provide a leading capability for this assessment. It was shown that the detachment process in a 3D edge solution for ITER follows the recycling regimes that are known from axisymmetric solutions, but that multiple plasma exhaust channels connected to the material surfaces are established which feature individual recycling characteristics. Because these channels touch the material surfaces in the divertor in a 3D geometry, the compatibility with the plasma material interaction (PMI), including erosion and impurity generation has been found to be an important part of the integration challenge. To address this, the fully 3D plasma material interaction code ERO2 has been adapted to these ITER specific geometries and a homogeneous mixing model was implemented, that allows to consider the mixing of Be and Was used at ITER in the PMI modeling. This model enhancement has been used to study non-local migration of Be in the JET ITER like wall configuration and it has been shown that with this model such complex migration processes in ITER relevant plasma shapes and with ITER relevant plasma boundary conditions can be addressed. The combined modeling approach using EMC3-EIRENE as a plasma boundary transport code and the ERO2 specialized PMI model will be an asset for the continued preparations of ITER operation as well as for Fusion Pilot Plant efforts that have emerged in the U.S. during the evolution of this grant. The predictive capability of this numerical tool has been validated at the DIII-D US national fusion facility. Here, dedicated plasma edge diagnostics were implemented to measure the impurity household around a 3D edge plasma during ELM suppression by 3D fields. Dedicated experiments with local material probes using these diagnostics and the state-of-the-art suite of boundary measurements at DIII-D have shown that the 3D perturbation of the plasma edge that is excreted by such 3D control fields yield a perturbation of the plasma boundary flux structure and hence also of the resulting PMI. The 3D boundary plasma is composed out of helical magnetic flux channels that intersect the divertor targets at an angle relative to the main guiding field, i.e., the toroidal magnetic field component of the tokamak. A similar effect has been measured as well on limiter surfaces during the startup campaign at the new stellarator experiment Wendelstein 7-X. These experiments ad initial analysis with the ERO plasma material interaction model, suggested that the place of erosion for a given particle from the surface and its re-deposition can be different in such 3D field geometries yielding potentially a significant level of net-erosion. This is not the case for axisymmetric solutions, where it was shown in the past that the eroded particles are effectively re-deposited into gaps produced by erosion at the same position and hence the net-erosion levels are small. For ITER, the quest to suppress the ELMs and at the same time maintain the integrity of the divertor is an issue, which these fundamental findings will help to resolve. The coupling of this work to the extrapolation in the ITER program has been addressed by both the PI and the lead numerical scientist being ITER Science Fellows in the duration of the contract and forward. A second focus in the exploration of 3D boundary effects on tokamaks and stellarators has been set on the measurement of helium exhaust features with such 3D fields. This is important because He represents the ash of the fusion process and needs to be exhausted. It was shown that 3D field application compatible with suppression of ELMs yields an increase of the helium exhaust performance. The ratio of the effective helium confinement time over the energy confinement time was reduced by almost 50% which demonstrated that the impact of helium accumulation in the plasma core with respect to the confinement of energy to sustain the fusion reaction is significantly improved with such 3D control fields. It was shown that this is the case for tokamaks as well as stellarators. At the Large helical Device in Japan, a similar enhancement of the helium exhaust features when small amplitude additional 3D fields were applied was measured. This is an important additional function of 3D field application and its impact on ITER is presently being studied in combination with investigations of helium exhaust in 3D field geometries of stellarator devices.

3D plasma edge transport↗
DOE OSTI2025

The AGORA High-Resolution Galaxy Simulations Comparison Project

Context. Satellite galaxies experience multiple physical processes when interacting with their host halos, often leading to the quenching of star formation. In the Local Group, satellite quenching has been shown to be highly efficient, affecting nearly all satellites except the most massive ones. While recent surveys study Milky Way-analogs to assess how representative our Local Group is, the dominant physical mechanisms behind satellite quenching in Milky Way-mass halos remain under debate. Aims. We analyze satellite quenching within the same Milky Way-mass halo simulated using various widely used astrophysical codes, each using different hydrodynamic methods and implementing different supernovae feedback recipes. The goal is to determine whether quenched fractions, quenching timescales, and the dominant quenching mechanisms are consistent across codes or if they show sensitivity to the specific hydrodynamic method and supernovae feedback physics employed. Methods. We used a subset of high-resolution cosmological zoom-in simulations of a Milky Way-mass halo from the multiple-code AGORA CosmoRun suite. Our analysis focuses on comparing satellite quenching across the different models and against observational data. We also analyzed the dominant mechanisms driving satellite quenching in each model. Results. We find that the quenched fraction is consistent with the latest SAGA Survey results within its 1σ host-to-host scatter across all the models. Regarding quenching timescales, all the models reproduce the trend observed in the ELVES survey, Local Group observations, and previous simulations: The less massive the satellite, the shorter its quenching timescale. All of our models converge on the dominant quenching mechanisms: Strangulation halts cold gas accretion in all satellites, while ram pressure stripping is the predominant mechanism for gas removal, and it is particularly effective in satellites with M * <10 8 M ⊙ . Nevertheless, the efficiency of the stripping mechanisms differs among the codes, showing a strong sensitivity to the different supernovae feedback implementations and/or hydrodynamic methods employed.

Local Group↗
DOE OSTI2023

Overview of interpretive modelling of fusion performance in JET DTE2 discharges with TRANSP

In the paper we present an overview of interpretive modelling of a database of JET-ILW 2021 D-T discharges using the TRANSP code. The main aim is to assess our capability of computationally reproducing the fusion performance of various D-T plasma scenarios using different external heating and D-T mixtures, and to understand the performance driving mechanisms. We find that interpretive simulations confirm a general power-law relationship between increasing external heating power and fusion output, which is supported by absolutely calibrated neutron yield measurements. A comparison of measured and computed D-T neutron rates shows that the calculations' discrepancy depends on the absolute neutron yield. The calculations are found to agree well with measurements for higher performing discharges with external heating power above ~20 MW, while low-neutron shots display an average discrepancy of around +40% compared to measured neutron yields. A similar trend is found for the ratio between thermal and beam-target fusion, where larger discrepancies are seen in shots with dominant beam-driven performance. We compare the observations to studies of JET-ILW D discharges, to find that on average the fusion performance is well modelled over a range of heating power, although an increased unsystematic deviation for lower-performing shots is observed. The ratio between thermal and beam-induced D-T fusion is found to be increasing weakly with growing external heating power, with a maximum value of ≳1 achieved in a baseline scenario experiment. An evaluation of the fusion power computational uncertainty shows a strong dependence on the plasma scenario type and fusion drive characteristics, varying between ±25% and 35%. D-T fusion alpha simulations show that the ratio between volume-integrated electron and ion heating from alphas is ≲10 for the majority of analysed discharges. Alphas are computed to contribute between ~15% and 40% to the total electron heating in the core of highest performing D-T discharges. An alternative workflow to TRANSP was employed to model JET D-T plasmas with the highest fusion yield and dominant non-thermal fusion component because of the use of fundamental radio-frequency heating of a large minority in the scenario, which is calculated to have provided ~10% to the total fusion power.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

MOSCATO Development and Integration in Fiscal Year 2022

During FY21, we conducted ongoing development work for the MOSCATO (Molten Salt Chemistry and Transport) solver. The code development work primarily consisted of transitioning capabilities from the original version of the solver, which was written in OpenFOAM, into Nek5000. In doing so, a fast, highly parallelizable solver was created that is capable of complex chemistry and corrosion simulations for engineering-scale molten salt systems. The Nek5000 version of MOSCATO is now fully featured and capable of higher-fidelity simulations than were previously possible. Demonstration cases including a thermal convection loop have been simulated to test these new capabilities. We built upon the work for FY22 and improved the code from several different perspectives. First, we improved the user interface by adding a new component to the official Nek5000 input file (.par). This new part contains documents parameters like, salt properties (density, viscosity, Cp, thermal conductivity), diffusion coefficients, standard potential, etc. Second, we built a conversion script to extract salt properties from the MSTDB-TP salt database and write to MOSCATO input file. Third, we migrated the code to NekRS, which is the GPU branch of Nek5000 and suitable for next generation supercomputers. Verification and Validation (V&V) work was also continued in FY22. Two tasks were performed. The first V&V task involved the validation of the Poisson-Nernst-Planck equation solver and Butler-Volmer electrode kinetics, by comparing with numerical and experimental data about thermoelectric cells. The second task involved the comparisons to corrosion results from a thermal convection loop run during the MSRE era. Satisfactory agreement was obtained from both tasks.

Yuan, Haomin↗
DOE OSTI2022

Source scaling comparison and validation in Central Italy: data intensive direct S waves versus the sparse data coda envelope methodology

SUMMARY Robustness of source parameter estimates is a fundamental issue in understanding the relationships between small and large events; however, it is difficult to assess how much of the variability of the source parameters can be attributed to the physical source characteristics or to the uncertainties of the methods and data used to estimate the values. In this study, we apply the coda method by Mayeda et al. using the coda calibration tool (CCT), a freely available Java-based code (https://github.com/LLNL/coda-calibration-tool) to obtain a regional calibration for Central Italy for estimating stable source parameters. We demonstrate the power of the coda technique in this region and show that it provides the same robustness in source parameter estimation as a data-driven methodology [generalized inversion technique (GIT)], but with much fewer calibration events and stations. The Central Italy region is ideal for both GIT and coda approaches as it is characterized by high-quality data, including recent well-recorded seismic sequences such as L'Aquila (2009) and Amatrice–Norcia–Visso (2016–2017). This allows us to apply data-driven methods such as GIT and coda-based methods that require few, but high-quality data. The data set for GIT analysis includes ∼5000 earthquakes and more than 600 stations, while for coda analysis we used a small subset of 39 events spanning 3.5 < Mw < 6.33 and 14 well-distributed broad-band stations. For the common calibration events, as well as an additional 247 events (∼1.7 < Mw < ∼5.0) not used in either calibration, we find excellent agreement between GIT-derived and CCT-derived source spectra. This confirms the ability of the coda approach to obtain stable source parameters even with few calibration events and stations. Even reducing the coda calibration data set by 75 per cent, we found no appreciable degradation in performance. This validation of the coda calibration approach over a broad range of event size demonstrates that this procedure, once extended to other regions, represents a powerful tool for future routine applications to homogeneously evaluate robust source parameters on a national scale. Furthermore, the coda calibration procedure can homogenize the Mw estimates for small and large events without the necessity of introducing any conversion scale between narrow-band measures such as local magnitude (ML) and Mw, which has been shown to introduce significant bias.

Morasca, Paola (ORCID:0000000265254867)↗
DOE OSTI2022

Metaplectic geometrical optics for ray-based modeling of caustics: Theory and algorithms

The optimization of radio frequency-wave (RF) systems for fusion experiments is often performed using ray-tracing codes, which rely on the geometrical-optics (GO) approximation. However, GO fails at caustics such as cutoffs and focal points, erroneously predicting the wave intensity to be infinite. This is a critical shortcoming of GO, since the caustic wave intensity is often the quantity of interest, e.g., RF heating. Full-wave modeling can be used instead, but the computational cost limits the speed at which such optimizations can be performed. Here, we have developed a less expensive alternative called metaplectic geometrical optics (MGO). Instead of evolving waves in the usual x (coordinate) or k (spectral) representation, MGO uses a mixed X$\equiv$Ax+Bk representation. By continuously adjusting the matrix coefficients A and B along the rays, one can ensure that GO remains valid in the X coordinates without caustic singularities. The caustic-free result is then mapped back onto the original x space using metaplectic transforms. Here, we overview the MGO theory and review algorithms that will aid the development of an MGO-based ray-tracing code. We show how using orthosymplectic transformations leads to considerable simplifications compared to previously published MGO formulas. We also prove explicitly that MGO exactly reproduces standard GO when evaluated far from caustics (an important property that until now has only been inferred from numerical simulations), and we relate MGO to other semiclassical caustic-removal schemes published in the literature. Finally this discussion is then augmented by an explicit comparison of the computed spectrum for a wave bounded between two cutoffs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Comparison of private flux region instability in conventional and super-X divertor configurations

Understanding turbulence in the divertor leg of tokamaks is essential to predicting the heat deposition profile on the divertor plate. This in turn is important for evaluating advanced divertor configurations, such as the super-X divertor. Within the divertor region, the private flux region is of interest because it is relatively unaffected by turbulence extending from the outboard midplane, so instabilities in this region could have a particularly pronounced effect on transport. These instabilities are modeled using the Arbitrary Topology Equation Reader (ArbiTER) eigenvalue code. Eigenmodes are examined further by comparing physics models to determine the fundamental mechanisms behind their formation, and quantifying the effect of individual terms. This analysis is conducted on both conventional and super-X divertors to compare these effects. Here, the resulting analysis reveals the presence of a geodesic curvature driven instability that is significantly more pronounced in the super-X configuration.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Comparison of spatial dynamics and point kinetics approaches in multiphysics modeling of the molten salt reactor experiment

In this work, we present validation test results of fully coupled neutronics and thermal-hydraulics models of the Molten Salt Reactor Experiment (MSRE) against experimental data of the zero power pump transients and the natural circulation tests at low power. To capture the strong coupling between neutronics and thermal-hydraulics due to fuel circulation, and to account for the delayed neutron precursor (DNP) distribution, the porous media thermal-hydraulics solver Pronghorn was fully coupled to the spatial neutron dynamics code Griffin, which solves the neutron diffusion equation, and to the 0-D point kinetics solver Squirrel, using a 2-D homogenized representation of the MSRE. The validation test results show very good agreement with experimental data for both point kinetics and spatial dynamics simulations, capturing the strong feedback effect and DNP losses in the MSRE. The 0-D code Squirrel accurately predicted the time-dependent behavior in the MSRE given the steady-state spatial dynamics solution of Griffin.

42 - ENGINEERING↗
DOE OSTI2020

SYSTEMATIC MULTI-INDEX VALIDATIONS OF SIDI ENGINE FLOW FIELD LES COMPUTATIONS USING CRANK ANGLE-RESOLVED PIV MEASUREMENTS

In-cylinder flow fields make significant impacts on the fuel atomization, fuel mixture formation, and combustion process in spark ignition direct injection (SIDI) engines. In recent years, model-based simulation approaches are preferred in regard to investigating the transient in-cylinder flow field characteristics. Most commonly, the simulation models are validated using single representative flow field at a typical crank angle measured by particle image velocimetry (PIV). However, it provides only limited knowledge about the flow field which is highly three-dimensional and of transient nature. In this study, crank angle-resolved Ply measurements are conducted on three distinct planes inside the cylinder to capture the transient process of flow field characteristics which vary with the crank angle. These three planes consist of one tumble plane through the spark plug tip, one tumble plane along two intake ports, and one swirl plane at 30 mm below the cylinder head. Large eddy simulation (LES) is employed for the numerical computations using the CONVERGE codes. On the basis of large datasets for both temporal and spatial domains, a multi-index systematic validation approach is conducted. Crank angle-resolved calculations of global indices and local indices are implemented using the flow fields velocity data obtained from both PIV and LES on select planes. Global indices reveal the trends in similarities of different crank angle degrees and locations, while local indices give the detail comparison results. In summary, with the systematic multi-index validation approach, the crucial crank angle degrees and locations for model verification will be detected. Furthermore, the corresponding critical flow features are analyzed. Practical guideline of flow field validation is proposed.

Crank angle-resolved PIV↗
DOE OSTI2020

Simulations of coherent scattering experiments at storage ring synchrotron radiation sources in the hard x-ray range

Detailed simulations of experiments carried out at modern light sources are directly related to the most efficient and productive use of these facilities for research in multiple branches of science and technology. The “Synchrotron Radiation Workshop” computer code with its Python interface, and Sirepo web-browser-based graphical user interface, currently supports physical optics simulations of coherent X-ray scattering and imaging experiments on user-defined virtual samples. We present examples of simulations of coherent scattering experiments that are typically performed at the Coherent Hard X-ray beamline at Brookhaven National Laboratory’s (BNL) National Synchrotron Light Source II. We also present several comparisons of the simulations with the results of actual coherent X-ray scattering experiments with nano-fabricated test samples produced at BNL’s Center for Functional Nanomaterials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Direct Numerical Simulation of Flow Over a Wall-Mounted Cube with the Nek5000 Spectral Element Code: DNS at Re h = 3900

The direct numerical simulation (DNS) of the canonical wall-mounted unit cube subjected to two distinct incident velocity profiles is performed at a Reynolds number where the bulk flow characteristics are known to become relatively Reynolds number insensitive. The aim of this work is to highlight the sensitivity of such bluff-body flows to mean shear and to provide a representative set of data for such flow scenarios where common turbulence modeling techniques often fail. Simple boundary conditions and a small domain are selected to allow for cost-effective and easy comparisons for model development purposes. In addition to mean velocity profiles, select turbulence statistics are presented in detail. Further, the basic efficacy of eddy viscosity models is evaluated and found to be adequate only for the shear stress components for the bluff-body flows examined here. Other failure mechanisms for RANS are proposed.

42 ENGINEERING↗
DOE OSTI2024

Development of spatially and temporally resolved electron density measurements for the assessment of radiation hydrodynamics simulations of laboratory X-ray photoionized plasmas

The photoionized plasma gas cell experiment is an established platform we use to make at-parameter (ξ > > 1 ergs cm s –1 ) measurements of plasma properties with application to high-energy astrophysical systems. We model the experiments with 1D radiation hydrodynamics simulations using the HELIOS-CR code to inform our understanding and assist in the interpretation of results. The simulations predict that the bulk of the plasma is in a quasi-uniform and hydrodynamically unperturbed state throughout the duration of the experiment. To evaluate this prediction, we introduced a photonic Doppler velocimetry (PDV) diagnostic to measure spatially and temporally resolved plasma electron density. The initial measurements were successful but had limitations that made model-data comparisons challenging. To address this, we re-designed the gas cell PDV diagnostic and doubled the number of measurement locations to sample across two thirds of the depth of the cell. We also present a comparison of the results from the upgraded PDV diagnostic to the HELIOS-CR simulations for the first time. As a result, the experimental data confirms the prediction of an unperturbed region in the bulk of the plasma but reveals discrepancies in the time evolution and spatial distribution of the simulated electron density.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Near-continuum, hypersonic oxygen flow over a double cone simulated by direct simulation Monte Carlo informed from quantum chemistry

A large-scale, fully resolved direct simulation Monte Carlo (DSMC) computation of a non-equilibrium, reactive flow of pure oxygen over a double cone is presented. Under the simulated near-continuum conditions, the computational demands are shown to be significant because of the wide range of length scales that must be resolved. Therefore, robust grid adaption capabilities and efficient parallelization of the Stochastic PArallel Rarefied-gas Time-accurate Analyzer (SPARTA) code that is utilized in this work are essential. The thermochemical and transport collision models were selected for efficiency and simplicity. First-principles data, obtained from the highly accurate direct molecular simulation method, were used to inform the collision models’ parameters. Importantly, because SPARTA implements molecular collision models using collision-specific energies, the resulting macroscopic relaxation rates were evaluated a posteriori via zero-dimensional heat bath simulations. The comparisons of surface properties, namely heat flux and pressure, show very close agreement with previous computational fluid dynamics (CFD) results. Differences with the measurements were found to be similar to the CFD simulations. The unresolved discrepancy with the measurements could be due to inconsistent free stream conditions with the actual experimental data or missing physical phenomena altogether, for example atomic and molecular oxygen electronically excited states, three-dimensional effects, or more complex gas–surface interactions. As shown in this work, the advantages of obtaining a DSMC particle solution for these flows reside in the method's ability to be directly informed from first principles and to seamlessly describe internal energy non-equilibrium for all modes. With the advent of exascale computing and beyond, particle methods will be an increasingly important tool to verify the validity of physical assumptions in reduced-order models via fully resolved, experimental-scale simulations, down to the level of molecular-level distributions.

Mechanics↗
DOE OSTI2024

Invariant regimes of Spencer scaling law for magnetic compression of rotating FRC plasma

Abstract The scaling laws for the magnetic compression of a toroidally rotating field reversed configuration (FRC) have been investigated in this work. The magnetohydrodynamics (MHD) simulations of the magnetic compression on rotating FRCs employing the NIMROD code (Sovinec et al 2004 J. Comput. Phys. 195 355), are compared with the Spencer’s one-dimensional (1D) theory (Spencer et al 1983 Phys. Fluids 26 1564) for a wide range of initial flow speeds and profiles. The toroidal flow can influence the scalings directly through the alteration of the compressional work as also evidenced in the 1D adiabatic model, and indirectly by reshaping the initial equilibrium. However, in comparison to the static initial FRC equilibrium cases, the pressure and the radius scalings remain invariant for the magnetic compression ratio B w 2 / B w 1 up to 6 in presence of the initial equilibrium flow, suggesting a broader applicable regime of the Spencer scaling law for FRC magnetic compression. The invariant scaling has been proven a natural consequence of the conservation of angular momentum of both fluid and magnetic field during the dynamic compression process.

Ma, Yiming↗
DOE OSTI2020

Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles

G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world’s most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Model Inputs, Outputs, and Scripts associated with: “Combined effects of stream hydrology and land use on basin-scale hyporheic zone denitrification in the Columbia River Basin”

This data package is associated with the publication “Combined effects of stream hydrology and land use on basin‐scale hyporheic zone denitrification in the Columbia River Basin”, published in Water Resource Research (Son et al.2022) available at https://doi.org/10.1029/2021WR031131. This data package includes the key model inputs/outputs of the river corridor model for the Columbia River Basin (CRB) and the model source codes used in the manuscript. The model is a carbon-nitrogen-coupled river corridor model (RCM), and the model is used to quantify hyporheic zone (HZ) denitrification at the NHDPLUS stream reach scales. The RCM used in this study combines empirical substrate models derived from observations and three microbially driven reactions, including two-step denitrification and aerobic respiration, are considered within the HZ. The key input data of the model are exchange flux, residence time, and stream solute (dissolved organic carbon (DOC), dissolved oxygen (DO), and nitrate concentrations). These inputs are constant over time and represent long-term averaged values. This study uses the RCM to explore the spatial patterns of HZ denitrification across reaches with different sizes and land use in the CRB. Our main objective is to use the RCM as a virtual reality model, and the machine-learning models as surrogates that encapsulate the complexities of the physics-based model while identifying the importance of different variables that are not evident in the model conceptualization. We do not include a direct comparison of the modeled HZ denitrification and measurements; however, the RCM can capture the overall spatial patterns of the HZ denitrification because the model inputs and its reaction networks are based on well-established theory and a physical-based model. The combination of the model-based predictions and a machine-learning approach (e.g., random forest) is used to improve our understanding of what variables of the model are associated with spatial patterns of the modeled denitrification across reaches with different sizes and land uses, and to develop a proxy model using measurable variables to reproduce the simulated patterns.This dataset contains five folders: (1) model_inputs, (2) model_outputs, (3) Rscripts, (4) figures, and (5) model_codes. It also contains a readme, file level metadata (FLMD), and data dictionary (dd). Please see the FLMD for a list of all the files contained in this data package and descriptions for each. The model_inputs folder contains the model inputs used to drive the model simulations. The model_outputs folder contains key model output files from the river corridor model. The Rscripts folder contains the Rscripts for pre- and post- processing model results. The figures folder contains the raw figures associated with the manuscript. The model_codes folder includes key model source codes/input files. All files are .jpg, .jpeg, .out, .e, .od, .dat, .sub, .F90, .0, .R, .sbx, .cpg, .sbn, .shx, .shp, .dbf, .prj, .tfw, .tif, .xml, .pdf, or .csv.

54 ENVIRONMENTAL SCIENCES↗