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At least 811 records · Page 45

All sources NASA NTRS DOE OSTI

DOE OSTI2023

Parameter dependencies of the separatrix density in low triangularity L-mode and H-mode JET-ILW plasmas

Abstract The midplane electron separatrix density, n e,sep , in JET-ILW L-mode and H-mode low triangularity deuterium fuelled plasmas exhibits a strong explicit dependence on the averaged outer divertor target electron temperature, n e,sep ∼ T e,ot −1/2 . This dependence is reproduced by analytic reversed two point model (rev-2PM), and arises from parallel pressure balance, as well as the ratio of the power and momentum volumetric loss factors, (1 − f cooling )/(1 − f mom-loss ). Quantifying the influence of the (1 − f cooling ) and (1 − f mom-loss ) loss factors on n e,sep has been enabled by measurement estimates of these quantities from L-mode density (fueling) ramps in the outer horizontal, VH(C), and vertical target, VV, divertor configurations. Rev-2PM n e,sep estimates from the extended H-mode and more limited L-mode datasets are recovered to within ±25% of the measurements, with a scaling factor applied to account for use of T e,ot , an averaged quantity, rather than flux tube resolved target values. Both the (1 − f cooling ) and (1 − f mom-loss ) trends and recovery of n e,sep using the rev-2PM formatting are reproduced in EDGE2D-EIRENE L-mode-like and H-mode-like density scan simulations. The general lack of a divertor configuration effect in the JET-ILW n e,sep trends can be attributed to a significant influence of main chamber recycling, which has been shown in the EDGE2D-EIRENE results to moderate n e,sep with respect to changes in divertor neutral leakage imposed by changes in the divertor configuration. The unified n e,sep vs T e,ot trends can, however, be broken if large modifications to the divertor geometry (e.g. complete removal of the outer divertor baffle structure) are introduced in the model. The more pronounced high-field side high density region formation in the VH(C) configuration with reduced clearance to the separatrix does not appear to have a significant influence on the outer midplane separatrix and pedestal parameters when mapped to T e,ot , although conditions at the inner midplane could not be assessed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Nonlinear gyrokinetic modelling of high confinement negative triangularity plasmas

Abstract Nonlinear gyrokinetic simulations correctly predict particle as well as ion and electron energy fluxes of high confinement plasmas with a negative triangularity cross sectional shape, showing that core transport in these plasmas is well described by standard gyrokinetic models. Experimentally inferred power balance fluxes are mostly reproduced within one standard deviation across a wide portion of the minor radius. Experimental conditions are reproduced by ion scale simulations, without the need to include density and temperature profile curvature effects. The experimental case is used as baseline to predict that the non-dimensional confinement scaling in negative triangularity plasmas increases strongly with plasma current while slightly degrading at increasing normalized pressure and decreasing collisionality. Recent experiments showed that low toroidal rotation negatively impacts confinement; consistent with the experiment, simulations predict that low rotational shear significantly affects confinement unless the plasma effective charge is maintained above a minimum level. Core confinement is predicted to significantly degrade in low aspect ratio devices.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Analysis of the linear and nonlinear stability of Alfven eigenmodes and fish-bones in JET DT discharges: mode identification and shear flows generation

The plasma in future nuclear fusion reactors will be heated by neutral beam injectors (NBIs) and high frequency electromagnetic waves as well as fusion born alpha particles. Energetic particles (EPs), with energies up to two orders of magnitude larger than the thermal plasma, can trigger EP driven modes and induce harmful EP losses, reducing the plasma heating efficiency and the economical viability of the reactor. The present study is dedicated to analyze the Alfven Eigenmode (AE) activity in JET D–T discharges, the closest experiment to reactor-like operation performed until now. There, EP driven modes are induced by the combined effect of tangential NBIs and ion cyclotron resonance heating (ICRH) driven EP. Linear and nonlinear simulations are performed with the gyro-fluid FAR3d code to analyze the AE activity observed in the discharge 99896. The linear simulations reproduce the unstable n = 3 to 5 toroidal AEs (TAE) at the inner plasma region observed in the experiment, triggered by highly energetic passing deuterium populations injected by the tangential NBIs, further accelerated by the effect of the ICRH up to 1 MeV. In addition, fish-bones triggered by energetic trapped hydrogen induced by the ICRH are also reproduced. On the other hand, the alpha particles density is too small to destabilize AEs in the experiment. Nonetheless, increasing artificially the alpha density by one order of magnitude, an n = 1 beta induced AE can be destabilized in the inner plasma region. Nonlinear simulations indicate the generation of zonal structures during the AE/fish-bone saturation phase. TAE and fish-bones causes a rather weak increase of the passing D and trapped H EP (around 2%), respectively. Shear flows and zonal currents are generated during the saturation of TAE and fish-bones. Nonlinear simulations performed for D–T and pure deuterium thermal plasma indicate AE/fish-bone activity is weaker and shear flows are less intense in the pure deuterium case, trends consistent with the experimental observations that also indicates a deterioration of the thermal plasma confinement. Therefore, both numerical studies and experimental evidence indicate the generation of shear flows by AE/fish-bones could be connected with an improvement of the thermal plasma confinement.

AE↗

DOE OSTI2020

Heavy flavor dynamics across system size at the LHC

One of the fundamental signatures of the Quark Gluon Plasma has been the suppression of heavy flavor (specifically D mesons), which has been measured via the nuclear modification factor, R AA and azimuthal anisotropies, v n , in large systems. However, multiple competing models can reproduce the same data for R AA to v n . In this talk we break down the competing effects that conspire together to successfully reproduce R AA and v n in experimental data using Trento+v-USPhydro+DAB-MOD. Then using our best fit model we make predictions for R AA and v n across system size for 208 PbPb, 129 XeXe, 40 ArAr, and 16 OO collisions. We find that 0–10% centrality has a non-trivial interplay between the system size and eccentricities such that system size effects are masked in v 2 whereas in 30–50% centrality the eccentricities are approximately constant across system size and, therefore, is a better centrality class to study D meson dynamics across system size.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Wind Farm Wakes and Farm-to-Farm Interactions: Lidar and Wind Tunnel Tests

Recent experimental and numerical evidence has shown that the cumulative wake generated from the overlapping of multiple wakes within a wind farm could reduce power performance and enhance fatigue loads of wind turbines installed in neighboring downstream wind farms and may also extend up to distances one order of magnitude larger than those typically considered for intra-farm wake interactions. Similar to individual wind turbine wakes, wind farm wakes have a velocity deficit and added turbulence intensity, both affected by the turbine rotor thrust forces and the incoming turbulence intensity. Therefore, the evolution of wind farm wakes will vary for different operational and atmospheric conditions. In this paper, lidar measurements collected during the American WAKE experimeNt (AWAKEN) and wind tunnel tests of wind farms reproduced by porous disks are leveraged to investigate wind farm wakes.

17 WIND ENERGY↗

DOE OSTI2026

Industrial deposition of wavelength-shifting films for liquid argon photon detection systems

The Deep Underground Neutrino Experiment (DUNE) Phase-II Far Detector is considering an approximately 2000 m 2 photon detection system to achieve a target mean light yield of 180 PE/MeV. Meeting this requirement demands scalable, cost-effective, and high-quality wavelength-shifter (WLS) coatings capable of converting 127 nm liquid-argon scintillation light into visible photons with controlled and reproducible optical performance. We report on the successful realization of an industrial physical vapor deposition (PVD) process forp-terphenyl (pTP) coatings, adapted from vacuum deposition techniques developed for OLED display manufacturing, to produce uniform WLS layers on large-area inorganic substrates, a task traditionally challenged by adhesion and uniformity issues at organic-inorganic interfaces. Surface characterization by profilometry and spectroscopic measurements demonstrates edge-region thickness variation below 10% and emission spectra consistent with high-quality pTP reference samples. The industrial process demonstrates reproducibility, scalability, and significantly reduced production time compared to laboratory-based methods, while maintaining optical characteristics consistent with established pTP reference samples. These results establish a viable pathway for mass production of high-performance pTP coatings for DUNE FD3 and future neutrino experiments, from a coating manufacturing and process standpoint. Detector-level performance validation, including quantitative VUV conversion efficiency measurements at 127 nm, is identified as future work.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

The Thomas theorem and the Efimov States within a generalized Bohr model

Using a generalized Bohr model and the hyper-spherical formalism for a three-body system, we derive the universal energy functions. We apply our model to 4He atom where only the Coulomb potential is dominant and find that its binding energy is well reproduced (less than 5.5% difference). Later, we focus on the equal mass three-body systems and derive the Thomas theorem assuming a simple interaction depending on the range of the potential. We discuss the conditions for which an unbound two-body system produces a bound three-body system and apply our model to 4He and triton atoms as well as to the triton nucleus. Using their scattering lengths and effective ranges, we are able to reproduce the two-body or the three-body binding energies (less than 5% difference) with only one parameter fitted. Prediction for excited (Efimov) levels are also given and in particular we demonstrate that for some hyper-angles two equal minima appear which indicate a phase (shape) transition similar to the Landau's theory of phase transition. We suggest that the observed excited levels in two different experiments for the triton nucleus are indeed Efimov levels and there may be more surprises.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2022

Best practices for photovoltaic performance loss rate calculations

Abstract The performance loss rate (PLR) is a vital parameter for the time-dependent assessment of photovoltaic (PV) system performance and health state. Although this metric can be calculated in a relatively straightforward manner, it is challenging to achieve accurate and reproducible results with low uncertainty. Furthermore, the temporal evolution of PV system performance is usually nonlinear, but in many cases a linear evaluation is preferred as it simplifies the assessment and it is easier to evaluate. As such, the search for a robust and reproducible calculation methodology providing reliable linear PLR values across different types of systems and conditions has been the focus of many research activities in recent years. In this paper, the determination of PV system PLR using different pipelines and approaches is critically evaluated and recommendations for best practices are given. As nonlinear PLR assessments are fairly new, there is no consent on how to calculate reliable values. Several promising nonlinear approaches have been developed recently and are presented as tools to evaluate the PV system performance in great detail. Furthermore, challenges are discussed with respect to the PLR calculation but also opportunities for differentiating individual performance losses from a generic PLR value having the potential of enabling actionable insights for maintenance.

14 SOLAR ENERGY↗

DOE OSTI2020

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Abstract Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability and implementation All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary data are available at Bioinformatics online.

Hagemeijer, Marne C.↗

DOE OSTI2021

Deep graph representations embed network information for robust disease marker identification

We report that the accurate disease diagnosis and prognosis based on omics data rely on the effective identification of robust prognostic and diagnostic markers that reflect the states of the biological processes underlying the disease pathogenesis and progression. In this article, we present GCNCC, a Graph Convolutional Network-based approach for Clustering and Classification, that can identify highly effective and robust network-based disease markers. Based on a geometric deep learning framework, GCNCC learns deep network representations by integrating gene expression data with protein interaction data to identify highly reproducible markers with consistently accurate prediction performance across independent datasets possibly from different platforms. GCNCC identifies these markers by clustering the nodes in the protein interaction network based on latent similarity measures learned by the deep architecture of a graph convolutional network, followed by a supervised feature selection procedure that extracts clusters that are highly predictive of the disease state. By benchmarking GCNCC based on independent datasets from different diseases (psychiatric disorder and cancer) and different platforms (microarray and RNA-seq), we show that GCNCC outperforms other state-of-the-art methods in terms of accuracy and reproducibility.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

A generative graph model for electrical infrastructure networks

We propose a generative graph model for electrical infrastructure networks that accounts for heterogeneity in both node and edge type. To inform the design of this model, we analyze the properties of power grid graphs derived from the U.S. Eastern Interconnection, Texas Interconnection, and Poland transmission system power grids. Across these datasets, we find subgraphs induced by nodes of the same voltage level exhibit shared structural properties atypical to small-world networks, including low local clustering, large diameter and large average distance. On the other hand, we find subgraphs induced by transformer edges linking nodes of different voltage types contain a more limited structure, consisting mainly of small, disjoint star graphs. The goal of our proposed model is to match both these inter and intra-network properties by proceeding in two phases: we first generate subgraphs for each voltage level and then generate transformer edges that connect these subgraphs. The first phase of the model adapts the Chung-Lu random graph model, taking desired vertex degrees and desired diameter as inputs, while the second phase of the model is based on a simpler random star graph generation process. We test the performance of our model by comparing its output across many runs to the aforementioned real data. In nearly all categories tested, we find our model is more accurate in reproducing the unusual mixture of properties apparent in the data than the Chung-Lu model. We also include graph visualization comparisons, as well as a brief analysis of edge-deletion resiliency. Ultimately, our model may be used to generate synthetic graph data, test hypotheses and algorithms at different scales, and serve as a baseline model on top of which further electrical network properties, device models, and interdependencies to other networks, may be appended.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

Temperature dependence of nitrate-reducing Fe(II) oxidation by Acidovorax strain BoFeN1 – evaluating the role of enzymatic vs. abiotic Fe(II) oxidation by nitrite

ABSTRACT Fe(II) oxidation coupled to nitrate reduction is a widely observed metabolism. However, to what extent the observed Fe(II) oxidation is driven enzymatically or abiotically by metabolically produced nitrite remains puzzling. To distinguish between biotic and abiotic reactions, we cultivated the mixotrophic nitrate-reducing Fe(II)-oxidizing Acidovorax strain BoFeN1 over a wide range of temperatures and compared it to abiotic Fe(II) oxidation by nitrite at temperatures up to 60°C. The collected experimental data were subsequently analyzed through biogeochemical modeling. At 5°C, BoFeN1 cultures consumed acetate and reduced nitrate but did not significantly oxidize Fe(II). Abiotic Fe(II) oxidation by nitrite at different temperatures showed an Arrhenius-type behavior with an activation energy of 80±7 kJ/mol. Above 40°C, the kinetics of Fe(II) oxidation were abiotically driven, whereas at 30°C, where BoFeN1 can actively metabolize, the model-based interpretation strongly suggested that an enzymatic pathway was responsible for a large fraction (ca. 62%) of the oxidation. This result was reproduced even when no additional carbon source was present. Our results show that at below 30°C, i.e. at temperatures representing most natural environments, biological Fe(II) oxidation was largely responsible for overall Fe(II) oxidation, while abiotic Fe(II) oxidation by nitrite played a less important role.

Microbiology↗

DOE OSTI2023

polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies

Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes, including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Open Hardware in Science: The Benefits of Open Electronics

Abstract Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global “maker” community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions, by improving access to customizable high-end technologies, sustainability, visibility, and interdisciplinary collaboration potential; and (III) the scientific community, by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. We further discuss how current barriers like poor awareness, knowledge access, and time investments can be resolved by increased documentation and collaboration, and provide guidelines for academics to enter this emerging field. We highlight that open electronics are a promising and powerful tool to help scientific research to become more innovative and reproducible and offer a key practical solution to improve democratic access to science.

Oellermann, Michael (ORCID:0000000153926737)↗

DOE OSTI2020

Perturbation theory approach to predict the covariance matrices of the galaxy power spectrum and bispectrum in redshift space

In this paper, we predict the covariance matrices of both the power spectrum and the bispectrum, including full non-Gaussian contributions, redshift space distortions, linear bias effects, and shot-noise corrections, using perturbation theory (PT). To quantify the redshift-space distortion effect, we focus mainly on the monopole and quadrupole components of both the power and bispectra. We, for the first time, compute the 5- and 6-point spectra to predict the cross-covariance between the power and bispectra, and the autocovariance of the bispectrum in redshift space. Further, we test the validity of our calculations by comparing them with the covariance matrices measured from the MultiDark-Patchy mock catalogues that are designed to reproduce the galaxy clustering measured from the Baryon Oscillation Spectroscopic Survey Data Release 12. We argue that the simple, leading-order PT works because the shot-noise corrections for the Patchy mocks are more dominant than other higher order terms we ignore. In the meantime, we confirm some discrepancies in the comparison, especially of the cross-covariance. We discuss potential sources of such discrepancies. We also show that our PT model reproduces well the cumulative signal-to-noise ratio of the power spectrum and the bispectrum as a function of maximum wavenumber, implying that our PT model captures successfully essential contributions to the covariance matrices.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Damped Ly α absorbers and atomic hydrogen in galaxies: the view of the GAEA model

ABSTRACT Using the GAEA semi-analytic model, we analyse the connection between Damped Ly α systems (DLAs) and H i in galaxies. Our state-of-the-art semi-analytic model is tuned to reproduce the local galaxy H i mass function, and that also reproduces other important galaxy properties, including the galaxy mass–gas metallicity relation. To produce catalogues of simulated DLAs we throw 105 random lines of sight in a composite simulated volume: dark matter haloes with log$(\frac{M_{200}}{ {\rm M}_{\odot }}) \ge 11.5$ are extracted from the Millennium Simulation, while for $9.2 \le \log (\frac{M_{200}}{ \mathrm{M}_{\odot }})\lt 11.5$ we use the Millennium II, and for $8 \le \log (\frac{M_{200}}{\mathrm{M}_{\odot }}) \lt 9.2$ a halo occupation distribution model. At 2 < z < 3, where observational data are more accurate, our fiducial model predicts the correct shape of the column density distribution function, but its normalization falls short of the observations, with the discrepancy increasing at higher redshift. The agreement with observations is significantly improved increasing both the H i masses and the disc radii of model galaxies by a factor of 2, as implemented ‘a posteriori’ in our 2M−2R model. In the redshift range of interest, haloes with $M_{200} \ge {10}^{11} \, \mathrm{M}_{\odot }$ give the major contribution to ΩDLA, and the typical DLA host halo mass is $\sim \!{10}^{11} \, \mathrm{M}_{\odot }$. The simulated DLA metallicity distribution is in relatively good agreement with observations, but our model predicts an excess of DLAs at low metallicities. Our results suggest possible improvements for the adopted modelling of the filtering mass and metal ejection in low-mass haloes.

Di Gioia, Serafina↗

DOE OSTI2020

Clues on the history of early-type galaxies from SDSS spectra and GALEX photometry

ABSTRACT Stellar population studies of early-type galaxies (ETGs) based on their optical stellar continuum suggest that these are quiescent systems. However, emission lines and ultraviolet photometry reveal a diverse population. We use a new version of the starlight spectral synthesis code and state-of-the-art stellar population models to simultaneously fit Sloan Digital Sky Survey spectra and Galaxy Evolution Explorer photometry for a sample of 3453 galaxies at z < 0.1 with near ultraviolet (NUV) − r > 5 that are classified as elliptical by Galaxy Zoo. We reproduce far ultraviolet (FUV) magnitudes for 80 per cent of UV upturn galaxies selected using criteria from the literature, suggesting that additional stellar population ingredients such as binaries and extreme horizontal branch stars may have a limited contribution to the UV upturn. The addition of ultraviolet data leads to a broadening of the distributions of mean stellar ages, metallicities, and attenuation. Stellar populations younger than $1\,$ Gyr are required to reproduce the ultraviolet emission in 17 per cent of our sample. These systems represent 43 per cent of the sample at 5 < NUV − r < 5.5 and span the same stellar mass range as other ETGs in our sample. ETGs with young stellar components have larger H α equivalent widths (WH α) and larger dust attenuation. Emission line ratios and WH α indicate that the ionizing source in these systems is a mixture of young and old stellar populations. Their young stellar populations are metal-poor, especially for high-mass galaxies, indicating recent star formation associated with rejuvenation events triggered by external processes, such as minor mergers.

Werle, A.↗

DOE OSTI2020

The star formation properties of the observed and simulated AGN Universe: BAT versus EAGLE

ABSTRACT In this paper, we present data from 72 low-redshift, hard X-ray selected active galactic nucleus (AGN) taken from the Swift–BAT 58 month catalogue. We utilize spectral energy distribution fitting to the optical to infrared photometry in order to estimate host galaxy properties. We compare this observational sample to a volume- and flux-matched sample of AGN from the Evolution and Assembly of GaLaxies and their Environments (EAGLE) hydrodynamical simulations in order to verify how accurately the simulations can reproduce observed AGN host galaxy properties. After correcting for the known +0.2 dex offset in the SFRs between EAGLE and previous observations, we find agreement in the star formation rate (SFR) and X-ray luminosity distributions; however, we find that the stellar masses in EAGLE are 0.2–0.4 dex greater than the observational sample, which consequently leads to lower specific star formation rates (sSFRs). We compare these results to our previous study at high redshift, finding agreement in both the observations and simulations, whereby the widths of sSFR distributions are similar (∼0.4–0.6 dex) and the median of the SFR distributions lie below the star-forming main sequence by ∼0.3–0.5 dex across all samples. We also use EAGLE to select a sample of AGN host galaxies at high and low redshift and follow their characteristic evolution from z = 8 to z = 0. We find similar behaviour between these two samples, whereby star formation is quenched when the black hole goes through its phase of most rapid growth. Utilizing EAGLE we find that 23 per cent of AGN selected at z ∼ 0 are also AGN at high redshift, and that their host galaxies are among the most massive objects in the simulation. Overall, we find EAGLE reproduces the observations well, with some minor inconsistencies (∼0.2 dex in stellar masses and ∼0.4 dex in sSFRs).

Jackson, Thomas M.↗