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DOE OSTI2020

Interpretive MHD modeling of dispersive shell pellet injection for rapid shutdown in tokamaks

Dispersive shell pellet (DSP) injection is modeled with the extended-MHD code NIMROD for interpretive insight into the results of recent DIII-D DSP experiments and to explore the dynamics of an inside-out thermal quench for disruption mitigation in tokamaks. Simulations of the pre-thermal quench (TQ) phase indicate that the upper bound for the quantity of ablated carbon shell material that will not perturb the flux surfaces is in the ballpark of, but somewhat below the experimental quantity. Even below this quantity, sufficient electrons are added to the plasma by the shell material to produce significant dilution cooling before the TQ is triggered. Simulations carried through the end of the TQ have very large amplitude MHD fluctuations (δB/B>10 -2 ) at the time of the plasma current spike associated with current profile redistribution. Finally, after the plasma current spike, which is of comparable amplitude to that measured in DIII-D experiments, none of the runaway electron test-particles whose orbits are tracked throughout the simulation remain confined.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Interpretative transport modeling of the WEST boundary plasma: main plasma and light impurities

Understanding impurity transport in tokamak plasmas is crucial to control radiative losses and material migration in future magnetic fusion reactors. In this work we deploy the SolEdge2D-EIRENE code to model the boundary plasma in a WEST discharge, satisfactorily reproducing measurements of both upstream and divertor plasma conditions. Additionally, the spatial distribution of oxygen, studied here as a representative light impurity, is compared to vacuum ultraviolet spectroscopy measurements acquired with an oscillating line of sight. The simulation captures a key feature of the experiment, namely a factor of sime2 higher oxygen brightness in the inner divertor region compared to the outer one. This spatial asymmetry in oxygen concentration is interpreted by analyzing the balance of friction forces and thermal gradient forces that the light impurity exchanges with the main plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Interpretive modelling of boron transport in the boundary plasma of WEST experiments with the impurity powder dropper

Abstract Boron (B) powder injection is a potential alternative to glow discharge boronization as a wall conditioning method for tokamaks. This technique is currently being studied in WEST experiments, during which B powder is injected by an Impurity Powder Dropper developed by PPPL. In order to interpret and analyse experimental trends, and to help develop future experiments, a modelling workflow using a boundary plasma simulation (SOLEDGE-EIRENE) and powder ablation simulation (Dust Injection Simulator) was developed and tested. The effect of adding a B neutral source to simulated deuterium + oxygen (D + O) plasmas was compared to experimental data from the WEST C5 campaign, where B powder was injected in a dedicated experiment. While the impact of B injection on radiated power P rad measurements at the upper divertor was similar, there were significant differences in measurements of P rad , outer strike point electron temperature T e OSP and O-II line intensity at the lower divertor between experiment and simulation. This discrepancy suggests that those parameters were affected by phenomena not present in the simulations, with the most likely candidates being reduced D recycling and a reduced O sourcing from the divertor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Interpretative 3D MHD modelling of deuterium SPI into a JET H-mode plasma

Abstract The pre-thermal quench (pre-TQ) dynamics of a pure deuterium ( D 2 ) shattered pellet injection (SPI) into a 3 MA / 7 MJ JET H-mode plasma is studied via 3D non-linear MHD modelling with the JOREK code. The interpretative modelling captures the overall evolution of the measured density and radiated power. The simulations also identify the importance of the drifts of ablation plasmoids towards the tokamak low field side (LFS) and the impurities in the background plasma in fragment penetration, assimilation, radiative cooling and MHD activity in D 2 SPI experiments. It is found that plasmoid drifts lead to an about 70% reduction of the central line-integrated density (compared to a simulation without drifts) in the JET D 2 SPI discharge considered. Impurities that pre-exist before the SPI as well as those from possible impurity influxes related to the SPI are shown to dominate the radiation in the considered discharge. With inputs from JOREK simulations, modelling with the Lagrangian particle-based pellet code PELOTON reproduces the deviation of the SPI fragments in the direction of the major radius as observed by the fast camera. This confirms the role of rocket effects and plasmoid drifts in the considered discharge and reinforces the validity of the JOREK modelling. The limited core density rise due to plasmoid drifts and the strong radiative cooling and MHD activity with impurities (depending on their species and concentration) could limit the effectiveness of LFS D 2 SPI in runaway electron avoidance and are worth considering in the design of the ITER disruption mitigation system.

Physics↗

DOE OSTI2024

Super-X and conventional divertor configurations in MAST-U ohmic L-mode; a comparison facilitated by interpretative modelling

Measurements are presented, alongside corresponding interpretative SOLPS-ITER simulations, of the first MAST-U experiments comparing ohmically heated L-mode fuelling scans in Conventional divertor (CD) and Super-X divertor (SXD) configurations. In experiment, at comparable outer mid-plane separatrix electron density, $n_{e,\textrm{sep,OMP}}$, the maximum lower outer target heat load was found to be a factor 16 $\,\pm\,7$ lower in SXD compared to CD. In simulation, a factor 26.8 reduction was found (slightly higher than the experimental range), suggesting an additional reduction in SXD compared to the factor 9.3 expected from geometric considerations alone. According to the simulations, this additional reduction in the SXD is due to a net radial transport of the energy remaining downstream of the $T_e = 5$ eV location. This energy is carried out of the critical (highest heat load) flux tube by deuterium atoms, demonstrating the importance of a longer legged divertor which provides space for this to occur. Importantly, in both simulation and experiment, the SXD has minimal impact on the upstream n e and T e profiles. Spectral inferences of detachment front movement in SXD compare well between simulation and experiment. In regions of high magnetic field gradient, the parallel movement of the front towards the X-point becomes less sensitive to increasing $n_{e,\textrm{sep,OMP}}$, in qualitative agreement with simplified models and previous predictive simulations. Additional aspects, regarding the target ion flux rollover, upstream separatrix temperature and drift effects, are also presented and discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Interpretive modeling of tungsten divertor leakage during experiments with neon gas seeding

Abstract Many existing and future tokamaks with tungsten divertors operate, or will operate, with low- Z impurity seeding, but the direct effect of these seeded impurities on tungsten Scrape-off-Layer (SOL) transport has not been explored in detail. This paper reports on a DIII-D experiment designed to test how tungsten divertor leakage from the Small-Angle Slot V-Shaped, tungsten-coated divertor is impacted by neon seeding at a variety of injection rates and poloidal injection locations. Measurements from the experiment show an inverse relationship between the neon injection rate and the tungsten core penetration factor. Interpretive modeling is performed with a combination of the SOLPS-ITER and DIVIMP codes to assess the underlying tungsten behavior. The modeling results show that the reduction in tungsten divertor leakage is driven by both an increase in the divertor collisionality as well as a reduction in the ion temperature gradient near the divertor target. Collisions between low- Z impurities and tungsten impurities are found to have a significant impact on the tungsten SOL transport, such that ignoring the low- Z impurity collisional effects on the tungsten transport can result in an overestimate of the divertor leakage by an order-of-magnitude. Given the importance of these localized interactions, neon seeding from the closed, slot-like divertor has a clear advantage in being able to reduce tungsten divertor leakage without the high levels of neon core contamination that occur when seeding from other poloidal locations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2015

Laboratory study supporting the interpretation of Solar Dynamics Observatory data

High-resolution extreme ultraviolet spectra of ions in an electron beam ion trap are investigated as a laboratory complement of the moderate-resolution observation bands of the AIA experiment on board the Solar Dynamics Observatory (SDO) spacecraft. Here, the latter observations depend on dominant iron lines of various charge states which in combination yield temperature information on the solar plasma. Our measurements suggest additions to the spectral models that are used in the SDO data interpretation. In the process, we also note a fair number of inconsistencies among the wavelength reference data bases.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Advances in scientific literature mining for interpreting materials characterization

Abstract Using synchrotron light sources, such as the National Synchrotron Light Source II at Brookhaven National Laboratory, scientists in fields as diverse as physics, biology, and materials science, identify the atomic structure, chemical composition, or other important properties of varied specimens. x-ray spectroscopy from light sources is particularly valuable for materials research with vast information available about reference spectra in the scientific literature. However, as the technique is applicable to many science domains, searching for information about select x-ray spectroscopy spectra is impeded by the sheer number of publications. Moreover, useful information about the context of an experiment or figures presented in papers can be buried among the details, which takes time to assess. This work presents a scientific literature mining system that supports data acquisition, information extraction, and user interaction for referencing x-ray spectra identification and spectral interpretation. The goal is to provide efficient access to useful spectral data to researchers who may spend only a few days at a synchrotron light source. With this system, users browse a classification tree for papers arranged according to x-ray spectroscopic methods, chemical elements, and x-ray absorption spectroscopy edges. Relevant figures are extracted with sentences from the paper that explain them, known as ‘figure explanatory text.’ Notably, this system focuses on semantic aspects (logical analysis) to find figure explanatory text using deep contextualized word embeddings techniques and contains an interface to obtain labeled data from domain experts that is used to evaluate and improve the model.

Park, Gilchan (ORCID:0000000201536646)↗

DOE OSTI2021

Variations in pharmacokinetic-pharmacodynamic target values across MICs and their potential impact on determination of susceptibility test interpretive criteria

Abstract Background An antibacterial drug’s susceptibility test interpretive criteria (STIC) are determined by integrating clinical, microbiological and pharmacokinetic-pharmacodynamic (PK-PD) data. PTA analysis plays a pivotal or supportive role in STIC determination and is heavily dependent on the PK-PD target values determined from animal PK-PD studies. Therefore, variations in PK-PD target values may impact STIC determination. Factors contributing to variation in the PK-PD target values include the number of and MICs for bacterial isolates used in animal PK-PD studies. Objectives To analyse the relationship between PK-PD target values and MICs, describe the variations in PK-PD target values of isolates and evaluate whether the proposed/target STICs were within the ranges of the MICs for isolates used in animal PK-PD studies. Methods A database was compiled for this research by screening animal PK-PD study reports submitted to the FDA from 10 new drug applications (NDAs). Results A relationship evaluation between PK-PD target values and MICs for tested isolates for seven drugs (that used AUC/MIC ratio as the PK-PD index) showed that, generally, the AUC/MIC values decreased with an increase in MIC. These target values were highly variable, with the percentage coefficient of variation ranging between 1% and 132% for isolates having the same MIC. For 16/27 (59%) drug/bacteria combinations from all 10 drugs, the proposed/target STICs were higher than the highest MIC for bacteria isolates evaluated, while 6/27 (22.5%) were lower. Conclusions This research suggests that careful considerations related to selection of bacterial isolates for animal PK-PD studies could strengthen the STIC determination process.

Waack, Ursula↗

DOE OSTI2022

Photometric redshifts from SDSS images with an interpretable deep capsule network

ABSTRACT Studies of cosmology, galaxy evolution, and astronomical transients with current and next-generation wide-field imaging surveys like the Rubin Observatory Legacy Survey of Space and Time are all critically dependent on estimates of photometric redshifts. Capsule networks are a new type of neural network architecture that is better suited for identifying morphological features of the input images than traditional convolutional neural networks. We use a deep capsule network trained on ugriz images, spectroscopic redshifts, and Galaxy Zoo spiral/elliptical classifications of ∼400 000 Sloan Digital Sky Survey galaxies to do photometric redshift estimation. We achieve a photometric redshift prediction accuracy and a fraction of catastrophic outliers that are comparable to or better than current methods for SDSS main galaxy sample-like data sets (r ≤ 17.8 and zspec ≤ 0.4) while requiring less data and fewer trainable parameters. Furthermore, the decision-making of our capsule network is much more easily interpretable as capsules act as a low-dimensional encoding of the image. When the capsules are projected on a two-dimensional manifold, they form a single redshift sequence with the fraction of spirals in a region exhibiting a gradient roughly perpendicular to the redshift sequence. We perturb encodings of real galaxy images in this low-dimensional space to create synthetic galaxy images that demonstrate the image properties (e.g. size, orientation, and surface brightness) encoded by each dimension. We also measure correlations between galaxy properties (e.g. magnitudes, colours, and stellar mass) and each capsule dimension. We publicly release our code, estimated redshifts, and additional catalogues at https://biprateep.github.io/encapZulate-1.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Interpreting Sunyaev–Zel’dovich observations with MillenniumTNG: mass and environment scaling relations

ABSTRACT Sunyaev–Zel’dovich (SZ) measurements can dramatically improve our understanding of the intergalactic medium and the role of feedback processes in galaxy formation, allowing us to calibrate important astrophysical systematics in cosmological constraints from weak lensing galaxy clustering surveys. However, the signal is only measured in a two-dimensional projection, and its correct interpretation relies on understanding the connection between observable quantities and the underlying intrinsic properties of the gas, in addition to the relation between the gas and the underlying matter distribution. One way to address these challenges is through the use of hydrodynamical simulations such as the high-resolution, large-volume MillenniumTNG suite. We find that measurements of the optical depth, τ, and the Compton-y parameter, Y, receive large line-of-sight contributions that can be removed effectively by applying a compensated aperture photometry filter. In contrast with other τ probes (e.g. X-rays and fast radio bursts), the kinematic SZ-inferred τ receives most of its signal from a confined cylindrical region around the halo due to the velocity decorrelation along the line of sight. Additionally, we perform fits to the Y–M and τ–M scaling relations and report best-fitting parameters adopting the smoothly broken power law formalism. We note that subgrid physics modelling can broaden the error bar on these by 30 per cent for intermediate-mass haloes (${\sim }10^{13} \, {\rm M}_{\odot }$). The scatter of the scaling relations can be captured by an intrinsic dependence on concentration and an extrinsic dependence on tidal shear. Finally, we comment on the effect of using galaxies rather than haloes in observations, which can bias the inferred profiles by ∼20 per cent for L* galaxies.

Hadzhiyska, Boryana (ORCID:0000000223123121)↗

DOE OSTI2025

Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence–function relationships across protein engineering campaigns

The discovery and engineering of new enzymes is important across the bioeconomy, with diverse applications from foods to pharmaceuticals, sensors to agriculture. However, enzyme engineering, in particular machine learning-guided engineering, is hampered by a lack of data. Currently there exists no database designed to capture and interpret datasets created in this domain, nor are there easy analysis and visualisation tools. We developed the Enzyme Engineering Database to provide a centralized resource and an online analysis tool to consolidate sequence-function data from enzyme engineering campaigns, thereby making three contributions: (i) a database into which researchers can deposit public data, (ii) visualisation and analysis tools for protein engineers to analyse their own data or compare enzyme variants to other engineering campaigns, and (iii) a gold-standard dataset for benchmarking automated extraction along with the first large language model extraction pipeline specific for enzyme engineering campaigns. The Enzyme Engineering Database is accessible at http://enzengdb.org/.

Long, Yueming [California Institute of Technology ↗

DOE OSTI2017

Interpretation of Urinary Excretion Data From Plutonium Wound Cases Treated With DTPA: Application of Different Models and Approaches

After a chelation treatment, assessment of intake and doses is the primary concern of an internal dosimetrist. Using the urinary excretion data from two actual wound cases encountered at Los Alamos National Laboratory (LANL), this study discusses several methods that can be used to interpret intakes from the urinary data collected after one or multiple chelation treatments. One of the methods uses only the data assumed to be unaffected by chelation (data collected beyond 100 d after the last treatment). This method, used by many facilities for official dose records, was implemented by employing maximum likelihood analysis and Bayesian analysis methods. The impacts of an improper assumption about the physicochemical behavior of a radioactive material and the importance of the use of a facility-specific biokinetic model when available have also been demonstrated. Another method analyzed both the affected and unaffected urinary data using an empirical urinary excretion model. This method, although case-specific, was useful in determining the actual intakes and the doses averted or the reduction in body burdens due to chelation treatments. Finally, this approach was important in determining the enhancement factors, the behavior of the chelate, and other observations that may be pertinent to several DTPA compartmental modeling approaches being conducted by the health physics community.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2020

Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testisspecific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Interpretable and Efficient Interferometric Contrast in Scanning Transmission Electron Microscopy with a Diffraction-Grating Beam Splitter

Efficient imaging of biomolecules, 2D materials and electromagnetic fields depends on retrieval of the phase of transmitted electrons. We demonstrate a method to measure phase in a scanning transmission electron microscope using a nanofabricated diffraction grating to produce multiple probe beams. The measured phase is more interpretable than phase-contrast scanning transmission electron microscopy techniques without an off-axis reference wave, and the resolution could surpass that of off-axis electron holography. Here, we apply the technique to image nanoparticles, carbon sub- strates and electric fields. The contrast observed in experiments agrees well with contrast predicted in simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Quantitative and interpretable order parameters for phase transitions from persistent homology

Here, we apply modern methods in computational topology to the task of discovering and characterizing phase transitions. As illustrations, we apply our method to four two-dimensional lattice spin models: the Ising, square ice, XY, and fully frustrated XY models. In particular, we use persistent homology, which computes the births and deaths of individual topological features as a coarse-graining scale or sublevel threshold is increased, to summarize multiscale and high-point correlations in a spin configuration. We employ vector representations of this information called persistence images to formulate and perform the statistical task of distinguishing phases. For the models we consider, a simple logistic regression on these images is sufficient to identify the phase transition. Interpretable order parameters are then read from the weights of the regression. This method suffices to identify magnetization, frustration, and vortex-antivortex structure as relevant features for phase transitions in our models. We also define “persistence” critical exponents and study how they are related to those critical exponents usually considered.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Interpretation of Ir L-edge isotropic x-ray absorption spectra across the pressure-induced dimerization transition in hyper-honeycomb beta-Li2IrO3

The extended nature of atomic 5d orbitals, together with a relatively short ~ 3 °A Ir-Ir distance across edge-shared octahedra in honeycomb iridate lattices, leads to a tendency to disrupt the local, spin-orbit entangled jeff = 1 2 moments of Ir4+ ions in favor of dimerization and formation of molecular orbitals, especially upon lattice compression. The sensitivity of Ir L-edge spectroscopy to both spin-orbit entanglement in jeff states and quenching of orbital degrees of freedom in dimerized states, results in a peculiar evolution of x-ray absorption spectra across dimerization transitions including energy shifts in opposite direction for L3 and L2 leading absorption edges, and substantial changes in their isotropic branching ratio. We present a theoretical description of the evolution of 5d electronic states, and related x-ray absorption spectra, in going from the single ion to the dimerized limit. The calculations reproduce the experimental results for hyper-honeycomb β-Li2IrO3[1, 2] and shed light into the weakening of the coupling between spin and orbital degrees of freedom as the strength of dimerization increases. The results provide a basis for interpretation of L-edge xray absorption spectra in 5d systems where competition between formation of local jeff states and molecular orbitals is at play.

van Veenendaal, Michel↗

DOE OSTI2019

Interpretable machine learning study of the many-body localization transition in disordered quantum Ising spin chains

We apply support vector machine (SVM) to study the phase transition between many-body localized and thermal phases in a disordered quantum Ising chain in a transverse external field. The many-body eigenstate energy E is bounded by a bandwidth W = E max – E min . The transition takes place on a phase diagram spanned by the energy density ε = 2(E – E min )/W and the disorder strength δJ of the spin interaction uniformly distributed within [ – δJ, δJ], formally parallel to the mobility edge in Anderson localization. In our paper, we use the labeled probability density of eigenstate wave functions belonging to the deeply localized and thermal regimes at two different energy densities (ε's) as the training set, i.e., providing labeled data at four corners of the phase diagram. Then we employ the trained SVM to predict the whole phase diagram. The obtained phase boundary qualitatively agrees with previous work using entanglement entropy to characterize these two phases. We further analyze the decision function of the SVM to interpret its physical meaning and find that it is analogous to the inverse participation ratio in configuration space. Our findings demonstrate the ability of the SVM to capture potential quantities that may characterize the many-body localization phase transition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗