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21. Overview of NSTX Upgrade Initial Results and Modelling Highlights

Author(s):
Menard, J.E.; Allain, J.P.; Battaglia, D.J.; Bedoya, F.; Bell, R.E.; Belova, E.; Berkery, J.W.; Boyer, M.D.; Crocker, N.; Diallo, A.; Ebrahimi, F.; Ferrraro, N.; Fredrickson, E.; Frerichs, H.; Gerhardt, S.; Gorelenkov, N.; Guttenfelder, W.; Heidbrink, W.; Kaita, R.; Kaye, S.M.; Kriete, D.M.; Kubota, S.; LeBlanc, B.P.; Liu, D.; Lunsford, R.; Mueller, D.; Myers, C.E.; Ono, M.; Park, J.-K.; Podesta, M.; Raman, R.; Reinke, M.; Ren, Y.; Sabbagh, S.A.; Schmitz, O.; Scotti, F.; Sechrest, Y.; Skinner, C.H.; Smith, D.R.; Soukhanovskii, V.; Stoltzfus-Dueck, T.; Yuh, H.; Wang, Z.; Waters, I.; Ahn, J.-W.; Andre, R.; Barchfeld, R.; Beiersdorfer, P.; Bertelli, N.; Bhattacharjee, A.; Boyle, D.; Brennan, D.; Buttery, R.; Capece, A.; Canal, G.; Canik, J.; Chang, C.S.; Darrow, D.; Delgado-Aparicio, L.; Domier, C.; Ethier, S.; Evans, T.; Ferron, J.; Finkenthal, M.; Fonck, R.; Gan, K.; Gates, D.; Goumiri, I.; Gray, T.; Hosea, J.; Humphreys, D.; Jarboe, T.; Jardin, S.; Jaworski, M.A.; Koel, B.; Kolemen, E.; Ku, S.; LaHaye, R.J.; Levinton, F.; Luhmann Jr., N.; Maingi, R.; Maqueda, R.; McKee, G.; Meier, E.; Myra, J.; Perkins, R.; Poli, F.; Rhodes, T.; Riquezes, J.; Rowley, C.; Russell, D.; Schuster, E.; Stratton, B.; Stutman, D.; Taylor, G.; Tritz, K.; Wang, W.; Wirth, B.; Zweben, S.J.
Abstract:
The National Spherical Torus Experiment (NSTX) has undergone a major upgrade, and the NSTX Upgrade (NSTX-U) Project was completed in the summer of 2015. NSTX-U first plasma was subsequently achieved, diagnostic and control systems have been commissioned, H-Mode accessed, magnetic error fields identified and mitigated, and the first physics research campaign carried out. During 10 run weeks of operation, NSTX-U surpassed NSTX-record pulse-durations and toroidal fields, and high-performance ~1MA H-mode plasmas comparable to the best of NSTX have been sustained near and slightly above the n=1 no-wall stability limit and with H-mode confinement multiplier H98y2 above 1. Transport and turbulence studies in L-mode plasmas have identified the coexistence of at least two ion-gyro-scale turbulent micro-instabilities near the same radial location but propagating in opposite (i.e. ion and electron diamagnetic) directions. These modes have the characteristics of ion-temperature gradient and micro-tearing modes, respectively, and the role of these modes in contributing to thermal transport is under active investigation. The new second more tangential neutral beam injection was observed to significantly modify the stability of two types of Alfven Eigenmodes. Improvements in offline disruption forecasting were made in the areas of identification of rotating MHD modes and other macroscopic instabilities using the Disruption Event Characterization and Forecasting (DECAF) code. Lastly, the Materials Analysis and Particle Probe (MAPP) was utilized on NSTX-U for the first time and enabled assessments of the correlation between boronized wall conditions and plasma performance. These and other highlights from the first run campaign of NSTX-U are described.
Type:
Dataset
Issue Date:
October 2017

22. Data for: Persistent hepatitis B virus and HIV coinfections in dually humanized mice engrafted with human liver and immune system

Author(s):
Ploss, Alexander; Hogan, Glenn; Winer, Benjamin; Ahodantin, James; Sellau, Julie; Huang, Tiffany; Douam, Florian; Funaki, Masaya; Chiriboga, Luis; Su, Lishan
Abstract:
Chronic hepatitis B (CHB), caused by hepatitis B virus (HBV), remains a major medical problem. HBV has a high propensity for progressing to chronicity and can result in severe liver disease, including fibrosis, cirrhosis and hepatocellular carcinoma. CHB patients frequently present with viral coinfection, including HIV and hepatitis delta virus. About 10% of chronic HIV carriers are also persistently infected with HBV which can result in more exacerbated liver disease. Mechanistic studies of HBV-induced immune responses and pathogenesis, which could be significantly influenced by HIV infection, have been hampered by the scarcity of immunocompetent animal models. Here, we demonstrate that humanized mice dually engrafted with components of a human immune system and a human liver supported HBV infection, which was partially controlled by human immune cells, as evidenced by lower levels of serum viremia and HBV replication intermediates in the liver. HBV infection resulted in priming and expansion of human HLA-restricted CD8+ T cells, which acquired an activated phenotype. Notably, our dually humanized mice support persistent coinfections with HBV and HIV which opens opportunities for analyzing immune dysregulation during HBV and HIV coinfection and preclinical testing of novel immunotherapeutics.
Type:
Dataset
Issue Date:
12 June 2023

23. Femtosecond X-ray Diffraction of Laser-shocked Forsterite (Mg2SiO4) to 122 GPa

Author(s):
Kim, Donghoon; Tracy, Sally J.; Smith, Raymond F.; Gleason, Arianna E.; Bolme, Cindy A.; Prakapenka, Vitali B.; Appel, Karen; Speziable, Sergio; Wicks, June K.; Berryman, Eleanor J.; Han, Sirus K.; Schoelmerich, Markus O.; Lee, Hae Ja; Nagler, Bob; Cunningham, Eric F.; Akin, Minta C.; Asimow, Paul D.; Eggert, Jon H.; Duffy, Thomas S.
Abstract:
The behavior of forsterite, Mg2SiO4, under dynamic compression is of fundamental importance for understanding its phase transformations and high-pressure behavior. Here, we have carried out an in situ X-ray diffraction study of laser-shocked poly- and single-crystal forsterite (a-, b-, and c- orientations) from 19 to 122 GPa using the Matter in Extreme Conditions end-station of the Linac Coherent Light Source. Under laser-based shock loading, forsterite does not transform to the high-pressure equilibrium assemblage of MgSiO3 bridgmanite and MgO periclase, as was suggested previously. Instead, we observe forsterite and forsterite III, a metastable polymorph of Mg2SiO4, coexisting in a mixed-phase region from 33 to 75 GPa for both polycrystalline and single-crystal samples. Densities inferred from X-ray diffraction data are consistent with earlier gas-gun shock data. At higher stress, the behavior observed is sample-dependent. Polycrystalline samples undergo amorphization above 79 GPa. For [010]- and [001]-oriented crystals, a mixture of crystalline and amorphous material is observed to 108 GPa, whereas the [100]-oriented crystal adopts an unknown crystal structure at 122 GPa. The Q values of the first two sharp diffraction peaks of amorphous Mg2SiO4 show a similar trend with compression as those observed for MgSiO3 glass in both recent static and laser-compression experiments. Upon release to ambient pressure, all samples retain or revert to forsterite with evidence for amorphous material also present in some cases. This study demonstrates the utility of femtosecond free-electron laser X-ray sources for probing the time evolution of high-pressure silicates through the nanosecond-scale events of shock compression and release.
Type:
Dataset
Issue Date:
November 2020

24. Fast animal pose estimation using deep neural networks

Author(s):
Pereira, Talmo D.; Aldarondo, Diego E.; Willmore, Lindsay; Kislin, Mikhail; Wang, Samuel S.-H.; Murthy, Mala; Shaevitz, Joshua W.
Abstract:
Recent work quantifying postural dynamics has attempted to define the repertoire of behaviors performed by an animal. However, a major drawback to these techniques has been their reliance on dimensionality reduction of images which destroys information about which parts of the body are used in each behavior. To address this issue, we introduce a deep learning-based method for pose estimation, LEAP (LEAP Estimates Animal Pose). LEAP automatically predicts the positions of animal body parts using a deep convolutional neural network with as little as 10 frames of labeled data for training. This framework consists of a graphical interface for interactive labeling of body parts and software for training the network and fast prediction on new data (1 hr to train, 185 Hz predictions). We validate LEAP using videos of freely behaving fruit flies (Drosophila melanogaster) and track 32 distinct points on the body to fully describe the pose of the head, body, wings, and legs with an error rate of <3% of the animal's body length. We recapitulate a number of reported findings on insect gait dynamics and show LEAP's applicability as the first step in unsupervised behavioral classification. Finally, we extend the method to more challenging imaging situations (pairs of flies moving on a mesh-like background) and movies from freely moving mice (Mus musculus) where we track the full conformation of the head, body, and limbs.
Type:
Dataset
Issue Date:
30 May 2018

25. Data corresponding to our paper on "Chemotactic smoothing of collective migration"

Author(s):
Bhattacharjee, Tapomoy; Amchin, Daniel; Alert, Ricard; Ott, Jenna; Datta, Sujit
Abstract:
Collective migration -- the directed, coordinated motion of many self-propelled agents -- is a fascinating emergent behavior exhibited by active matter that has key functional implications for biological systems. Extensive studies have elucidated the different ways in which this phenomenon may arise. Nevertheless, how collective migration can persist when a population is confronted with perturbations, which inevitably arise in complex settings, is poorly understood. Here, by combining experiments and simulations, we describe a mechanism by which collectively migrating populations smooth out large-scale perturbations in their overall morphology, enabling their constituents to continue to migrate together. We focus on the canonical example of chemotactic migration of Escherichia coli, in which fronts of cells move via directed motion, or chemotaxis, in response to a self-generated nutrient gradient. We identify two distinct modes in which chemotaxis influences the morphology of the population: cells in different locations along a front migrate at different velocities due to spatial variations in (i) the local nutrient gradient and in (ii) the ability of cells to sense and respond to the local nutrient gradient. While the first mode is destabilizing, the second mode is stabilizing and dominates, ultimately driving smoothing of the overall population and enabling continued collective migration. This process is autonomous, arising without any external intervention; instead, it is a population-scale consequence of the manner in which individual cells transduce external signals. Our findings thus provide insights to predict, and potentially control, the collective migration and morphology of cell populations and diverse other forms of active matter.
Type:
Dataset
Issue Date:
24 June 2021

26. Raw Data for GrsA Sub-domain Dynamics

Author(s):
Sun, Xun; Alfermann, Jonas; Li, Hao; Watkins, Maxwell B.; Chen, Yi-Tsao; Chu, Jhih-Wei; Ando, Nozomi
Abstract:
This repository contains the raw photon-by-photon single-molecule FRET (smFRET) trajectories, SAXS data, and MD simulation trajectories, multi-sequence alignment, and gel images for the paper titled "Sub-Domain Dynamics Enables Chemical Chain Reactions in Nonribosomal Peptide Synthetases."
Type:
Dataset
Issue Date:
2 August 2023

27. Hydrogen Retention in Lithium on Metallic Walls from “In Vacuo” Analysis in LTX and Implications for High-Z Plasma-Facing Components in NSTX-U

Author(s):
Kaita, R.; Lucia, M.; Allain, J. P.; Bedoya, F.; Capece, A.; Jaworski, M.; Koel, B. E.; Majeski, R.; Roszell, J.; Schmitt, J.; Scotti, F.; Skinner, C. H.; Soukhanovskii, V.
Abstract:
The application of lithium to plasma-facing components (PFCs) has long been used as a technique for wall conditioning in magnetic confinement devices to improve plasma performance. Determining the characteristics of PFCs at the time of exposure to the plasma, however, is difficult because they can only be analyzed after venting the vacuum vessel and removing them at the end of an operational period. The Materials Analysis and Particle Probe (MAPP) addresses this problem by enabling PFC samples to be exposed to plasmas, and then withdrawn into an analysis chamber without breaking vacuum. The MAPP system was used to introduce samples that matched the metallic PFCs of the Lithium Tokamak Experiment (LTX). Lithium that was subsequently evaporated onto the walls also covered the MAPP samples, which were then subject to LTX discharges. In vacuo extraction and analysis of the samples indicated that lithium oxide formed on the PFCs, but improved plasma performance persisted in LTX. The reduced recycling this suggests is consistent with separate surface science experiments that demonstrated deuterium retention in the presence of lithium oxide films. Since oxygen decreases the thermal stability of the deuterium in the film, the release of deuterium was observed below the lithium deuteride dissociation temperature. This may explain what occurred when lithium was applied to the surface of the NSTX Liquid Lithium Divertor (LLD). The LLD had segments with individual heaters, and the deuterium-alpha emission was clearly lower in the cooler regions. The plan for NSTX-U is to replace the graphite tiles with high-Z PFCs, and apply lithium to their surfaces with lithium evaporation. Experiments with lithium coatings on such PFCs suggest that deuterium could still be retained if lithium compounds form, but limiting their surface temperatures may be necessary.
Type:
Dataset
Issue Date:
2016

28. Advances in boronization on NSTX-Upgrade

Author(s):
Skinner, C.H.; Bedoya, F.; Scotti, F.; Allain, J.P.; Blanchard, W.; Cai, D.; Jaworski, M.; Koel, B.E.
Abstract:
Boronization has been effective in reducing plasma impurities and enabling access to higher density, higher confinement plasmas in many magnetic fusion devices. The National Spherical Torus eXperiment, NSTX, has recently undergone a major upgrade to NSTX-U in order to develop the physics basis for a ST-based Fusion Nuclear Science Facility (FNSF) with capability for double the toroidal field, plasma current, and NBI heating power and increased pulse duration from 1–1.5 s to 5–8 s. A new deuterated tri-methyl boron conditioning system was implemented together with a novel surface analysis diagnostic. We report on the spatial distribution of the boron deposition versus discharge pressure, gas injection and electrode location. The oxygen concentration of the plasma facing surface was measured by in-vacuo XPS and increased both with plasma exposure and with exposure to trace residual gases. This increase correlated with the rise of oxygen emission from the plasma.
Type:
Dataset
Issue Date:
January 2017