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1. A novel scheme for error field correction in permanent magnet stellarators

Author(s):
Rutkowski, Adam; Hammond, Kenneth; Zhu, Caoxiang; Gates, David; Chambliss, Amelia
Abstract:
Stellarators offer a promising path towards fusion reactors, but their design and construction are complicated by stringent tolerance requirements on highly complex 3D coils. A potential way to simplify the engineering requirements for stellarators is to use simple planar toroidal field coils along with permanent magnet arrays to generate shaping fields. In order to ensure sufficient field accuracy while minimizing engineering complexity and system cost, new techniques are required to correct the field produced by the permanent magnet arrays to within requirements set by plasma physics. This work describes a novel correction method developed for this purpose. This analysis is applied to the design of a quasi-axisymmetric stellarator that employs a combination of permanent magnets and planar toroidal field coils to generate its magnetic field. Analysis techniques and initial results using the method for error correction on a proposed permanent magnet stellarator are shown, and it is demonstrated that the method successfully meets the design requirements of the project.
Type:
Dataset
Issue Date:
7 December 2022

2. CLEVR-Matrices

Author(s):
Mondal, Shanka Subhra; Webb, Taylor; Cohen, Jonathan
Abstract:
A dataset of Raven’s Progressive Matrices (RPM)-like problems using realistically rendered 3D shapes, based on source code from CLEVR (a popular visual-question-answering dataset) (Johnson, J., Hariharan, B., Van Der Maaten, L., Fei-Fei, L., Lawrence Zitnick, C., & Girshick, R. (2017). Clevr: A diagnostic dataset for compositional language and elementary visual reasoning. In Proceedings of the IEEE conference on computer vision and pattern recognition (pp. 2901-2910)).
Type:
Dataset
Issue Date:
1 March 2023

3. Electromagnetic total-f algorithm for gyrokinetic particle-in-cell simulations of boundary plasma in XGC

Author(s):
Hager, Robert; Ku, Seung-Hoe; Sharma, Amil Y.; Churchill, Randy Michael; Chang, C. S.; Scheinberg, Aaron
Abstract:
The simplified delta-f mixed-variable/pull-back electromagnetic simulation algorithm implemented in XGC for core plasma simulations by Cole et al. [Phys. Plasmas 28, 034501 (2021)] has been generalized to a total-f electromagnetic algorithm that can include, for the first time, the boundary plasma in diverted magnetic geometry with neutral particle recycling, turbulence and neoclassical physics. The delta-f mixed-variable/pull-back electromagnetic implementation is based on the pioneering work by Kleiber and Mischenko et al. [Kleiber et al., Phys. Plasmas 23, 032501 (2016); Mishchenko et al., Comput. Phys. Commun. 238, 194 (2019)]. An electromagnetic demonstration simulation is performed in a DIII-D-like, H-mode boundary plasma, including a corresponding comparative electrostatic simulation, which confirms that the electromagnetic simulation is necessary for a higher fidelity understanding of the electron particle and heat transport even at the low-beta pedestal foot in the vicinity of the magnetic separatrix.
Type:
Dataset
Issue Date:
21 November 2022

4. Laboratory study of the failed torus mechanism in arched, line-tied, magnetic flux ropes

Author(s):
Alt, Andrew; Ji, Hantao; Yoo, Jongsoo; Bose, Sayak; Goodman, Aaron; Yamada, Masaaki
Abstract:
Coronal mass ejections (CMEs) are some of the most energetic and violent events in our solar system. The prediction and understanding of CMEs is of particular importance due to the impact that they can have on Earth-based satellite systems, and in extreme cases, ground-based electronics. CMEs often occur when long-lived magnetic flux ropes (MFRs) anchored to the solar surface destabilize and erupt away from the Sun. One potential cause for these eruptions is an ideal magnetohydrodynamic (MHD) instability such as the kink or torus instability. Previous experiments on the Magnetic Reconnection eXperiment (MRX) revealed a class of MFRs that were torus-unstable but kink-stable, which failed to erupt. These “failed-tori” went through a process similar to Taylor relaxation where the toroidal current was redistributed before the eruption ultimately failed. We have investigated this behavior through additional diagnostics that measure the current distribution at the foot points and the energy distribution before and after an event. These measurements indicate that ideal MHD effects are sufficient to explain the energy distribution changes during failed torus events. This excludes Taylor relaxation as a possible mechanism of current redistribution during an event. A new model that only requires non-ideal effects in a thin layer above the electrodes is presented to explain the observed phenomena. This work broadens our understanding of the stability of MFRs and the mechanism behind the failed torus through the improved prediction of the torus instability and through new diagnostics to measure the energy inventory and current profile at the foot points.
Type:
Dataset
Issue Date:
2023

5. Reduced Physics Model of the Tokamak Scrape-off-Layer for Pulse Design

Author(s):
Zhang, Xin
Abstract:
The dynamic interplay between the core and the edge plasma has important consequences in the confinement and heating of fusion plasma. The transport of the Scrape-Off-Layer (SOL) plasma imposes boundary conditions on the core plasma, and neutral transport through the SOL influences the core plasma sourcing. In order to better study these effects in a self-consistent, time-dependent fashion with reasonable turn-around time, a reduced model is needed. In this paper we introduce the SOL Box Model, a reduced SOL model that calculates the plasma temperature and density in the SOL given the core-to-edge particle and power fluxes and recycling coefficients. The analytic nature of the Box Model allows one to readily incorporate SOL physics in time-dependent transport solvers for pulse design applications in the control room. Here we demonstrate such a coupling with the core transport solver TRANSP and compare the results with density and temperature measurements, obtained through Thomson scattering and Langmuir probes, of an NSTX discharge. Implications for future interpretive and predictive simulations are discussed.
Type:
Dataset
Issue Date:
January 2023

6. Telomere Length in Preterm Infants

Author(s):
Notterman, Daniel A; Schneper, Lisa M; Drake, Amanda; Piyasena, Chinthika
Abstract:
This entry contains the data used in the PLOS ONE publication entitled, "Characteristics of salivary telomere length shortening in preterm infants" by Schneper et al. The objective of the study was to examine the association between gestational age, telomere length (TL) and rate of shortening in newborns. Genomic DNA was isolated from buccal samples of 39 term infants at birth and one year and 32 preterm infants at birth, term-adjusted age (40 weeks post-conception) and age one-year corrected for gestational duration. Telomere length was measured by quantitative real-time PCR. Demographic and clinical data were collected during clinic or research visits and from hospital records. Socioeconomic status was estimated using the deprivation category (DEPCAT) scores derived from the Carstairs score of the subject's postal code.
Type:
Dataset
Issue Date:
5 January 2023

7. Topological Langmuir-cyclotron wave

Author(s):
Qin, Hong; Fu, Yichen
Abstract:
The data set consists of the figures in a manuscript tilted Topological Langmuir-cyclotron wave. There are 10 figures with captions.
Type:
Image
Issue Date:
2022

10. Data and code for “Structured foraging of soil predators unveils functional responses to bacterial defenses”

Author(s):
Gregor, Thomas; Rossine, Fernando
Abstract:
Microscopy images are part of a paper entitled "Structured foraging of soil predators unveils functional responses to bacterial defenses" by Fernando Rossine, Gabriel Vercelli, Corina Tarnita, and Thomas Gregor. For detailed acquisition methods see the paper. Experiments were performed between 2019 and 2020 at Princeton University. Two types of images are provided, macroscopic and microscopic widefiled Images. Macroscopic images all show Petri dishes covered in fluorescent bacteria being consumed by amoebae. Images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum. Images used for the creation of a profile were all taken within 30 minutes of each other. Within each directory numbered images are independent replicates. The raw video directory contains time series for dishes under drug treatments. Each numbered folder is a sequence of photos (taken 30 minutes apart of each other) of a single dish. Microscopic images all show amoebae consuming bacteria on a petri dish. The 45 minute videos show either edge cells (located at the edge of amoebae colonies), or inner cells (located 2.5 millimeters towards the center of the colony, from the edge). Videos are confocal stacks, with bacteria showing in green and amoebae appearing as black holes within the bacterial lawn. As was for the macroscopic images, images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum.
Type:
Dataset and Software
Issue Date:
11 November 2022

11. Data for "The value of fusion energy to a decarbonized United States electric grid"

Author(s):
Schwartz, Jacob A.; Ricks, Wilson; Kolemen, Egemen; Jenkins, Jesse D.
Abstract:
Fusion could be a part of future decarbonized electricity systems, but it will need to compete with other technologies. In particular, pulsed tokamaks plants have a unique operational mode, and evaluating which characteristics make them economically competitive can help select between design pathways. Using a capacity expansion and operations model, we determined cost thresholds for pulsed tokamaks to reach a range of penetration levels in a future decarbonized US Eastern Interconnection. The required capital cost to reach a fusion capacity of 100 GW varied from $3000 to $7200/kW, and the equilibrium penetration increases rapidly with decreasing cost. The value per unit power capacity depends on the variable operational cost and on cost of its competition, particularly fission, much more than on the pulse cycle parameters. These findings can therefore provide initial cost targets for fusion more generally in the United States.
Type:
Dataset
Issue Date:
2022

12. Data for “Global adjoint tomography—model GLAD-M25”

Author(s):
Lei, Wenjie
Abstract:
The dataset contains the model file for the Global Adjoint Tomography Model 25 (GLAD-M25). The model file contains parameters defined on the spectral-element mesh and is recommend to be used in SPECFEM3D GLOBE for seismic wave simulation at the global scale.
Type:
Dataset
Issue Date:
5 April 2022

13. Data for: "Structure and Density of Silicon Carbide to 1.5 TPa and Implications for Extrasolar Planets"

Author(s):
Kim, Donghoon
Abstract:
There has been considerable recent interest in the high-pressure behavior of silicon carbide, a potential major constituent of carbon-rich exoplanets. In this work, the atomic-level structure of SiC was determined through in situ X-ray diffraction under laser-driven ramp compression up to 1.5 TPa; stresses more than seven times greater than previous static and shock data. Here we show that the B1-type structure persists over this stress range and we have constrained its equation of state (EOS). Using this data we have determined the first experimentally based mass-radius curves for a hypothetical pure SiC planet. Interior structure models are constructed for planets consisting of a SiC-rich mantle and iron-rich core. Carbide planets are found to be ~10% less dense than corresponding terrestrial planets.
Type:
Dataset
Issue Date:
28 April 2022

14. Data for: "The origin of non-skeletal carbonate mud and implications for global climate"

Author(s):
Geyman, Emily C.; Wu, Ziman; Nadeau, Matthew D.; Edmonsond, Stacey; Turner, Andrew; Purkis, Sam J.; Howes, Bolton; Dyer, Blake; Ahm, Anne-Sofie C.; Yao, Nan; Deutsch, Curtis A.; Higgins, John A.; Stolper, Daniel A.; Maloof, Adam C.
Abstract:
Carbonate mud represents one of the most important geochemical archives for reconstructing ancient climatic, environmental, and evolutionary change from the rock record. Mud also represents a major sink in the global carbon cycle. Yet, there remains no consensus about how and where carbonate mud is formed. In this contribution, we present new geochemical data that bear on this problem, including stable isotope and minor and trace element data from carbonate sources in the modern Bahamas such as ooids, corals, foraminifera, and green algae.
Type:
Dataset
Issue Date:
16 June 2022

15. Data set for "NAPS: Integrating pose estimation and tag-based tracking"

Author(s):
Wolf, Scott W.
Abstract:
Data set corresponding to "NAPS: Integrating pose estimation and tag-based tracking." This dataset contains the corresponding videos, tracking scripts, and SLEAP models along with SLEAP, NAPS, and ArUco tracking results.
Type:
Dataset
Issue Date:
7 December 2022

16. Design of an arrangement of cubic magnets for a quasi-axisymmetric stellarator experiment

Author(s):
Hammond, Kenneth; Zhu, Caoxiang; Korrigan, Keith; Gates, David; Lown, Robert; Mercurio, Robert; Qian, Tony; Zarnstorff, Michael
Abstract:
The usage of permanent magnets to shape the confining field of a stellarator has the potential to reduce or eliminate the need for non-planar coils. As a proof-of-concept for this idea, we have developed a procedure for designing an array of cubic permanent magnets that works in tandem with a set of toroidal-field coils to confine a stellarator plasma. All of the magnets in the design are constrained to have identical geometry and one of three polarization types in order to simplify fabrication while still producing sufficient field accuracy. We present some of the key steps leading to the design, including the geometric arrangement of the magnets around the device, the procedure for optimizing the polarizations according to three allowable magnet types, and the choice of magnet types to be used. We apply these methods to design an array of rare-Earth permanent magnets that can be paired with a set of planar toroidal-field coils to confine a quasi-axisymmetric plasma with a toroidal magnetic field strength of about 0.5 T on axis.
Type:
Dataset
Issue Date:
2022

17. Effects of collisional ion orbit loss on neoclassical tokamak radial electric fields

Author(s):
Zhu, Hongxuan; Stoltzfus-Dueck, T; Hager, R; Ku, S; Chang, C. S.
Abstract:
Ion orbit loss is considered important for generating the radially inward electric field Er in a tokamak edge plasma. In particular, this effect is emphasized in diverted tokamaks with a magnetic X point. In neoclassical equilibria, Coulomb collisions can scatter ions onto loss orbits and generate a radially outward current, which in steady state is balanced by the radially inward current from viscosity. To quantitatively measure this loss-orbit current in an edge pedestal, an ion-orbit-flux diagnostic has been implemented in the axisymmetric version of the gyrokinetic particle-in-cell code XGC. As the first application of this diagnostic, a neoclassical DIII-D H-mode plasma is studied using gyrokinetic ions and adiabatic electrons. The validity of the diagnostic is demonstrated by studying the collisional relaxation of Er in the core. After this demonstration, the loss-orbit current is numerically measured in the edge pedestal in quasisteady state. In this plasma, it is found that the radial electric force on ions from Er approximately balances the ion radial pressure gradient in the edge pedestal, with the radial force from the plasma flow term being a minor component. The effect of orbit loss on Er is found to be only mild.
Type:
Dataset
Issue Date:
2022

18. Electron Temperature Gradient Driven Transport Model for Tokamak Plasmas

Author(s):
Rafiq, Tariq; Wilson, Christopher; Luo, Lixiang; Weiland, Jan; Schuster, Eugenio; Pankin, Alexei; Guttenfelder, Walter; Kaye, Stan
Abstract:
A new model for electron temperature gradient (ETG) modes is developed as a component of the Multi-Mode anomalous transport module [T. Rafiq \textit{et al.,} Phys Plasmas \textbf{20}, 032506 (2013)] to predict a time dependent electron temperature profile in conventional and low aspect ratio tokamaks. This model is based on two-fluid equations that govern the dynamics of low-frequency short- and long-wavelength electromagnetic toroidal ETG driven drift modes. A low collisionality NSTX discharge is used to scan the plasma parameter dependence on the ETG real frequency, growth rate, and electron thermal diffusivity. Electron thermal transport is discovered in the deep core region where modes are more electromagnetic in nature. Several previously reported gyrokinetic trends are reproduced, including the dependencies of density gradients, magnetic shear, $\beta$ and gradient of $\beta$ $(\betap)$, collisionality, safety factor, and toroidicity, where $\beta$ is the ratio of plasma pressure to the magnetic pressure. The electron heat diffusivity associated with the ETG mode is discovered to be on a scale consistent with the experimental diffusivity determined by power balance analysis.
Type:
Dataset
Issue Date:
30 August 2022

20. Energetic particle optimization of quasi-axisymmetric stellarator equilibria

Author(s):
LeViness, Alexandra; Schmitt, John; Lazerson, Samuel; Bader, Aaron; Faber, Benjamin; Hammond, Kenneth; Gates, David
Abstract:
An important goal of stellarator optimization is to achieve good confinement of energetic particles such as, in the case of a reactor, alphas created by Deuterium-Tritium (D-T) fusion. In this work, a fixed-boundary stellarator equilibrium was re-optimized for energetic particle confinement via a two-step process: first, by minimizing deviations from quasi-axisymmetry (QA) on a single flux surface near the mid-radius, and secondly by maintaining this improved quasi-axisymmetry while minimizing the analytical quantity ΓC , which represents the angle between magnetic flux surfaces and contours of J||, the second adiabatic invariant. This was performed multiple times, resulting in a group of equilibria with significantly reduced energetic particle losses, as evaluated by Monte Carlo simulations of alpha particles in scaled-up versions of the equilibria. This is the first time that energetic particle losses in a QA stellarator have successfully been reduced by optimizing ΓC . The relationship between energetic particle losses and metrics such as QA error (Eqa) and ΓC in this set of equilibria were examined via statistical methods and a nearly linear relationship between volume-averaged ΓC and prompt particle losses was found.
Type:
Dataset
Issue Date:
2022

22. Fusion Pilot Plant performance and the role of a Sustained High Power Density tokamak

Author(s):
Menard, Jonathan; Grierson, Brian; Brown, Tom; Rana, Chirag; Zhai, Yuhu; Poli, Francesca; Maingi, Rajesh; Guttenfelder, Walter; Snyder, Philip
Abstract:
Recent U.S. fusion development strategy reports all recommend that the U.S. should pursue innovative science and technology to enable construction of a Fusion Pilot Plant (FPP) that produces net electricity from fusion at low capital cost. Compact tokamaks have been proposed as a means of potentially reducing the capital cost of a fusion pilot plant. However, compact steady-state tokamak FPPs face the challenge of integrating a high fraction of self-driven current with high core confinement, plasma pressure, and high divertor parallel heat flux. This integration is sufficiently challenging that a dedicated sustained-high-power-density (SHPD) tokamak facility is proposed by the U.S. community as the optimal way to close this integration gap. Performance projections for the steady-state tokamak FPP regime are presented and a preliminary SHPD device with substantial flexibility in lower aspect ratio (A=2-2.5), shaping, and divertor configuration to narrow gaps to a FPP is described.
Type:
Dataset
Issue Date:
January 2022

23. Global gyrokinetic study of shaping effects on electromagnetic modes at NSTX aspect ratio with ad hoc parallel magnetic perturbation effects

Author(s):
Sharma, A. Y.; Cole, M. D. J.; Görler, T.; Chen, Y.; Hatch, D. R.; Guttenfelder, W.; Hager, R.; Sturdevant, B. J.; Ku, S.; Chang, C. S.
Abstract:
Plasma shaping may have a stronger effect on global turbulence in tight-aspect-ratio tokamaks than in conventional-aspect-ratio tokamaks due to the higher toroidicity and more acute poloidal asymmetry in the magnetic field. In addition, previous local gyrokinetic studies have shown that it is necessary to include parallel magnetic field perturbations in order to accurately compute growth rates of electromagnetic modes in tight-aspect-ratio tokamaks. In this work, the effects of elongation and triangularity on global, ion-scale, linear electromagnetic modes are studied at NSTX aspect ratio and high plasma beta using the global gyrokinetic particle-in-cell code XGC. The effects of compressional magnetic perturbations are approximated via a well-known modification to the particle drifts that was developed for flux-tube simulations [N. Joiner et al., Phys. Plasmas 17, 072104 (2010)], without proof of its validity in a global simulation. Magnetic equilibria are re-constructed for each distinct plasma profile that is used. Coulomb collision effects are not considered. Within the limitations imposed by the present study, it is found that linear growth rates of electromagnetic modes (collisionless microtearing modes and kinetic ballooning modes) are significantly reduced by NSTX-like shaping. For example, growth rates of kinetic ballooning modes at high beta are reduced to the level of that of collisionless trapped electron modes.
Type:
Dataset
Issue Date:
2022

24. Gyrokinetic simulations of momentum flux parasitic to free-energy transfer

Author(s):
Stoltzfus-Dueck, T; Hornsby, W A; Grosshauser, S R
Abstract:
Ion Landau damping interacts with a portion of the E×B drift to cause a non-diffusive outward flux of co-current toroidal angular momentum. Quantitative evaluation of this momentum flux requires nonlinear simulations to determine fL, the fraction of fluctuation free energy that passes through ion Landau damping, in fully developed turbulence. Nonlinear gyrokinetic simulations with the GKW code confirm the presence of the systematic symmetry-breaking momentum flux. For simulations with adiabatic electrons, fL scales inversely with the ion temperature gradient, because only the ion curvature drift can transfer free energy to the electrostatic potential. Although kinetic electrons should in principle relax this restriction, the ion Landau damping measured in collisionless kinetic-electron simulations remained at low levels comparable with ion-curvature-drift transfer, except when magnetic shear was strong. A set of simulations scanning the electron pitch-angle scattering rate showed only a weak variation of fL with the electron collisionality. However, collisional-electron simulations with electron temperature greater than ion temperature unambiguously showed electron-curvature-drift transfer supporting ion Landau damping, leading to a corresponding enhancement of the symmetry-breaking momentum flux.
Type:
Dataset
Issue Date:
2022

25. Identification of a non-axisymmetric mode in laboratory experiments searching for standard magnetorotational instability

Author(s):
Wang, Yin; Gilson, Erik P.; Ebrahimi, Fatima; Goodman, Jeremy; Caspary, Kyle J.; Winarto, Himawan W.; Ji, Hantao
Abstract:
This dataset provides the source data of figures in the main text of the paper "Identification of a non-axisymmetric mode in laboratory experiments searching for standard magnetorotational instability" accepted by Nature Communications.
Type:
Dataset
Issue Date:
2022

26. Initial Results from Boron Powder Injection Experiments in WEST Lower Single Null L-mode Plasmas

Author(s):
Bodner, Grant; Gallo, Alberto; Diallo, Ahmed; Lunsford, Robert; Moreau, Philippe; Nagy, Alex; Pellissier, Francis-Pierre; Guillemaut, Christophe; Gunn, James; Bourdelle, Clarisse; Desgranges, Corinne; Manas, Pierre; Bortolon, Alessandro; Klepper, Christopher; Tsitrone, Emanuelle; Unterberg, Ezekial; Vermare, Laure
Abstract:
Using a recently installed impurity powder dropper (IPD), boron powder (< 150 μm) was injected into lower single null (LSN) L-mode discharges in WEST. IPDs possibly enable real-time wall conditioning of the plasma-facing components and may help to facilitate H-mode access in the full-tungsten environment of WEST. The discharges in this experiment featured Ip = 0.5 MA, BT = 3.7 T, q95 = 4.3, tpulse = 12–30 s, ne,0 ~ 4×1019 m-2, and PLHCD ~ 4.5 MW. Estimates of the deuterium and impurity particle fluxes, derived from a combination of visible spectroscopy measurements and their corresponding S/XB coefficients, showed decreases of ~ 50% in O+, N+, and C+ populations during powder injection and a moderate reduction of these low-Z impurities (~ 50%) and W (~ 10%) in the discharges that followed powder injection. Along with the improved wall conditions, WEST discharges with B powder injection observed improved confinement, as the stored energy WMHD, neutron rate, and electron temperature Te increased significantly (10–25% for WMHD and 60–200% for the neutron rate) at constant input power. These increases in confinement scale up with the powder drop rate and are likely due to the suppression of ion temperature gradient (ITG) turbulence from changes in Zeff and/or modifications to the electron density profile.
Type:
Dataset
Issue Date:
2022

27. Internal Rotation of ELM Filaments on NSTX

Author(s):
Lampert, Mate; Diallo, Ahmed; Zweben, Stewart; Myra, Jim
Abstract:
The data is formatted to text files. A corresponding file is provided for each figure.
Type:
Dataset
Issue Date:
September 2022

30. Nonlinear growth of magnetic islands by passing fast ions in NSTX

Author(s):
Yang, James; Fredrickson, Eric; Podestà, Mario; Poli, Francesca
Abstract:
The growth of magnetic islands in NSTX is modeled successfully, with the consideration of passing fast ions. It is shown that a good quantitative agreement between simulation and experimental measurement can be achieved when the uncompensated cross-field current induced by passing fast ions is included in the island growth model. The fast ion parameters, along with other equilibrium parameters, are obtained self-consistently using the TRANSP code with the assumptions of the ‘kick’ model (Podestà et al 2017 Plasma Phys. Control. Fusion 59 095008). The results show that fast ions can contribute to overcoming the stabilizing effect of polarization current for magnetic island growth.
Type:
Dataset
Issue Date:
2022

32. Parametric dependencies of resonant layer responses across linear, two-fluid, drift-MHD regimes

Author(s):
Park, Jong-Kyu
Abstract:
Non-axisymmetric magnetic fields arising in a tokamak either by external or internal perturbations can induce complex non-ideal MHD responses in their resonant surfaces while remaining ideally evolved elsewhere. This layer response can be characterized in a linear regime by a single parameter called the inner-layer Delta, which enables outer-layer matching and the prediction of torque balance to non-linear island regimes. Here, we follow strictly one of the most comprehensive analytic treatments including two-fluid and drift MHD effects and keep the fidelity of the formulation by incorporating the numerical method based on the Riccati transformation when quantifying the inner-layer Delta. The proposed scheme reproduces not only the predicted responses in essentially all asymptotic regimes but also with continuous transitions as well as improved accuracies. In particular, the Delta variations across the inertial regimes with viscous or semi-collisional effects have been further resolved, in comparison with additional analytic solutions. The results imply greater shielding of the electromagnetic torque at the layer than what would be expected by earlier work when the viscous or semi-collisional effects can compete against the inertial effects, and also due to the intermediate regulation by kinetic Alfven wave resonances as rotation slows down. These are important features that can alter the nonaxisymmetric plasma responses including the field penetration by external fields or island seeding process in rotating tokamak plasmas.
Type:
Dataset
Issue Date:
26 July 2022

33. Plasma Facing Components with Capillary Porous System and Liquid Metal Coolant Flow

Author(s):
Khodak, Andrei; Maingi, Rajesh
Abstract:
Liquid metal can create a renewable protective surface on plasma facing components (PFC), with an additional advantage of deuterium pumping and the prospect of tritium extraction if liquid lithium (LL) is used and maintained below 450 C, the temperature above which LL vapor pressure begins to contaminate the plasma. LM can also be utilized as an efficient coolant, driven by the Lorentz force created with the help of the magnetic field in fusion devices. Capillary porous systems can serve as a conduit of LM and simultaneously provide stabilization of the LM flow, protecting against spills into the plasma. Recently a combination of a fast-flowing LM cooling system with a porous plasma facing wall (CPSF) was investigated [Khodak and Maingi (2021)]. The system takes an advantage of a magnetohydrodynamics velocity profile, as well as attractive LM properties to promote efficient heat transfer from the plasma to the LL at low pumping energy cost, relative to the incident heat flux on the PFC. In case of a disruption leading to excessive heat flux from the plasma to the LM PFCs, LL evaporation can stabilize the PFC surface temperature, due to high evaporation heat and apparent vapor shielding. The proposed CPSF was optimized analytically for the conditions of a Fusion Nuclear Science Facility [Kessel et al. (2019)]: 10T toroidal field and 10 MW/m2 peak incident heat flux. Computational fluid dynamics analysis confirmed that a CPSF system with 2.5 mm square channels can pump enough LL so that no additional coolant is needed.
Type:
Dataset and Image
Issue Date:
2021

34. Shock Compression of Fluorapatite to 120 GPa: Wave Profile Data

Author(s):
Rucks, Melinda
Abstract:
The item included here is a collection of wave profiles collected and presented in the accompanying paper: Rucks, M. J., Winey, J. M., Toyoda, T., Gupta, Y. M., & Duffy, T. S. (in review). "Shock compression of fluorapatite to 120 GPa" Submitted to Journal of Geophysical Research: Planets.
Type:
Dataset
Issue Date:
19 October 2022

35. Single-crystal X-ray diffraction of fluorapatite to 61 GPa: Structural Data

Author(s):
Rucks, Melinda J.
Abstract:
This dataset includes individual CIF files with the refined structure of fluorapatite under compression to 61 GPa. The structures have been discussed in detail in the accompanying manuscript "Single-crystal X-ray diffraction of fluorapatite to 61 GPa"
Type:
Dataset
Issue Date:
8 April 2022

37. Spike Trains of Retinal Ganglion Cells Viewing a Repeated Natural Movie

Author(s):
Berry II, Michael J.
Abstract:
This archive contains spike trains simultaneously recorded from ganglion cells in the tiger salamander retina with a multi-electrode array while viewing a repeated natural movie clip. These data have been analyzed in previous papers, notably Puchalla et al. Neuron 2005 and Schneidman et al. Nature 2006.
Type:
Dataset
Issue Date:
8 March 2022

38. Streaked Sub-ps-resolution X-ray Line Shapes and Implications for Solid-density Plasma Dynamics

Author(s):
Kraus, B. Frances; Gao, Lan; Hill, K. W.; Bitter, M.; Efthimion, P. C.; Hollinger, R.; Wang, Shoujun; Song, Huanyu; Nedbailo, R.; Rocca, J. J.; Mancini, R. C.; MacDonald, M. J.; Beatty, C. B.; Shepherd, R.
Abstract:
A high-resolution x-ray spectrometer was coupled with an ultrafast x-ray streak camera to produce time-resolved line shape spectra measured from hot, solid-density plasmas. A Bragg crystal was placed near a laser-produced plasma to maximize throughput; alignment tolerances were established by raytracing. The streak camera produced single-shot time-resolved spectra, heavily sloped due to photon time-of-flight differences, with sufficient reproducibility to accumulate photon statistics. The images are time-calibrated by the slope of streaked spectra and dewarped to generate spectra emitted at different times defined at the source. The streaked spectra demonstrate the evolution of spectral shoulders and other features on ps timescales, showing the feasibility of plasma parameter measurements on the rapid timescales necessary to study high-energy-density plasmas.
Type:
Dataset
Issue Date:
2022

39. Study of Stark Broadening of Krypton Helium-beta Lines and Estimation of Electron Density and Temperature in NIF Compressed Capsules

Author(s):
Hill, K. W.; Gao, L.; Kraus, B. F.; Bitter, M.; Efthimion, P. C.; Pablant, N. A.; Schneider, M. B.; Thorn, D. B.; Chen, H.; Kauffman, R. L.; Liedahl, D. A.; MacDonald, M. J.; MacPhee, A. G.; Scott, H. A.; Stoupin, S.; Doron, R.; Stambulchik, E.; Maron, Y.; Lahmann, B.
Abstract:
Numerical data used to draw the figures in the manuscript
Type:
Dataset
Issue Date:
6 June 2022

40. Supplemental material for: Verification, validation, and results of an approximate model for the stress of a Tokamak toroidal field coil at the inboard midplane

Author(s):
Swanson, CPS; Kahn, S; Rana, C; Titus, PH; Brooks, AW; Guttenfelder, W; Zhai, Y; Brown, TG; Menard, JE
Abstract:
This is the supplemental material for the manuscript "Verification, validation, and results of an approximate model for the stress of a Tokamak toroidal field coil at the inboard midplane" submitted to Fusion Engineering and Design. This material includes PDF writeups of the derivations of the axisymmetric extended plane strain model, the elastic properties smearing model, and 20+ MATLAB scripts and functions which implement the model and generate the figures in the paper.
Type:
collection, Dataset, and Software
Issue Date:
2022

44. Three dimensional archaeocyathide and coral imagery for morphologic analysis

Author(s):
Manzuk, Ryan; Maloof, Adam
Abstract:
In our study, we compare the three dimensional (3D) morphologic characteristics of Earth's first reef-building animals (archaeocyath sponges) with those of modern, photosynthetic corals. Within this repository are the 3D image data products for both groups of animals. The archaeocyath images were produced through serial grinding and imaging with the Grinding, Imaging, and Reconstruction Instrument at Princeton University. The images in this repository are the downsampled data products used in our study, and the full resolution (>2TB) image stacks are available upon request from the author. For the coral image data, the computed tomography (CT) images of all samples are included at full resolution. Also included in this repository are the manual and automated outline coordinates of the archaeocyath and coral branches, which can be directly used for morphological study.
Type:
Dataset, Image, MovingImage, and StillImage
Issue Date:
August 2022

45. To dee or not to dee: costs and benefits of altering the triangularity of a steady-state DEMO-like reactor

Author(s):
Schwartz, Jacob A.; Nelson, A. O.; Kolemen, Egemen
Abstract:
Shaping a tokamak plasma to have a negative triangularity may allow operation in an ELM-free L-mode regime and with a larger strike-point radius, ameliorating divertor power-handling requirements. However, the shaping has a potential drawback in the form of a lower no-wall ideal beta limit, found using the MHD codes CHEASE and DCON. Using the new fusion systems code FAROES, we construct a steady-state DEMO2 reactor model. This model is essentially zero-dimensional and neglects variations in physical mechanisms like turbulence, confinement, and radiative power limits, which could have a substantial impact on the conclusions deduced herein. Keeping its shape otherwise constant, we alter the triangularity and compute the effects on the levelized cost of energy (LCOE). If the tokamak is limited to a fixed B field, then unless other means to increase performance (such as reduced turbulence, improved current drive efficiency or higher density operation) can be leveraged, a negative-triangularity reactor is strongly disfavored in the model due to lower \beta_N limits at negative triangularity, which leads to tripling of the LCOE. However, if the reactor is constrained by divertor heat fluxes and not by magnet engineering, then a negative-triangularity reactor with higher B0 could be favorable: we find a class of solutions at negative triangularity with lower peak heat flux and lower LCOE than those of the equivalent positive triangularity reactors.
Type:
Dataset
Issue Date:
April 2022

46. Wall conditioning and ELM mitigation with boron nitride powder injection in KSTAR

Author(s):
Gilson, Erik; Lee, H; Bortolon, A; Choe, W; Diallo, A; Hong, SH; Lee, HM; Maingi, R; Mansfield, DK; Nagy, A; Park, SH; Song, IW; Song, JI; Yun, SW; Nazikian, R
Abstract:
Results from KSTAR powder injection experiments, in which tens of milligrams of boron nitride (BN) were dropped into low-power H-mode plasmas, show an improvement in wall conditions in subsequent discharges and, in some cases, a reduction or elimination of edge-localized modes (ELMs). Injected powder is distributed by the plasma flow and is deposited on the wall and, over the course of several discharges, was observed to gradually reduce recycling by 33%, and decrease both the ELM amplitude and frequency. This is the first demonstration of the use of BN for ELM mitigation. In all of these experiments, an Impurity Powder Dropper (IPD) was used to introduce precise, controllable amounts of the materials into ELMy H-mode KSTAR discharges. The plasma duration was between 10 s and 15 s, 𝐼𝑝 = 500 kA, 𝐵𝑇 = 1.8 T, 𝑃NBI = 1.6 MW, and 𝑃ECH = 0.6 MW. Plasma densities were between 2 and 3 × 1019 m−3. In all cases, the pre-fill and startup gas-fueling was kept constant, suggesting that the decrease in baseline D𝛼 emission is in fact due to a reduction in recycling. The results presented herein highlight the viability of powder injection for intra-shot and between-shot wall conditioning.
Type:
Dataset
Issue Date:
September 2021

47. A software package for plasma facing component analysis and design: the Heat flux Engineering Analysis Toolkit (HEAT)

Author(s):
Looby, Tom; Reinke, Matthew; Wingen, Andreas; Menard, Jonathan; Gerhardt, Stefan; Gray, Travis; Donovan, David; Unterberg, Ezekial; Klabacha, Jonathan; Messineo, Mike
Abstract:
The engineering limits of plasma facing components (PFCs) constrain the allowable operational space of tokamaks. Poorly managed heat fluxes that push the PFCs beyond their limits not only degrade core plasma performance via elevated impurities, but can also result in PFC failure due to thermal stresses or melting. Simple axisymmetric assumptions fail to capture the complex interaction between 3D PFC geometry and 2D or 3D plasmas. This results in fusion systems that must either operate with increased risk or reduce PFC loads, potentially through lower core plasma performance, to maintain a nominal safety factor. High precision 3D heat flux predictions are necessary to accurately ascertain the state of a PFC given the evolution of the magnetic equilibrium. A new code, the Heat flux Engineering Analysis Toolkit (HEAT), has been developed to provide high precision 3D predictions and analysis for PFCs. HEAT couples many otherwise disparate computational tools together into a single open source python package. Magnetic equilibrium, engineering CAD, finite volume solvers, scrape off layer plasma physics, visualization, high performace computing, and more, are connected in a single web-based user interface. Linux users may use HEAT without any software prerequisites via an appImage. This manuscript introduces HEAT, discusses the software architecture, presents first HEAT results, and outlines physics modules in development.
Type:
Dataset
Issue Date:
March 2021

48. A thermodynamic phase transition in magnetic reconnection

Author(s):
Jara-Almonte, Jonathan; Hantao, Ji
Abstract:
Data supporting the manuscript "A thermodynamic phase transition in magnetic reconnection" published in Physical Review Letters.
Type:
Dataset
Issue Date:
7 July 2021

49. Code and data from "Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections"

Author(s):
King, Sean
Abstract:
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively. Included in this repository are the instructions and corresponding code required to build the dataset and run the analysis in the manuscript.
Type:
Dataset
Issue Date:
28 September 2021

50. Coupling between Alfven wave and Kelvin-Helmholtz waves in the low latitude boundary layer

Author(s):
Kim, Eun-Hwa; Johnson, Jay; Nykyri, Katariina
Abstract:
The Kelvin-Helmholtz (KH) instability of magnetohydrodynamic surface waves at the low latitude boundary layer is examined using both an eigenfrequency analysis and a time-dependent wave simulation. The analysis includes the effects of sheared flow and Alfven velocity gradient. When the magnetosheath flows are perpendicular to the ambient magnetic field direction, unstable KH waves that propagate obliquely to the sheared flow direction occur at the sheared flow surface when the Alfv\'en Mach number is higher than an instability threshold. Including a shear transition layer between the magnetosphere and magnetosheath leads to secondary KH waves (driven by the sheared flow) that are coupled to the resonant surface Alfven wave. There are remarkable differences between the primary and the secondary KH waves including wave frequency, the growth rate, and the ratio between transverse and the compressional component. The secondary KH wave energy is concentrated near the shear Alfven wave frequency at the magnetosheath with a lower frequency than the primary KH waves. Although the growth rate of the secondary KH waves is lower than the primary KH waves, the threshold condition is lower, so it is expected that these types of waves will dominate at lower Mach number. Because the transverse component of the secondary KH waves is stronger than the primary KH waves, more efficient wave energy transfer from the boundary layer to the inner magnetosphere is also predicted.
Type:
Dataset
Issue Date:
December 2021

51. CrvA and CrvB form a curvature-inducing module sufficient to induce cell shape complexity in Gram-negative bacteria

Author(s):
Martin, Nicholas R; Blackman, Edith; Bratton, Benjamin P; Chase, Katelyn J; Bartlett, Thomas M; Gitai, Zemer
Abstract:
Bacterial species have diverse cell shapes that enable motility, colonization, and virulence. The cell wall defines bacterial shape and is primarily built by two cytoskeleton-guided synthesis machines, the elongasome and the divisome. However, the mechanisms producing complex shapes, like the curved-rod shape of Vibrio cholerae, are incompletely defined. Previous studies have reported that species-specific regulation of cytoskeleton-guided machines enables formation of complex bacterial shapes such as cell curvature and cellular appendages. In contrast, we report that CrvA and CrvB are sufficient to induce complex cell shape autonomously of the cytoskeleton in V. cholerae. The autonomy of the CrvAB module also enables it to induce curvature in the Gram-negative species Escherichia coli, Pseudomonas aeruginosa, Caulobacter crescentus, and Agrobacterium tumefaciens. Using inducible gene expression, quantitative microscopy, and biochemistry we show that CrvA and CrvB circumvent the need for patterning via cytoskeletal elements by regulating each other to form an asymmetrically-localized, periplasmic structure that directly binds to the cell wall. The assembly and disassembly of this periplasmic structure enables dynamic changes in cell shape. Bioinformatics indicate that CrvA and CrvB may have diverged from a single ancestral hybrid protein. Using fusion experiments in V. cholerae, we find that a synthetic CrvA/B hybrid protein is sufficient to induce curvature on its own, but that expression of two distinct proteins, CrvA and CrvB, promotes more rapid curvature induction. We conclude that morphological complexity can arise independently of cell shape specification by the core cytoskeleton-guided synthesis machines.
Type:
Dataset
Issue Date:
2021

53. Data for: 'Facies control on carbonate δ13C on the Great Bahama Bank'

Author(s):
Geyman, Emily C.; Maloof, Adam C.
Abstract:
The carbon isotopic (δ13C) composition of shallow-water carbonates often is interpreted to reflect the δ13C of the global ocean and is used as a proxy for changes in the global carbon cycle. However, local platform processes, in addition to meteoric and marine diagenesis, may decouple carbonate δ13C from that of the global ocean. To shed light on the extent to which changing sediment grain composition may produce δ13C shifts in the stratigraphic record, we present new δ13C measurements of benthic foraminifera, solitary corals, calcifying green algae, ooids, coated grains, and lime mud from the modern Great Bahama Bank (GBB). This survey of a modern carbonate environment reveals δ13C variability comparable to the largest δ13C excursions in the last two billion years of Earth history.
Type:
Dataset
Issue Date:
6 May 2021

54. Data for: 'How is sea level change encoded in carbonate stratigraphy?'

Author(s):
Geyman, Emily C.; Maloof, Adam C.; Dyer, Blake
Abstract:
The history of organismal evolution, seawater chemistry, and paleoclimate is recorded in layers of carbonate sedimentary rock. Meter-scale cyclic stacking patterns in these carbonates often are interpreted as representing sea level change. A reliable sedimentary proxy for eustasy would be profoundly useful for reconstructing paleoclimate, since sea level responds to changes in temperature and ice volume. However, the translation from water depth to carbonate layering has proven difficult, with recent surveys of modern shallow water platforms revealing little correlation between carbonate facies (i.e., grain size, sedimentary bed forms, ecology) and water depth. We train a convolutional neural network with satellite imagery and new field observations from a 3,000 km2 region northwest of Andros Island (Bahamas) to generate a facies map with 5 m resolution. Leveraging a newly-published bathymetry for the same region, we test the hypothesis that one can extract a signal of water depth change, not simply from individual facies, but from sequences of facies transitions analogous to vertically stacked carbonate strata. Our Hidden Markov Model (HMM) can distinguish relative sea level fall from random variability with ∼90% accuracy. Finally, since shallowing-upward patterns can result from local (autogenic) processes in addition to forced mechanisms such as eustasy, we search for statistical tools to diagnose the presence or absence of external forcings on relative sea level. With a new data-driven forward model that simulates how modern facies mosaics evolve to stack strata, we show how different sea level forcings generate characteristic patterns of cycle thicknesses in shallow carbonates, providing a new tool for quantitative reconstruction of ancient sea level conditions from the geologic record.
Type:
Dataset
Issue Date:
1 February 2021

55. Data for: Three-Dimensional Morphometry of Ooids in Oolites: a new tool for more accurate and precise paleoenvironmental interpretation

Author(s):
Howes, Bolton; Mehra, Akshay; Maloof, Adam
Abstract:
The prevalence of ooids in the stratigraphic record, and their association with shallow-water carbonate environments, make ooids an important paleoenvironmental indicator. Recent advances in the theoretical understanding of ooid morphology, along with empirical studies from Turks and Caicos, Great Salt Lake, and The Bahamas, have demonstrated that the morphology of ooids is indicative of depositional environment and hydraulic conditions. To apply this knowledge from modern environments to the stratigraphic record of Earth history, researchers measure the size and shape of lithified ooids on two-dimensional surfaces (i.e., thin sections or polished slabs), often assuming that random 2D slices intersect the nuclei and that the orientation of the ooids is known. Here we demonstrate that these assumptions rarely are true, resulting in errors of up to 35% on metrics like major axis length. We present a method for making 3D reconstructions by serial grinding and imaging, which enables accurate measurement of the morphology of individual ooids within an oolite, as well as the sorting and porosity of a sample. We also provide three case studies that use the morphology of ooids in oolites to extract environmental information. Each case study demonstrates that 2D measurements can be useful if the environmental signal is large relative to the error from 2D measurements. However, 3D measurements substantially improve the accuracy and precision of environmental interpretations. This study focuses on oolites, but errors from 2D measurements are not unique to oolites; this method can be used to extract accurate grain and porosity measurements from any lithified granular sample.
Type:
Dataset
Issue Date:
22 February 2021

58. Developments on two lithium vapor-box linear test-stand experiments

Author(s):
Schwartz, Jacob A.; Goldston, Robert J.
Abstract:
The lithium vapor-box divertor is a possible fusion power exhaust solution.It uses condensation pumping to create a gradient of vapor density in a divertor slot; this should allow a stable detachment front without active feedback.As initial explorations of the concept, two test stands which take the form of three connected cylindrical stainless steel boxes are being developed: one without plasma at PPPL, to test models of lithium evaporation and flow; and one for the linear plasma device Magnum-PSI (at DIFFER in Eindhoven, The Netherlands) to test the ability of a lithium vapor cloud to induce volumetric detachment and redistribute the plasma power.The first experiment uses boxes with diameters of 6 cm, joined by apertures with diameters of 2.2 cm. Up to 1 g of Li is placed in one box, which is heated to up to 600 degrees C. The Li evaporates, then flows to and condenses in the two other, cooler boxes over several minutes. The quantity of Li transported is assessed by weighing the boxes before and after the heating cycle, and is compared to the quantity predicted to flow for the box at its measured temperature using a Direct Simulation Monte Carlo code, SPARTA. With good experimental conditions, the two values agree to within 15%.The experiment on Magnum-PSI is in the conceptual design stage.The design is assessed by simulations using the code B2.5-Eunomia.They show that when the hydrogen-ion plasma beam, with n_e = 4e20 per cubic meter, T_e = 1.5 eV, and r = 1 cm, is passed through a 16 cm long, 12 Pa, 625 degree C Li vapor cloud, the plasma heat flux and pressure on the target are significantly reduced compared to the case without Li.With the Li present, the plasma is cooled by excitation of Li neutrals followed by radiation until it volumetrically recombines, lowering the heat flux from 3.7 MW/m^2 to 0.13 MW/m^2, and the pressure is reduced by 93%, largely by collisions of hydrogen ions with neutral Li.
Type:
Dataset
Issue Date:
January 2021

59. Dynamics of filaments during the edge-localized mode crash on NSTX

Author(s):
Lampert,Mate; Diallo,Ahmed; Myra,James R.; Zweben, Stewart J.
Abstract:
Edge localized modes (ELMs) are routinely observed in H-mode plasma regimes of the National Spherical Torus Experiment (NSTX). Due to the explosive nature of the instability, only diagnostics with high temporal and spatial resolution could provide a detailed insight into the dynamics associated with the ELMs. Gas-puff imaging (GPI) at NSTX provides 2D measurements of the magnetic field aligned fluctuations (e.g. ELM filaments) in the scrape-off layer and the at the plasma edge with 2.5 us temporal and 10 mm optical resolution.A novel analysis technique was developed to estimate the frame-by-frame velocities and the spatial parameters of the dominant structures associated with the ELMs. The analysis was applied to single ELM events to characterize the ELM crash dynamics, and then extended to a database of 169 ELM events.Statistical analysis was performed in order to find the characterizing dynamics of the ELM crash. The results show that on average an ELM crash consists of a filament with a circular cross-section which is propelled outwards with a characterizing peak radial velocity of ~3.3 km/s. The radial velocity was found to be linearly dependent on the distance of the filament from the separatrix, which has never been seen before. The ELM filament is characterized by propagation in the ion-diamagnetic direction poloidally with a peak velocity of 11.4 km/s. The ELM crash lasts for approximately 100us until the radial propulsion settles back to the pre-ELM level. The experimental findings were compared with analytical theory. Two possible mechanisms were identified for explaining the observations: the curvature interchange model and the current-filament interaction model.
Type:
Dataset
Issue Date:
January 2021

61. Enhancement of edge turbulence concomitant with ELM suppression during boron powder injection in EAST

Author(s):
Sun, Zhen; Maingi, Rajesh; Diallo, Ahmed; Xu, Wei; Qian, Yuzhong; Tritz, Kevin; Ye, Yang; Li, Chenglong; Xu, Zhong; Wang, Yifeng; Kaixuan, Ye; Bortolon, A.; Nagy, Alex; Zhang, Ling; Duan, Yanmin; Lu, Zhiyuan; Wang, Huiqian; Shi, Tonghui; Zhao, Hailin; Gao, Wei; Xu, Jichan; Chen, Ran; Huang, Ming; Zuo, Guizhong; Xu, Guosheng; Gong, Xianzu; Hu, Jiansheng
Abstract:
Data supporting the manuscript "Enhancement of edge turbulence concomitant with ELM suppression during boron powder injection in EAST" published in Plasma of Physics, 2021.
Type:
Dataset and Image
Issue Date:
August 2021

62. Experimental data for paper "hydraulic transmissivity inferred from ice-sheet relaxation following Greenland supraglacial lake drainages"

Author(s):
Lai, Ching-Yao
Abstract:
This setup mimics ice lying above the drainage system. In the experiment, a fluid-filled blister is generated via liquid injection into the interface between a transparent elastic layer and a porous substrate. After injection of liquid, the fluid permeates from the blister through the porous substrate, the blister volume V(t) relaxes exponentially with time. Our lab experiments show that varying the permeability of the porous substrate k significantly impacts the relaxation timescale in the experiments.
Type:
Dataset
Issue Date:
18 May 2021

63. Hybrid simulations of sub-cyclotron compressional and global Alfven Eigenmode stability in spherical tokamaks

Author(s):
Lestz, J.B.; Belova, E.V.; Gorelenkov, N.N
Abstract:
A comprehensive numerical study has been conducted in order to investigate the stability of beam-driven, sub-cyclotron frequency compressional (CAE) and global (GAE) Alfven Eigenmodes in low aspect ratio plasmas for a wide range of beam parameters. The presence of CAEs and GAEs has previously been linked to anomalous electron temperature profile flattening at high beam power in NSTX experiments, prompting further examination of the conditions for their excitation. Linear simulations are performed with the hybrid MHD-kinetic initial value code HYM in order to capture the general Doppler-shifted cyclotron resonance that drives the modes. Three distinct types of modes are found in simulations -- co-CAEs, cntr-GAEs, and co-GAEs -- with differing spectral and stability properties. The simulations reveal that unstable GAEs are more ubiquitous than unstable CAEs, consistent with experimental observations, as they are excited at lower beam energies and generally have larger growth rates. Local analytic theory is used to explain key features of the simulation results, including the preferential excitation of different modes based on beam injection geometry and the growth rate dependence on the beam injection velocity, critical velocity, and degree of velocity space anisotropy. The background damping rate is inferred from simulations and estimated analytically for relevant sources not present in the simulation model, indicating that co-CAEs are closer to marginal stability than modes driven by the cyclotron resonances.
Type:
Dataset
Issue Date:
March 2021

64. Hyperdiffusion of dust particles in a turbulent tokamak plasma

Author(s):
Nespoli, Federico; Kaganovich, Igor; Autricque, Adrien; Marandet, Yannick; Tamain, Patrick
Abstract:
The effect of plasma turbulence on the trajectories of dust particles is investigated for the first time. The dynamics of dust particles is computed using the ad-hoc developed Dust Injection Simulator code, using a 3D turbulent plasma background computed with the TOKAM3X code. As a result, the evolution of the particle trajectories is governed by the ion drag force, and the shape of the trajectory is set by the Stokes number $St\propto a_d/n_0$, with $a_d$ the dust radius and $n_0$ the density at the separatrix. The plasma turbulence is observed to scatter the dust particles, exhibiting a hyperdiffusive regime in all cases. The amplitude of the turbulent spread of the trajectories $\Delta r^2$ is shown to depend on the ratio $Ku/St$, with $Ku\propto u_{rms}$ the Kubo number and $u_{rms}$ the fluctuation level of the plasma flow. These results are compared with a simple analytical model, predicting $\Delta r^2\propto (Ku/St)^2t^3$, or $\Delta r^2\propto (u_{rms}n_0/a_d)^2t^3$. As the dust is heated by the plasma fluxes, thermionic emission sets the dust charge, originally negative, to slightly positive values. This results in a substantial reduction of the ion drag force through the suppression of its Coulomb scattering component. The dust grain inertia is then no longer negligible, and drives the transition from a hyperdiffusive regime towards a ballistic one.
Type:
Article
Issue Date:
July 2021

65. Impact of edge harmonic oscillations on the divertor heat flux in NSTX

Author(s):
Gan, Kaifu; Gray, Travis; Zweben, Stewart; Eric, Fredrickson; Maingi, Rajesh; Battaglia, Devon; McLean, Adam; Wirth, Brian
Abstract:
All the data was uploaded with .cvs file, we have not uploaded the figure 1 data since it is just photo show field of view of IR and GPI diagnostic.
Type:
Dataset
Issue Date:
6 December 2021

66. Implementation of higher-order velocity mapping between marker particles and grid in the particle-in-cell code XGC

Author(s):
Mollen Albert; Adams Mark F.; Knepley Matthew G.; Hager Robert; Chang C. S.
Abstract:
The global total-f gyrokinetic particle-in-cell code XGC, used to study transport in magnetic fusion plasmas or to couple with a core gyrokinetic code while functioning as an edge gyrokinetic code, implements a 5-dimensional (5D) continuum grid to perform the dissipative operations, such as plasma collisions, or to exchange the particle distribution function information with a core code. To transfer the distribution function between marker particles and a rectangular 2D velocity-space grid, XGC employs a bilinear mapping. The conservation of particle density and momentum is accurate enough in this bilinear operation, but the error in the particle energy conservation can become undesirably large and cause non-negligible numerical heating in a steep edge pedestal. In the present work we update XGC to use a novel mapping technique, based on the calculation of a pseudo-inverse, to exactly preserve moments up to the order of the discretization space. We describe the details of the implementation and we demonstrate the reduced interpolation error for a tokamak test plasma by using 1st- and 2nd-order elements with the pseudo-inverse method and comparing to the bilinear mapping.
Type:
Dataset
Issue Date:
March 2021

67. Initial operation and data processing on a system for real-time evaluation of Thomson scattering signals on the Large Helical Device

Author(s):
Hammond, K. C.; Laggner, F. M.; Diallo, A.; Doskoczynski, S.; Freeman, C.; Funaba, H.; Gates, D.A.; Rozenblat, R.; Tchilinguirian, G.; Xing, Z.; Yamada, I.; Yasuhara, R.; Zimmer, G.; Kolemen, E.
Abstract:
A scalable system for real-time analysis of electron temperature and density based on signals from the Thomson scattering diagnostic, initially developed for and installed on the NSTX-U experiment, was recently adapted for the Large Helical Device (LHD) and operated for the first time during plasma discharges. During its initial operation run, it routinely recorded and processed signals for four spatial points at the laser repetition rate of 30 Hz, well within the system's rated capability for 60 Hz. We present examples of data collected from this initial run and describe subsequent adaptations to the analysis code to improve the fidelity of the temperature calculations.
Type:
Dataset
Issue Date:
2021

68. Integrative Mechanisms of Social Attention

Author(s):
Bio, Branden; Graziano, Michael
Abstract:
Monitoring the attention of others is fundamental to social cognition. Most of the literature on the topic assumes that our social cognitive machinery is tuned specifically to the gaze direction of others as a proxy for attention. This standard assumption reduces attention to an externally visible parameter. Here we show that this assumption is wrong and a deeper, more meaningful representation is involved. We presented subjects with two cues about the attentional state of a face: direction of gaze and emotional expression. We tested whether people relied predominantly on one cue, the other, or both. If the traditional view is correct, then the gaze cue should dominate. Instead, people employed a variety of strategies, some relying on gaze, some on expression, and some on an integration of cues. We also assessed people’s social cognitive ability using two, independent, standard tests. If the traditional view is correct, then social cognitive ability, as assessed by the independent tests, should correlate with the degree to which people successfully use the gaze cue to judge the attention state of the face. Instead, social cognitive ability correlated best with the degree to which people successfully integrated the cues together, instead of with the use of any one specific cue. The results suggest a rethink of a fundamental component of social cognition: monitoring the attention of others involves constructing a deep model that is informed by a combination of cues. Attention is a rich process and monitoring the attention of others involves a similarly rich representation.
Type:
Dataset
Issue Date:
22 July 2021

69. Inversion technique to obtain local ion temperature profiles for an axisymmetric plasma with toroidal and radial velocities

Author(s):
Bell, Ronald E.
Abstract:
A matrix inversion technique is derived to calculate local ion temperature from line-integrated measurements of an extended emission source in an axisymmetric plasma which exactly corrects for both toroidal velocity and radial velocity components. Local emissivity and toroidal velocity can be directly recovered from line-integrated spectroscopic measurements, but an independent measurement of the radial velocity is necessary to complete the temperature inversion. The extension of this technique to handle the radial velocity is relevant for magnetic reconnection and merging compression devices where temperature inversion from spectroscopic measurements is desired. A simulation demonstrates the effects of radial velocity on the determination of ion temperature.
Type:
Dataset
Issue Date:
February 2021

70. Lower Hybrid Drift Waves During Guide Field Reconnection

Author(s):
Yoo, Jongsoo; Jeong-Young, Ji; M. V., Ambat; Shan, Wang; Hantao, Ji; Jenson, Lo; Bowen, Li; Yang, Ren; J., Jara-Almonte; William, Fox; Masaaki, Yamada; Andrew, Alt; Aaron, Goodman
Abstract:
Digital data for figures used in Lower Hybrid Drift Waves During Guide Field Reconnection, Geophysical Research Letters, 47, e2020GL087192, 2020.
Type:
Dataset
Issue Date:
29 October 2020

71. Microtearing Instabilities and Electron Thermal Transport in Low and High Collisionality NSTX Discharges

Author(s):
Rafiq T; Kaye S; Guttenfelder W; Weiland J; Schuster E; Anderson J; Luo L;
Abstract:
Microtearing mode (MTM) real frequency, growth rate, magnetic fluctuation amplitude and resulting electron thermal transport are studied in systematic NSTX scans of relevant plasma parameters. The dependency of the MTM real frequency and growth rate on plasma parameters, suitable for low and high collision NSTX discharges, is obtained by using the reduced MTM transport model [T. Rafiq, et al., Phys. Plasmas 23, 062507 (2016)]. The plasma parameter dependencies are compared and found to be consistent with the results obtained from MTM using the Gyrokinetic GYRO code. The scaling trend of collision frequency and plasma beta is found to be consistent with the global energy confinement trend observed in the NSTX experiment. The strength of the magnetic fluctuation is found to be consistent with the gyrokinetic estimate.In earlier studies, it was found that the version of the Multi-Mode (MM) anomalous transport model, which did not contain the effect of MTMs, provided an appropriate description of the electron temperature profiles in standard tokamak discharges and not in spherical tokamaks. When the MM model, which involves transport associated with MTMs, is incorporated in the TRANSP code and is used in the study of electron thermal transport in NSTX discharges, it is observed that the agreement with the experimental electron temperature profile is substantially improved.
Type:
Dataset
Issue Date:
February 2021

72. Multi-Fluid and Kinetic Models of Partially Ionized Magnetic Reconnection

Author(s):
Jara-Almonte, J.; Murphy, N.A.; Ji, H.
Abstract:
Magnetic reconnection in partially ionized plasmas is a ubiquitous and important phenomena in both laboratory and astrophysical systems. Here, simulations of partially ionized magnetic reconnection with well-matched initial conditions are performed using both multi-fluid and fully-kinetic approaches. Despite similar initial conditions, the time-dependent evolution differs between the two models. In multi-fluid models, the reconnection rate locally obeys either a decoupled Sweet-Parker scaling, where neutrals are unimportant, or a fully coupled Sweet-Parker scaling, where neutrals and ions are strongly coupled, depending on the resistivity. In contrast, kinetic models show a faster reconnection rate that is proportional to the fully-coupled, bulk Alfv\'en speed, $v_A^\star$. These differences are interpreted as the result of operating in different collisional regimes. Multi-fluid simulations are found to maintain $\nu_{ni}L/v_A^\star \gtrsim 1$, where $\nu_{ni}$ is the neutral-ion collision frequency and $L$ is the time-dependent current sheet half-length. This strongly couples neutrals to the reconnection outflow, while kinetic simulations evolve to allow $\nu_{ni}L/v_A^\star < 1$, decoupling neutrals from the reconnection outflow. Differences in the way reconnection is triggered may explain these discrepancies.
Type:
Dataset
Issue Date:
2021

75. Observation of synergy between lower hybrid waves at two frequencies in EAST

Author(s):
Choi, W.; Poli, F. M.; Li, M. H.; Baek, S. G.; Gorenlenkova, M.; Ding, B. J.; Gong, X. Z.; Chan, A.; Duan, Y. M.; Hu, J. H.; Lian, H.; Lin, S. Y.; Liu, H. Q.; Qian, J. P.; Wallace, G.; Wang, Y. M.; Zang, Q.; Zhao, H. L.
Abstract:
Synergistic effects between two frequencies of lower hybrid (LH) waves—operating at 2.45 and 4.6 GHz—were observed in experiment on EAST for the first time. At low density (n_e,lin ≈ 2.0 × 10^19m^−3), simultaneous injection of a 65/35 mix of 2.45 GHz/4.6 GHz power achieved an LHCD efficiency that was 25% higher than what should be expected from the linear combination of the two sources. The experiment was interpreted with time-dependent simulations, using the equilibrium and transport solver TRANSP, coupled with the ray-tracing code GENRAY and the Fokker-Planck solver CQL3D. For each discharge, profiles of current and hard x-ray from simulation and measurement agree within uncertainties. An examination of the electron distribution function indicates that the LH synergy is supported by the increased width of the LH resonance plateau in the simultaneous injection case compared to independent injection.
Type:
Dataset
Issue Date:
June 2021

77. Prediction of electron density and pressure profile shapes on NSTX-U using neural networks

Author(s):
Boyer, Mark; Chadwick, Jason
Abstract:
A new model for prediction of electron density and pressure profile shapes on NSTX and NSTX-U has been developed using neural networks. The model has been trained and tested on measured profiles from experimental discharges during the first operational campaign of NSTX-U. By projecting profiles onto empirically derived basis functions, the model is able to efficiently and accurately reproduce profile shapes. In order to project the performance of the model to upcoming NSTX-U operations, a large database of profiles from the operation of NSTX is used to test performance as a function of available data. The rapid execution time of the model is well suited to the planned applications, including optimization during scenario development activities, and real-time plasma control. A potential application of the model to real-time profile estimation is demonstrated.
Type:
Dataset
Issue Date:
February 2021

78. Princeton Open Ventilation Monitor

Author(s):
Bourrianne, Philippe; Chidzik, Stanley; Cohen, Daniel; Elmer, Peter; Hallowell, Thomas; Kilbaugh, Todd J.; Lange, David; Leifer, Andrew M.; Marlow, Daniel R.; Meyers, Peter D.; Normand, Edna; Nunes, Janine; Oh, Myungchul; Page, Lyman; Periera, Talmo; Pivarski, Jim; Schreiner, Henry; Stone, Howard A.; Tank, David W.; Thiberge, Stephan; Tully, Christopher
Abstract:
The detailed information on the design and construction of the Princeton Open Ventilation Monitor device and software are contained in this data repository. This information consists of the electrical design files, mechanical design files, bill of materials, human subject recording and analysis code, and a copy of the code repository for operating the patient monitors and central station.
Type:
Dataset, Software, and Image
Issue Date:
22 November 2021

82. Supporting data for Baldwin et al 2019 "Temporally Compound Heat Waves and Global Warming: An Emerging Hazard"

Author(s):
Baldwin, Jane W; Dessy, Jay Benjamin; Vecchi, Gabriel A; Oppenheimer, Michael; Jia, Liwei; Gudgel, Richard G; Paffendorf, Karen
Abstract:
This data is compiled to support a publication in the journal Earth's Future: Baldwin et al 2019 "Temporally Compound Heat Waves and Global Warming: An Emerging Hazard". The GCM GFDL CM2.5-FLOR was used to produce the raw climate model data. The model code for FLOR is freely available and can be downloaded at https://www.gfdl.noaa.gov/cm2-5-and-flor/. Code used to calculate the derived heat wave statistics data and produce figures in the paper is available at https://github.com/janewbaldwin/Compound-Heat-Waves The heat wave statistics derived output for only one definition is provided (daily minimum temperature, 90th percentile threshold, temporal structure 3114) which is the definition used the most in the paper figures. Statistics for the other definitions can be created by running the HWSTATS code provided in the corresponding github folder, which includes python scripts which do the analysis and PBS job scheduling and submission scripts which show how to run the python scripts. For more information on this, please see the github readme.
Type:
Dataset
Issue Date:
17 February 2019

83. Synergy of Coupled Kink and Tearing Modes in Fast Ion Transport

Author(s):
Yang, J.; Podesta, M.; Fredrickson, E.
Abstract:
One aspect of the interaction between fast ions and magnetohydrodynamic (MHD) instabilities is the fast ion transport. Coupled kink and tearing MHD instabilities have also been reported to cause fast ion transport. Recently, the ''kick" model has been developed to compute the evolution of the fast ion distribution from the neutral beam injection using instabilities as phase space resonance sources. The goal of this paper is to utilize the kick model to understand the physics of fast ion transport caused by the coupled kink and tearing modes. Soft X-ray diagnostics are used to identify the mode parameters in NSTX. The comparison of neutron rates measured and computed from time-dependent TRANSP simulation with the kick model shows the coupling of kink and tearing mode is important in determination of the fast ion transport. The numerical scan of the mode parameters shows that the relative phase of the kink and tearing modes and the overlapping of kink and tearing mode resonances in the phase space can affect the fast ion transport, suggesting that the synergy of the coupled modes may be causing the fast ion transpor
Type:
Dataset
Issue Date:
February 2021

84. The 21st year: transcription, motif list, and relation score

Author(s):
Chang, Claire H. C.; Lazaridi, Christina; Yeshurun, Yaara; Norman, Kenneth A.; Hasson, Uri
Abstract:
This study examined how the brain dynamically updates event representations by integrating new information over multiple minutes while segregating irrelevant input. A professional writer custom-designed a narrative with two independent storylines, interleaving across minute-long segments (ABAB). In the last (C) part, characters from the two storylines meet and their shared history is revealed. Part C is designed to induce the spontaneous recall of past events, upon the recurrence of narrative motifs from A/B, and to shed new light on them. Our fMRI results showed storyline-specific neural patterns, which were reinstated (i.e. became more active) during storyline transitions. This effect increased along the processing timescale hierarchy, peaking in the default mode network. Similarly, the neural reinstatement of motifs was found during part C. Furthermore, participants showing stronger motif reinstatement performed better in integrating A/B and C events, demonstrating the role of memory reactivation in information integration over intervening irrelevant events.
Type:
Dataset and text
Issue Date:
2021

85. The Attention Schema Theory in an Artificial Neural Network Agent: Controlling Visuospatial Attention Using a Descriptive Model of Attention

Author(s):
Wilterson, Andrew; Graziano, Michael
Abstract:
In the attention schema theory, the brain constructs a model of attention, the attention schema, to aid in the endogenous control of attention. Growing behavioral evidence appears to support this proposal. However, a central question remains: does a controller of attention actually benefit by having access to an attention schema? We constructed an artificial, deep Q-learning, neural network agent that was trained to control a simple form of visuospatial attention, tracking a stimulus with its attention spotlight in order to solve a catch task. The agent was tested with and without access to an attention schema. In both conditions, the agent received sufficient information such that it should, theoretically, be able to learn the task. We found that with an attention schema present, the agent learned to control its attention spotlight and learned the catch task to a high degree of performance. Once the agent learned, if the attention schema was disabled, the agent could no longer perform effectively. If the attention schema was removed before learning began, the agent was drastically impaired at learning. The results show how the presence of even a simple attention schema provides a profound benefit to a controller of attention. We interpret these results as supporting the central argument of AST: the brain evolved an attention schema because of its practical benefit in the endogenous control of attention.
Type:
Dataset and Software
Issue Date:
2021

86. The updated ITPA global H-mode confinement database: description and analysis

Author(s):
Verdoolaege, G.; Kaye, S.M.; Angioni, C.; Kardaunn, O.W.J.F.; Maslov, M.; Romanelli, M.; Ryter, F.; Thomsen, K.
Abstract:
The multi-machine ITPA Global H-mode Confinement Database has been upgraded with new data from JET with the ITER-like wall and ASDEX Upgrade with the full tungsten wall. This paper describes the new database and presents results of regression analysis to estimate the global energy confinement scaling in H-mode plasmas using a standard power law. Various subsets of the database are considered, focusing on type of wall and divertor materials, confinement regime (all H-modes, ELMy H or ELM-free) and ITER-like constraints. Apart from ordinary least squares, two other, robust regression techniques are applied, which take into account uncertainty on all variables. Regression on data from individual devices shows that, generally, the confinement dependence on density and the power degradation are weakest in the fully metallic devices. Using the multi-machine scalings, predictions are made of the confinement time in a standard ELMy H-mode scenario in ITER. The uncertainty on the scaling parameters is discussed with a view to practically useful error bars on the parameters and predictions. One of the derived scalings for ELMy H-modes on an ITER-like subset is studied in particular and compared to the IPB98(y,2) confinement scaling in engineering and dimensionless form. Transformation of this new scaling from engineering variables to dimensionless quantities is shown to result in large error bars on the dimensionless scaling. Regression analysis in the space of dimensionless variables is therefore proposed as an alternative, yielding acceptable estimates for the dimensionless scaling. The new scaling, which is dimensionally correct within the uncertainties, suggests that some dependencies of confinement in the multi- machine database can be reconciled with parameter scans in individual devices. This includes vanishingly small dependence of confinement on line-averaged density and normalized plasma pressure (β), as well as a noticeable, positive dependence on effective atomic mass and plasma triangularity. Extrapolation of this scaling to ITER yields a somewhat lower confinement time compared to the IPB98(y, 2) prediction, possibly related to the considerably weaker dependence on major radius in the new scaling (slightly above linear). Further studies are needed to compare more flexible regression models with the power law used here. In addition, data from more devices concerning possible ‘hidden variables’ could help to determine their influence on confinement, while adding data in sparsely populated areas of the parameter space may contribute to further disentangling some of the global confinement dependencies in tokamak plasmas.
Type:
Dataset
Issue Date:
March 2021

88. Type-I ELM mitigation by continuous lithium granule gravitational injection into the upper tungsten divertor in EAST

Author(s):
Sun, Zhen; Yuzhong, Qian; Maingi, Rajesh; Wang, Yifeng; Wang, Yumin; Nagy, Alex; Tritz, Kevin; Lunsford, Robert; Gilson, Erik; Zuo, Guizhong; Xu, Wei; Huang, Ming; Meng, Xiancai; Mansfield, Dennis K.; Zang, Qing; Zhu, Xiang; Lin, Xin; Liu, Haiqing; Duan, Yanmin; Zhang, Ling; Lyu, Bo; Liu, Yong; Wang, Liang; Bortolon, Ale; Xu, Guosheng; Gong, Xianzu; Hu, Jiansheng
Abstract:
Large edge-localized modes (ELMs) were mitigated by gravitational injection of lithium granules into the upper X-point region of the EAST device with tungsten plasma-facing components. The maximum ELM size was reduced by ~ 70% in high βN H-mode plasmas. Large ELM stabilization was sustained for up to about 40 energy confinement times, with constant core radiated power and no evidence of high-Z or low-Z impurity accumulation. The lithium granules injection reduced the edge plasma pedestal density and temperature and their gradients, due to increased edge radiation and reduced recycling from the plasma-facing components. Ideal stability calculations using the ELITE code indicate that the stabilization of large ELMs correlates with improved stability of intermediate-n peeling-ballooning modes, due to reduced edge current resulting from the profile changes. The pedestal pressure reduction was partially offset by a core density increase, which resulted in a modest ~ 7% drop in core stored energy and normalized energy confinement time. We surmise that the remnant small ELMs are triggered by the penetration of multiple Li granules just past the separatrix, similar to small ELMs triggered by deuterium pellet [S. Futatani et al., Nucl. Fusion 54 (2014) 073008]. This study extends previous ELM elimination with Li powder injection [R. Maingi et al., Nucl. Fusion 58 (2018) 024003] in EAST because 1) use of small, dust-like powder and the related potential health hazards were eliminated, and 2) use of macroscopic granules should be more applicable to future devices, due to deeper penetration than dust particles, e.g. inside the separatrix with velocities ~ 10 m/s in EAST.
Type:
Article
Issue Date:
April 2021

89. Wave-kinetic approach to zonal-flow dynamics: recent advances

Author(s):
Zhu, Hongxuan; Dodin, I. Y.
Abstract:
Basic physics of drift-wave turbulence and zonal flows has long been studied within the framework of wave-kinetic theory. Recently, this framework has been re-examined from first principles, which has led to more accurate yet still tractable "improved" wave-kinetic equations. In particular, these equations reveal an important effect of the zonal-flow "curvature" (the second radial derivative of the flow velocity) on dynamics and stability of drift waves and zonal flows. We overview these recent findings and present a consolidated high-level picture of (mostly quasilinear) zonal-flow physics within reduced models of drift-wave turbulence.
Type:
Dataset
Issue Date:
March 2021

90. Why is El Nino warm?

Author(s):
Hogikyan, Allison; Resplandy, Laure; Yang, Wenchang; Fueglistaler, Stephan
Abstract:
Dataset constructed from GFDL-FLOR preindustrial control experiment run by Wenchang Yang (wenchang@princeton.edu) on Princeton University's tiger CPU. Processing by Allison Hogikyan (hogikyan@princeton.edu) on Princeton University's tigress data processing node. June 2021.
Type:
Dataset
Issue Date:
28 June 2021

91. A dual-mechanism antibiotic kills Gram-negative bacteria and avoids drug resistance

Author(s):
Martin, James K; Sheehan, Joseph P; Bratton, Benjamin P; Moore, Gabriel M; Mateus, André; Li, Sophia Hsin-Jung; Kim, Hahn; Rabinowitz, Joshua D; Typas, Athanasios; Savitski, Mikhail M; Wilson, Maxwell Z; Gitai, Zemer
Abstract:
The rise of antibiotic resistance and declining discovery of new antibiotics have created a global health crisis. Of particular concern, no new antibiotic classes have been approved for treating Gram-negative pathogens in decades. Here, we characterize a compound, SCH-79797, that kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism of action (MoA) with undetectably-low resistance frequencies. To characterize its MoA, we combined quantitative imaging, proteomic, genetic, metabolomic, and cell-based assays. This pipeline demonstrates that SCH-79797 has two independent cellular targets, folate metabolism and bacterial membrane integrity, and outperforms combination treatments in killing MRSA persisters. Building on the molecular core of SCH-79797, we developed a derivative, Irresistin-16, with increased potency and showed its efficacy against Neisseria gonorrheae in a mouse vaginal infection model. This promising antibiotic lead suggests that combining multiple MoAs onto a single chemical scaffold may be an underappreciated approach to targeting challenging bacterial pathogens.
Type:
Dataset
Issue Date:
20 May 2020

92. Analytic stability boundaries for compressional and global Alfven eigenmodes driven by fast ions. I. Interaction via ordinary and anomalous cyclotron resonances.

Author(s):
Lestz J.B., Gorelenkov N.N., Belova E.V., Tang S.X., Crocker N.A.
Abstract:
Conditions for net fast ion drive are derived for beam-driven, sub-cyclotron compressional (CAE) and global (GAE) Alfven eigenmodes, such as those routinely observed in spherical tokamaks such as NSTX(-U) and MAST. Both co- and counter-propagating CAEs and GAEs are investigated, driven by the ordinary and anomalous Doppler-shifted cyclotron resonance with fast ions. Whereas prior results were restricted to vanishingly narrow distributions in velocity space, broad parameter regimes are identified in this work which enable an analytic treatment for realistic fast ion distributions generated by neutral beam injection. The simple, approximate conditions derived in these regimes for beam distributions of realistic width compare well to the numerical evaluation of the full analytic expressions for fast ion drive. Moreover, previous results in the very narrow beam case are corrected and generalized to retain all terms in omega/omega_{ci} and k_{||}/kperp, which are often assumed to be small parameters but can significantly modify the conditions of drive and damping when they are non-negligible. Favorable agreement is demonstrated between the approximate stability criterion, simulation results, and a large database of NSTX observations of cntr-GAEs.
Type:
Dataset
Issue Date:
September 2019

93. Analytic stability boundaries for compressional and global Alfven eigenmodes driven by fast ions. II. Interaction via Landau resonance.

Author(s):
Lestz, J.B.; Gorelenkov, N.N.; Belova, E.V.; Tang, S.X.; Crocker, N.A.
Abstract:
Conditions for net fast ion drive are derived for beam-driven, co-propagating, sub-cyclotron compressional (CAE) and global (GAE) Alfven eigenmodes driven by the Landau resonance with super-Alfvenic fast ions. Approximations applicable to realistic neutral beam distributions and mode characteristics observed in spherical tokamaks enable the derivation of marginal stability conditions for these modes. Such conditions successfully reproduce the stability boundaries found from numerical integration of the exact expression for local fast ion drive/damping. Coupling between the CAE and GAE branches of the dispersion due to finite \omega/\omega_{ci} and k_\parallel/k_\perp is retained and found to be responsible for the existence of the GAE instability via this resonance. Encouraging agreement is demonstrated between the approximate stability criterion, simulation results, and a database of NSTX observations of co-CAEs.
Type:
Dataset
Issue Date:
January 2020

94. Attention and awareness in the dorsal attention network

Author(s):
Wilterson, Andrew; Nastase, Samuel; Bio, Branden; Guterstam, Arvid; Graziano, Michael
Abstract:
The attention schema theory (AST) posits a specific relationship between subjective awareness and attention, in which awareness is the control model that the brain uses to aid in the endogenous control of attention. We proposed that the right temporoparietal junction (TPJ) is involved in that interaction between awareness and attention. In previous experiments, we developed a behavioral paradigm in human subjects to manipulate awareness and attention. The paradigm involved a visual cue that could be used to guide a shift of attention to a target stimulus. In task 1, subjects were aware of the visual cue, and their endogenous control mechanism was able to use the cue to help control attention. In task 2, subjects were unaware of the visual cue, and their endogenous control mechanism was no longer able to use it to control attention, even though the cue still had a measurable effect on other aspects of behavior. Here we tested the two tasks while scanning brain activity in human volunteers. We predicted that the right TPJ would be active in relation to the cue in task 1, but not in task 2. This prediction was confirmed. The right TPJ was active in relation to the cue in task 1; it was not measurably active in task 2; the difference was significant. In our interpretation, the right TPJ is involved in a complex interaction in which awareness aids in the control of attention.
Type:
Dataset
Issue Date:
2020

95. Data from a flume experiment of passive scalar diffusion within vegetation canopies using laser-induced fluorescence

Author(s):
Ghannam, Khaled; Poggi, Davide; Katul, Gabriel; Bou-Zeid, Elie
Abstract:
This dataset is a sequence of laser-induced fluorescence images of a dye injected in a channel flow with canopy-like stainless steel rods simulating a vegetation canopy stand. The data is acquired close to the channel bottom at z/h=0.2, where z is the height referenced to the channel bed and h is the canopy height. The dataset provides spatial distribution of scalar concentration in a plane parallel to the channel bed. The data has been used (but the data itself has not been published or available to the public) in previous work. The references are: Ghannam, K., Poggi, D., Porporato, A., & Katul, G. (2015). The spatio-temporal statistical structure and ergodic behaviour of scalar turbulence within a rod canopy. Boundary-Layer Meteorology,157(3), 447–460. Ghannam, K, Poggi, D., Bou-Zeid, E., Katul, G. (2020). Inverse cascade evidenced by information entropy of passive scalars in submerged canopy flows. Geophysical Research Letters (accepted).
Type:
Dataset
Issue Date:
22 April 2020

96. Dataset for 'Auditory Activity is Diverse and Widespread Throughout the Central Brain of Drosophila'

Author(s):
Pacheco, Diego A; Thiberge, Stephan; Pnevmatikakis, Eftychios; Murthy, Mala
Abstract:
Sensory pathways are typically studied starting at receptor neurons and following postsynaptic neurons into the brain. However, this leads to a bias in analysis of activity towards the earliest layers of processing. Here, we present new methods for volumetric neural imaging with precise across-brain registration, to characterize auditory activity throughout the entire central brain of Drosophila and make comparisons across trials, individuals, and sexes. We discover that auditory activity is present in most central brain regions and in neurons responsive to other modalities. Auditory responses are temporally diverse, but the majority of activity is tuned to courtship song features. Auditory responses are stereotyped across trials and animals in early mechanosensory regions, becoming more variable at higher layers of the putative pathway, and this variability is largely independent of spontaneous movements. This study highlights the power of using an unbiased, brain-wide approach for mapping the functional organization of sensory activity.
Type:
Dataset
Issue Date:
October 2020

97. Deep convolutional neural networks for multi-scale time-series classification and application to disruption prediction in fusion devices

Author(s):
Churchill, R.M; the DIII-D team
Abstract:
The multi-scale, mutli-physics nature of fusion plasmas makes predicting plasma events challenging. Recent advances in deep convolutional neural network architectures (CNN) utilizing dilated convolutions enable accurate predictions on sequences which have long-range, multi-scale characteristics, such as the time-series generated by diagnostic instruments observing fusion plasmas. Here we apply this neural network architecture to the popular problem of disruption prediction in fusion tokamaks, utilizing raw data from a single diagnostic, the Electron Cyclotron Emission imaging (ECEi) diagnostic from the DIII-D tokamak. ECEi measures a fundamental plasma quantity (electron temperature) with high temporal resolution over the entire plasma discharge, making it sensitive to a number of potential pre-disruptions markers with different temporal and spatial scales. Promising, initial disruption prediction results are obtained training a deep CNN with large receptive field ({$\sim$}30k), achieving an $F_1$-score of {$\sim$}91\% on individual time-slices using only the ECEi data.
Type:
Dataset
Issue Date:
October 2019

98. Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis in Helicobacter pylori

Author(s):
Taylor, Jenny A.; Bratton, Benjamin P.; Sichel, Sophie R.; Blair, Kris M.; Jacobs, Holly M.; DeMeester, Kristen E.; Kuru, Erkin; Gray, Joe; Biboy, Jacob; VanNieuwenhze, Michael S.; Vollmer, Waldemar; Grimes, Catherine L.; Shaevitz, Joshua W.; Salama, Nina R.
Abstract:
Helical cell shape is necessary for efficient stomach colonization by Helicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. We show that the helical centerline pitch and radius of wild-type H. pylori cells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of short pulses with either N-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape.
Type:
Dataset and Image
Issue Date:
April 2019

99. Enhanced Pedestal H-mode at low edge ion collisionality on NSTX

Author(s):
Battaglia, D.J.; Guttenfelder, W.; Bell, R.E.; Diallo, A.; Ferraro, N.;, Fredrickson, E.; Gerhardt, S.P.; Kaye, S.M.; Maingi, R.; Smith, D.R.
Abstract:
The Enhanced Pedestal (EP) H-mode regime is an attractive wide-pedestal ELM-free high-betap scenario for NSTX-U and next-step devices as it achieves enhanced energy confinement (H98y,2 > 1.5), large normalized pressure (betaN > 5) and significant bootstrap fraction (f_BS > 0.6) at I_p/B_T = 2 MA/T. This regime is realized when the edge ion collisionality becomes sufficiently small that a positive feedback interaction occurs between a reduction in the ion neoclassical energy transport and an increase in the particle transport from pressure-driven edge instabilities. EP H-mode was most often observed as a transition following a large ELM in conditions with low edge neutral recycling. It is hypothesized that the onset of pressure-driven instabilities prior to the full recovery of the neutral density leads to a temporary period with elevated ion temperature gradient that triggers the transition to EP H-mode. Linear CGYRO and M3D-C1 calculations are compared to beam emission spectroscopy (BES) and magnetic spectroscopy in order to describe the evolution of the edge particle transport mechanisms during the ELM recovery and the saturated EP H-mode state. The observations are consistent with the hypothesis that the onset of pressure-driven edge instabilities, such as the KBM and kink-peeling, can be responsible for the increased particle transport in EP H-mode.
Type:
Dataset
Issue Date:
June 2020

100. 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