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Start Over Domain Natural Sciences

1. 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

2. 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

3. 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

4. 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

7. 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

8. 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

9. 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

10. 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

11. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

22. 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

23. 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

24. 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

25. 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

29. 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

30. 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

31. 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

32. 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

33. 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

34. 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

36. 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

37. 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

38. 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

41. 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

42. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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

50. 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