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31. 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

32. Data from "Vapor-liquid equilibrium of water with the MB-pol many-body potential"

Author(s):
Muniz, Maria Carolina; Gartner III, Thomas E.; Riera, Marc; Knight, Christopher; Yue, Shuwen; Paesani, Francesco; Panagiotopoulos, Athanassios Z.
Abstract:
This dataset contains all data (including input files, simulation trajectories as well as other data files and analysis scripts) related to the publication "Vapor-liquid equilibrium of water with the MB-pol many-body potential" by Muniz et al. in preparation (2021). In this work, we assessed the performance of the MB-pol many-body potential with respect to water's vapor-liquid equilibrium properties. Through the use of direct coexistence molecular dynamics, we calculated properties such as coexistence densities, surface tension, vapor pressures and enthalpy of vaporization. We found that MB-pol is able to predict these properties in good agreement with experimental data. The results attest to the chemical accuracy of MB-pol and its large range of application across water's phase diagram.
Type:
Dataset
Issue Date:
2021

33. 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

34. 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

36. 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

37. 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

38. 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

39. 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

40. 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