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Start Over Domain Natural Sciences Year Published 2020

1. Modeling of resistive plasma response in toroidal geometry using an asymptotic matching approach

Author(s):
Z. R. Wang; A. H. Glasser; D. Brennan; Y. Q. Liu; J-K. Park
Abstract:
The method of solving linear resistive plasma response, based on the asymptotic matching approach, is developed for full toroidal tokamaks by upgrading the Resistive DCON code [A.H. Glasser, Z.R. Wang and J.-K. Park, Physics of Plasmas, \textbf{23}, 112506 (2016)]. The derived matching matrix, asymptotically matching the outer and inner regions, indicates that the applied three dimension (3-D) magnetic perturbations contribute additional small solutions at each resonant surface due to the toroidal coupling of poloidal modes. In contrast, the resonant harmonic only affects the corresponding resonant surface in the cylindrical plasma. Since the solution of ideal outer region is critical to the asymptotic matching and is challenging to be solved in the toroidal geometry due to the singular power series solution at the resonant surfaces, systematic verification of the outer region $\Delta^\prime$ matrix is made by reproducing the well known analytical $\Delta^{\prime}$ result in [H.P. Furth, P.H. Rutherford and H. Selberg, The Physics of Fluids, \textbf{16}, 1054-1063 (1073)] as well as by making a quantitative benchmark with the PEST3 code [A. Pletzer and R.L. Dewar, J. Plasma Physics, \textbf{45}, 427-451 (1991)]. Finally, the reconstructed numerical solution of resistive plasma response from the toroidal matching matrix is presented. Comparing with the ideal plasma response, the global structure of the response can be affected by the small finite island at the resonant surfaces.
Type:
Dataset
Issue Date:
October 2020

2. 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

3. March Mathness: Effects of basketball on the brain

Author(s):
Antony, James; McDougle, Sam
Abstract:
Surprise signals a discrepancy between past and current beliefs. It is theorized to be linked to affective experiences, the creation of particularly resilient memories, and segmentation of the flow of experience into discrete perceived events. However, the ability to precisely measure naturalistic surprise has remained elusive. We used advanced basketball analytics to derive a quantitative measure of surprise and characterized its behavioral, physiological, and neural correlates in human subjects observing basketball games. We found that surprise was associated with segmentation of ongoing experiences, as reflected by subjectively perceived event boundaries and shifts in neocortical patterns underlying belief states. Interestingly, these effects differed by whether surprising moments contradicted or bolstered current predominant beliefs. Surprise also positively correlated with pupil dilation, activation in subcortical regions associated with dopamine, game enjoyment, and long-term memory. These investigations support key predictions from event segmentation theory and extend theoretical conceptualizations of surprise to real-world contexts.
Type:
Dataset
Issue Date:
2020

4. 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

5. 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

6. Statistical properties of magnetic structures and energy dissipation during turbulent reconnection in the Earth's magnetotail

Author(s):
Bergstedt, K.; Ji, H.; Jara-Almonte, J.; Yoo, J.; Ergun, R. E.; Chen, L.-J.
Abstract:
We present the first statistical study of magnetic structures and associated energy dissipation observed during a single period of turbulent magnetic reconnection, by using the in situ measurements of the Magnetospheric Multiscale mission in the Earth's magnetotail on 26 July 2017. The structures are selected by identifying a bipolar signature in the magnetic field and categorized as plasmoids or current sheets via an automated algorithm which examines current density and plasma flow. The size of the plasmoids forms a decaying exponential distribution ranging from subelectron up to ion scales. The presence of substantial number of current sheets is consistent with a physical picture of dynamic production and merging of plasmoids during turbulent reconnection. The magnetic structures are locations of significant energy dissipation via electric field parallel to the local magnetic field, while dissipation via perpendicular electric field dominates outside of the structures. Significant energy also returns from particles to fields.
Type:
Dataset
Issue Date:
14 September 2020

7. 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

8. 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

9. 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

10. 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