scholarly journals Density enhancements associated with equatorial spread <I>F</I>

2010 ◽  
Vol 28 (2) ◽  
pp. 327-337 ◽  
Author(s):  
J. Krall ◽  
J. D. Huba ◽  
G. Joyce ◽  
T. Yokoyama
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Simulation Code ◽  
Equatorial Spread F ◽  
Equatorial Ionization Anomaly ◽  
Spread F ◽  
Key Features ◽  
Field Lines ◽  
Dimensional Simulation

Abstract. Forces governing the three-dimensional structure of equatorial spread-F (ESF) plumes are examined using the NRL SAMI3/ESF three-dimensional simulation code. As is the case with the equatorial ionization anomaly (IA), density crests within the plume occur where gravitational and diffusive forces are in balance. Large E×B drifts within the ESF plume place these crests on field lines with apex heights higher than those of the background IA crests. Large poleward field-aligned ion velocities within the plume result in large ion-neutral diffusive forces that support these ionization crests at altitudes higher than background IA crest altitudes. We show examples in which density enhancements associated with ESF, also called "plasma blobs," can occur within an ESF plume on density-crest field lines, at or above the density crests. Simulated ESF density enhancements reproduce all key features of those that have been observed in situ.

scholarly journals Equatorial spread <I>F</I> fossil plumes

2010 ◽  
Vol 28 (11) ◽  
pp. 2059-2069 ◽  
Author(s):  
J. Krall ◽  
J. D. Huba ◽  
S. L. Ossakow ◽  
G. Joyce
Keyword(s):  
High Altitude ◽  
Field Line ◽  
Mass Density ◽  
Three Dimensional ◽  
Simulation Code ◽  
Airglow Image ◽  
Spread F ◽  
Field Lines ◽  
Dimensional Simulation ◽  
Constant Altitude

Abstract. Behaviour of equatorial spread F (ESF) fossil plumes, i.e., ESF plumes that have stopped rising, is examined using the NRL SAMI3/ESF three-dimensional simulation code. We find that fossil bubbles, plasma density depletions associated with fossil plumes, can persist as high-altitude equatorial depletions even while being "blown" by zonal winds. Corresponding airglow-proxy images of fossil plumes, plots of electron density versus longitude and latitude at a constant altitude of 288 km, are shown to partially "fill in" in most cases, beginning with the highest altitude field lines within the plume. Specifically, field lines upon which the E field has fallen entirely to zero are affected and only the low altitude (≤600 km) portion if each field line fills in. This suggests that it should be possible to observe a bubble at high altitude on a field line for which the corresponding airglow image no longer shows a depletion. In all cases ESF plumes stop rising when the flux-tube-integrated ion mass density inside the upper edge of the bubble is equal to that of the nearby background, further supporting the result of Krall et al. (2010b).

scholarly journals Three-dimensional simulation of equatorial spread-F with meridional wind effects

2009 ◽  
Vol 27 (5) ◽  
pp. 1821-1830 ◽  
Author(s):  
J. Krall ◽  
J. D. Huba ◽  
G. Joyce ◽  
S. T. Zalesak
Keyword(s):  
Field Line ◽  
Three Dimensional ◽  
Meridional Wind ◽  
Two Dimensions ◽  
Simulation Code ◽  
Equatorial Spread F ◽  
Meridional Winds ◽  
Spread F ◽  
Field Geometry ◽  
Dimensional Simulation

Abstract. The NRL SAMI3 three-dimensional simulation code is used to examine the effect of meridional winds on the growth and suppression of equatorial spread F (ESF). The simulation geometry conforms to a dipole field geometry with field-line apex heights from 200 to 1600 km at the equator, but extends over only 4 degrees in longitude. The full SAMI3 ionosphere equations are included, providing ion dynamics both along and across the field. The potential is solved in two dimensions in the equatorial plane under a field-line equipotential approximation. By selectively including terms in the potential equation, the reduced growth predicted by Maruyama (1988) and the stabilization predicted by Zalesak and Huba (1991) are separately realized. We find that ESF is stabilized by a sufficiently large constant meridional wind (60 m/s in our example).

scholarly journals A guided approach for subtomogram averaging of challenging macromolecular assemblies

2020 ◽  
Author(s):  
Danielle Grotjahn ◽  
Saikat Chowdhury ◽  
Gabriel C. Lander
Keyword(s):  
Electron Tomography ◽  
A Priori ◽  
Three Dimensional ◽  
Structural Heterogeneity ◽  
Dimensional Structure ◽  
Diverse Range ◽  
Macromolecular Assemblies ◽  
Cryo Electron Tomography ◽  
Subtomogram Averaging

AbstractCryo-electron tomography is a powerful biophysical technique enabling three-dimensional visualization of complex biological systems. Macromolecular targets of interest identified within cryo-tomograms can be computationally extracted, aligned, and averaged to produce a better-resolved structure through a process called subtomogram averaging (STA). However, accurate alignment of macromolecular machines that exhibit extreme structural heterogeneity and conformational flexibility remains a significant challenge with conventional STA approaches. To expand the applicability of STA to a broader range of pleomorphic complexes, we developed a user-guided, focused refinement approach that can be incorporated into the standard STA workflow to facilitate the robust alignment of particularly challenging samples. We demonstrate that it is possible to align visually recognizable portions of multi-subunit complexes by providing a priori information regarding their relative orientations within cryo-tomograms, and describe how this strategy was applied to successfully elucidate the first three-dimensional structure of the dynein-dynactin motor protein complex bound to microtubules. Our approach expands the application of STA for solving a more diverse range of heterogeneous biological structures, and establishes a conceptual framework for the development of automated strategies to deconvolve the complexity of crowded cellular environments and improve in situ structure determination technologies.

Three-dimensional simulation code for SPring-8 RF gun system

2004 ◽  
pp. 387-391
Author(s):  
A. Mizuno ◽  
T. Asaka ◽  
H. Dewa ◽  
T. Kobayashi ◽  
S. Suzuki ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Simulation Code ◽  
Rf Gun ◽  
Dimensional Simulation
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