Vortices, shocks, and heating in the solar photosphere: effect of a magnetic field

Aims: We study the differences between non-magnetic and magnetic regions in the flow and thermal structure of the upper solar photosphere. Methods: Radiative MHD simulations representing a quiet region and a plage region, respectively, which extend into the layers around the temperature minimum, are analyzed. Results: The flow structure in the upper photospheric layers of the two simulations is considerably different: the non-magnetic simulation is dominated by a pattern of moving shock fronts while the magnetic simulation shows vertically extended vortices associated with magnetic flux concentrations. Both kinds of structures induce substantial local heating. The resulting average temperature profiles are characterized by a steep rise above the temperature minimum due to shock heating in the non-magnetic case and by a flat photospheric temperature gradient mainly caused by Ohmic dissipation in the magnetic run. Conclusions: Shocks in the quiet Sun and vortices in the strongly magnetized regions represent the dominant flow structures in the layers around the temperature minimum. They are closely connected with dissipation processes providing localized heating.Comment: Accepted for publicaton in A&

Non-equilibrium hydrogen ionization in 2D simulations of the solar atmosphere

The ionization of hydrogen in the solar chromosphere and transition region does not obey LTE or instantaneous statistical equilibrium because the timescale is long compared with important hydrodynamical timescales, especially of magneto-acoustic shocks. We implement an algorithm to compute non-equilibrium hydrogen ionization and its coupling into the MHD equations within an existing radiation MHD code, and perform a two-dimensional simulation of the solar atmosphere from the convection zone to the corona. Analysis of the simulation results and comparison to a companion simulation assuming LTE shows that: a) Non-equilibrium computation delivers much smaller variations of the chromospheric hydrogen ionization than for LTE. The ionization is smaller within shocks but subsequently remains high in the cool intershock phases. As a result, the chromospheric temperature variations are much larger than for LTE because in non-equilibrium, hydrogen ionization is a less effective internal energy buffer. The actual shock temperatures are therefore higher and the intershock temperatures lower. b) The chromospheric populations of the hydrogen n = 2 level, which governs the opacity of Halpha, are coupled to the ion populations. They are set by the high temperature in shocks and subsequently remain high in the cool intershock phases. c) The temperature structure and the hydrogen level populations differ much between the chromosphere above photospheric magnetic elements and above quiet internetwork. d) The hydrogen n = 2 population and column density are persistently high in dynamic fibrils, suggesting that these obtain their visibility from being optically thick in Halpha also at low temperature.Comment: 10 pages, 4 figure

Parallel Mapper

The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint trees. In this paper, we study the parallel analysis of the construction of Mapper. We give a provably correct parallel algorithm to execute Mapper on multiple processors and discuss the performance results that compare our approach to a reference sequential Mapper implementation. We report the performance experiments that demonstrate the efficiency of our method

Order-N Density-Matrix Electronic-Structure Method for General Potentials

A new order-N method for calculating the electronic structure of general (non-tight-binding) potentials is presented. The method uses a combination of the ``purification''-based approaches used by Li, Nunes and Vanderbilt, and Daw, and a representation of the density matrix based on ``travelling basis orbitals''. The method is applied to several one-dimensional examples, including the free electron gas, the ``Morse'' bound-state potential, a discontinuous potential that mimics an interface, and an oscillatory potential that mimics a semiconductor. The method is found to contain Friedel oscillations, quantization of charge in bound states, and band gap formation. Quantitatively accurate agreement with exact results is found in most cases. Possible advantages with regard to treating electron-electron interactions and arbitrary boundary conditions are discussed.Comment: 13 pages, REVTEX, 7 postscript figures (not quite perfect

Morphology and Dynamics of the Low Solar Chromosphere

The Interferometric Bidimensional Spectrometer (IBIS) installed at the Dunn Solar Telescope of the NSO/SP is used to investigate the morphology and dynamics of the lower chromosphere and the virtually non-magnetic fluctosphere below. The study addresses in particular the structure of magnetic elements that extend into these layers. We choose different quiet Sun regions in and outside coronal holes. In inter-network regions with no significant magnetic flux contributions above the detection limit of IBIS, we find intensity structures with the characteristics of a shock wave pattern. The magnetic flux elements in the network are long lived and seem to resemble the spatially extended counterparts to the underlying photospheric magnetic elements. We suggest a modification to common methods to derive the line-of-sight magnetic field strength and explain some of the difficulties in deriving the magnetic field vector from observations of the fluctosphere.Comment: accepted by ApJ, 16 pages, 8 figure

Second-harmonic generation in vortex-induced waveguides

We study the second-harmonic generation and localization of light in a reconfigurable waveguide induced by an optical vortex soliton in a defocusing Kerr medium. We show that the vortex-induced waveguide greatly improves conversion efficiency from the fundamental to the second harmonic field.Comment: 3 pages, 4 figures, submitted to Optics Letter

Branching, Capping, and Severing in Dynamic Actin Structures

Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to study steady-state network morphology. In bulk, we identify several scaling regimes in severing and branching protein concentrations and find that the coupling between severing and branching is optimally exploited for conditions {\it in vivo}. Near the leading edge, we find qualitative agreement with the {\it in vivo} morphology.Comment: 4 pages, 2 figure