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Solar partially ionized plasma is frequently modeled using single-fluid (1F) or two-fluid (2F) approaches. In the 1F case, charge-neutral interactions are often described through ambipolar diffusion, while the 2F model fully considers charge-neutral drifts. Here, we expand the definition of the ambipolar diffusion coefficient to include inelastic collisions (ion/rec) in two cases: a VAL3C 1D model and a 2F simulations of the Rayleigh-Taylor instability (RTI) in a solar prominence thread based on \cite{PopLukKho2021aa, PopLukKho2021ab}. On one side, we evaluate the relative importance of the inelastic contribution, compared to elastic and charge-exchange collisions. On the other side, we compare the contributions of ion/rec, thermal pressure, viscosity, and magnetic forces to the charge-neutral drift velocity of the turbulent flow of the RTI. Our analysis reveals that the contribution of inelastic collisions to the ambipolar diffusion coefficient is negligible across the chromosphere, allowing the classical definition of this coefficient to be safely used in 1F modeling. However, in the transition region, the contribution of inelastic collisions can become as significant as that of elastic collisions. Furthermore, we ascertain that the thermal pressure force predominantly influences the charge-neutral drifts in the RTI model, surpassing the impact of the magnetic force., Comment: Accepted

This study explores non-linear development of the magnetized Rayleigh-Taylor instability (RTI) in a prominence-corona transition region. Using a two-fluid model of a partially ionized plasma, we compare RTI simulations for several different magnetic field configurations. We follow prior descriptions of the numerical prominence model [Popescu Braileanu et al., 2021a,b, 2023] and explore the charged-neutral fluid coupling and plasma heating in a two-dimensional mixing layer for different magnetic field configurations. We also investigate how the shear in magnetic field surrounding a prominence may impact the release of the gravitational potential energy of the prominence material. We show that the flow decoupling is strongest in the plane normal to the direction of the magnetic field, where neutral pressure gradients drive ion-neutral drifts and frictional heating is balanced by adiabatic cooling of the expanding prominence material. We also show that magnetic field within the mixing plane can lead to faster non-linear release of the gravitational energy driving the RTI, while more efficiently heating the plasma via viscous dissipation of associated plasma flows. We relate the computational results to potential observables by highlighting how integrating over under-resolved two-fluid sub-structure may lead to misinterpretation of observational data., Comment: accepted to Philosophical Transactions A

The Mancha3D code is a versatile tool for numerical simulations of magnetohydrodynamic processes in solar/stellar atmospheres. The code includes non-ideal physics derived from plasma partial ionization, a realistic equation of state and radiative transfer, which allows performing high quality realistic simulations of magneto-convection, as well as idealized simulations of particular processes, such as wave propagation, instabilities or energetic events. The paper summarizes the equations and methods used in the Mancha3D code. It also describes its numerical stability and parallel performance and efficiency. The code is based on a finite difference discretization and memory-saving Runge-Kutta (RK) scheme. It handles non-ideal effects through super-time stepping and Hall diffusion schemes, and takes into account thermal conduction by solving an additional hyperbolic equation for the heat flux. The code is easily configurable to perform different kinds of simulations. Several examples of the code usage are given. It is demonstrated that splitting variables into equilibrium and perturbation parts is essential for simulations of wave propagation in a static background. A perfectly matched layer (PML) boundary condition built into the code greatly facilitates a non-reflective open boundary implementation. Spatial filtering is an important numerical remedy to eliminate grid-size perturbations enhancing the code stability. Parallel performance analysis reveals that the code is strongly memory bound, which is a natural consequence of the numerical techniques used, such as split variables and PML boundary conditions. Both strong and weak scalings show adequate performance up till several thousands of CPUs.

Solar prominences contain a significant amount of neutral species. The dynamics of the ionised and neutral fluids composing the prominence plasma can be slightly different if the collisional coupling is not strong enough. Large-scale velocities can be quantified by Doppler effect. Small-scale velocities leave their imprint on the width of spectral lines. Here we use one spectral line of ionised and two spectral lines of neutral elements to measure the resolved and unresolved velocities in a prominence with the aim to investigate the possible decoupling of the observed charged and neutral species. A prominence was observed with the German Vacuum Tower Telescope on June 17, 2017. Time series consisting of repeated 10-position scans were performed while recording simultaneously the intensity spectra of the Ca II 854.2 nm, H{\alpha} 656.28 nm, and HeD3 587.56 nm lines. The line-of-sight velocities and the Doppler width of the three spectral lines were determined at every spatial position and temporal moment. To make sure all spectral lines were sampling the same plasma volume, we applied selection criteria to identify locations with optically thin plasma. The velocities of the three spectral lines turned out to be very similar over this region, with the ionised Ca II showing velocity excursions systematically larger compared to those of the neutral lines of H{\alpha} and He I at some moments. The latter were found to be much closer to each other. The analysis of the Doppler widths indicated that the C aII line shows an excess of unresolved motions. The dynamics of the ionised and neutral plasma components in the observed prominence was very close one to the other. The differences found may indicate that a localised decoupling between ions and neutrals may appear at particular spatial locations or instants of time., Comment: Accepted for publication in Astronomy & Astrophysics, 12 pages, 12 figures

Context. Realistic 3D time-dependent simulations of stellar near-surface convection employ the opacity binning method for efficient and accurate computation of the radiative energy exchange. The method provides several orders of magnitude of speed-up, but its implementation includes a number of free parameters. Aims. Our aim is to evaluate the accuracy of the opacity binning method as a function of the choice of these free parameters. Methods. The monochromatic opacities computed with the SYNSPEC code are used to construct opacity distribution function (ODF) that is then verified through detailed comparison with the results of the ATLAS code. The opacity binning method is implemented with the SYNSPEC opacities for four representative cool main-sequence stellar spectral types (F3V, G2V, K0V, and M2V). Results. The ODFs from SYNSPEC and ATLAS show consistent results for the opacity and bolometric radiative energy exchange rate Q in case of the F, G, and K -- type stars. Significant differences, coming mainly from the molecular line lists, are found for the M -- type star. It is possible to optimise a small number of bins to reduce the deviation of the results coming from the opacity grouping with respect to the ODF for the F, G, and K -- type stars. In the case of the M -- type star, the inclusion of splitting in wavelength is needed in the grouping to get similar results, with a subsequent increase in computing time. In the limit of a large number of bins, the deviation for all the binning configurations tested saturates and the results do not converge to the ODF solution. Due to this saturation, the Q rate cannot be improved by increasing the number of bins to more than about 20 bins. The more effective strategy is to select the optimal location of fewer bins., Comment: 26 pages, 29 figures. Accepted for publication in section 15 (Numerical methods and codes) of Astronomy and Astrophysics

In this work, we study the accuracy that can be achieved when inferring the atmospheric information from realistic numerical magneto-hydrodynamic simulations that reproduce the spatial resolution we will obtain with future observations made by the 4m class telescopes DKIST and EST. We first study multiple inversion configurations using the SIR code and the Fe I transitions at 630 nm until we obtain minor differences between the input and the inferred atmosphere in a wide range of heights. Also, we examine how the inversion accuracy depends on the noise level of the Stokes profiles. The results indicate that when the majority of the inverted pixels come from strongly magnetised areas, there are almost no restrictions in terms of the noise, obtaining good results for noise amplitudes up to 1$\times10^{-3}$ of $I_c$. At the same time, the situation is different for observations where the dominant magnetic structures are weak, and noise restraints are more demanding. Moreover, we find that the accuracy of the fits is almost the same as that obtained without noise when the noise levels are on the order of 1$\times10^{-4}$of $I_c$. We, therefore, advise aiming for noise values on the order of or lower than 5$\times10^{-4}$ of $I_c$ if observers seek reliable interpretations of the results for the magnetic field vector reliably. We expect those noise levels to be achievable by next-generation 4m class telescopes thanks to an optimised polarisation calibration and the large collecting area of the primary mirror., Comment: 14 pages, 13 figures

The goal of helioseismology is to provide accurate information about the Sun's interior from the observations of the wave field at its surface. In the last three decades, both global and local helioseismology studies have made significant advances and breakthroughs in solar physics. However, 3-d mapping of the structure and dynamics of sunspots and active regions below the surface has been a challenging task and are among the longest standing and intriguing puzzles of solar physics due to the complexity of the turbulent and dynamic nature of sunspots. Thus the key problems that need to be addressed during the next decade are: (i) Understanding the wave excitation mechanisms in the quiet Sun and magnetic regions, (ii) Characterizing the wave propagation and transformation in strong and inclined magnetic field regions and understanding the magnetic portals in the chromosphere, (iii) Improving helioseismology techniques and investigating the whole life cycle of active regions, from magnetic flux emergence to dissipation, and (iv) Detecting helioseismic signature of the magnetic flux of active regions before it becomes visible on the surface so as to provide warnings several days before the emergence. For a transformative progress on these problems require full disk, simultaneous Doppler and vector magnetic field measurements of the photosphere up to the chromosphere with a spatial resolution of about 2 arc-sec as well as large-scale radiative MHD simulations of the plasma dynamics from the sub-photosphere to the chromosphere., Comment: A White Paper Submitted to the Decadal Survey for Solar and Space Physics (Heliophysics) -- SSPH 2024-2033

Recurrent, arc-shaped intensity disturbances were detected by EUV channels in an active region. The fronts were observed to propagate along a coronal loop bundle rooted in a small area within a sunspot umbra. Previous works have linked these intensity disturbances to slow magnetoacoustic waves that propagate from the lower atmosphere to the corona along the magnetic field. The slow magnetoacoustic waves propagate at the local cusp speed. However, the measured propagation speeds from the intensity images are usually smaller as they are subject to projection effects due to the inclination of the magnetic field with respect to the line-of-sight. Here, we aim to understand the effect of projection by comparing observed speeds with those from a numerical model. Using multi-wavelength data we determine the periods present in the observations at different heights of the solar atmosphere through Fourier analysis. We calculate the plane-of-sky speeds along one of the loops from the cross-correlation time lags obtained as a function of distance along the loop. We perform a 2D ideal MHD simulation of an active region embedded in a stratified atmosphere. We drive slow waves from the photosphere with a 3 minutes periodicity. Synthetic time-distance maps are generated from the forward-modelled intensities in coronal wavelengths and the projected propagation speeds are calculated. The intensity disturbances show a dominant period between [2-3] minutes at different heights of the atmosphere. The apparent propagation speeds calculated for coronal channels exhibit an accelerated pattern with values increasing from 40 to 120 km/s as the distance along the loop rises. The propagation speeds obtained from the synthetic time-distance maps also exhibit accelerated profiles within a similar range of speeds. We conclude that the accelerated propagation in our observations is due to the projection effect., Comment: 12 pages, 12 figures

The European Solar Telescope (EST) is a project aimed at studying the magnetic connectivity of the solar atmosphere, from the deep photosphere to the upper chromosphere. Its design combines the knowledge and expertise gathered by the European solar physics community during the construction and operation of state-of-the-art solar telescopes operating in visible and near-infrared wavelengths: the Swedish 1m Solar Telescope (SST), the German Vacuum Tower Telescope (VTT) and GREGOR, the French T\'elescope H\'eliographique pour l'\'Etude du Magn\'etisme et des Instabilit\'es Solaires (TH\'EMIS), and the Dutch Open Telescope (DOT). With its 4.2 m primary mirror and an open configuration, EST will become the most powerful European ground-based facility to study the Sun in the coming decades in the visible and near-infrared bands. EST uses the most innovative technological advances: the first adaptive secondary mirror ever used in a solar telescope, a complex multi-conjugate adaptive optics with deformable mirrors that form part of the optical design in a natural way, a polarimetrically compensated telescope design that eliminates the complex temporal variation and wavelength dependence of the telescope Mueller matrix, and an instrument suite containing several (etalon-based) tunable imaging spectropolarimeters and several integral field unit spectropolarimeters. This publication summarises some fundamental science questions that can be addressed with the telescope, together with a complete description of its major subsystems., Comment: 38 pages, 24 figures

Thermal conductivity is one of the important mechanisms of heat transfer in the solar corona. In the limit of strongly magnetized plasma, it is typically modeled by Spitzer's expression where the heat flux is aligned with the magnetic field. This paper describes the implementation of the heat conduction into the code MANCHA3D with an aim of extending single-fluid MHD simulations from the upper convection zone into the solar corona. Two different schemes to model heat conduction are implemented: (1) a standard scheme where a parabolic term is added to the energy equation, and (2) a scheme where the hyperbolic heat flux equation is solved. The first scheme limits the time step due to the explicit integration of a parabolic term, which makes the simulations computationally expensive. The second scheme solves the limitations on the time step by artificially limiting the heat conduction speed to computationally manageable values. The validation of both schemes is carried out with standard tests in one, two, and three spatial dimensions. Furthermore, we implement the model for heat flux derived by Braginskii (1965) in its most general form, when the expression for the heat flux depends on the ratio of the collisional to cyclotron frequencies of the plasma, and, therefore on the magnetic field strength. Additionally, our implementation takes into account the heat conduction in parallel, perpendicular, and transverse directions, and provides the contributions from ions and electrons separately. The model also transitions smoothly between field-aligned conductivity and isotropic conductivity for regions with a low or null magnetic field. Finally, we present a two-dimensional test for heat conduction using realistic values of the solar atmosphere where we prove the robustness of the two schemes implemented., Comment: 11 pages, 8 figures

Several generalizations of the well-known fluid model of Braginskii (Rev. of Plasma Phys., 1965) are considered. We use the Landau collisional operator and the moment method of Grad. We focus on the 21-moment model that is analogous to the Braginskii model, and we also consider a 22-moment model. Both models are formulated for general multi-species plasmas with arbitrary masses and temperatures, where all the fluid moments are described by their evolution equations. The 21-moment model contains two "heat flux vectors" (3rd and 5th-order moments) and two "viscosity-tensors" (2nd and 4th-order moments). The Braginskii model is then obtained as a particular case of a one ion-electron plasma with similar temperatures, with de-coupled heat fluxes and viscosity-tensors expressed in a quasi-static approximation. We provide all the numerical values of the Braginskii model in a fully analytic form (together with the 4th and 5th-order moments). For multi-species plasmas, the model makes calculation of transport coefficients straightforward. Formulation in fluid moments (instead of Hermite moments) is also suitable for implementation into existing numerical codes. It is emphasized that it is the quasi-static approximation which makes some Braginskii coefficients divergent in a weakly-collisional regime. Importantly, we show that the heat fluxes and viscosity-tensors are coupled even in the linear approximation, and that the fully contracted (scalar) perturbations of the 4th-order moment, which are accounted for in the 22-moment model, modify the energy exchange rates. We also provide several Appendices, which can be useful as a guide for deriving the Braginskii model with the moment method of Grad., Comment: Updated version. Title change from "Braginskii-type" to "Braginskii Type" to match the published version (accepted to ApJ Supplements, 29 Jan 2022). Bookmarks included, TOC is now at the beginning, numbering in Appendix I is fixed, few typos corrected

We report on results of high resolution two fluid non-linear simulations of the Rayleigh Taylor Instability (RTI) at the interface between a solar prominence and the corona. These follow results reported earlier by Popescu Braileanu et al. (2021a,b) on linear and early non-linear RTI dynamics in this environment. The simulations use a two fluid model that includes collisions between neutrals and charges, including ionization/recombination, energy and momentum transfer, and frictional heating. High resolution 2.5D magnetized RTI simulations with the magnetic field dominantly normal to and slightly sheared with respect to the prominence plane demonstrate that in a fully developed state of RTI a large fraction of the gravitational energy of a prominence thread can be converted into quasi-turbulent energy of the magnetic field. RTI magnetic energy generation is further accompanied by magnetic and plasma density structure formation, including dynamic formation, break-up, and merging of current sheets and plasmoid sub-structures. The simulations show the role of flow decoupling and ionization/recombination reactions between the neutrals and charges on the structure formation in magnetized RTI. We provide a careful examination of sources and form of numerical dissipation of the evolving magnetic field structures.

The importance of the chromosphere in the mass and energy transport within the solar atmosphere is now widely recognised. This review discusses the physics of magnetohydrodynamic (MHD) waves and instabilities in large-scale chromospheric structures as well as in magnetic flux tubes. We highlight a number of key observational aspects that have helped our understanding of the role of the solar chromosphere in various dynamic processes and wave phenomena, and the heating scenario of the solar chromosphere is also discussed. The review focuses on the physics of waves and invokes the basics of plasma instabilities in the context of this important layer of the solar atmosphere. Potential implications, future trends and outstanding questions are also delineated., Comment: This is an invited review article in the special issue "Solar and Heliospheric Plasma Structures: Waves, Turbulence, and Dissipation" of JGR - Space Physics (57 pages, 9 figures, Paper #2020JA029097R) with Editors: Leon Ofman and Shreekrishna Tripathi

In this work, we explore the dynamical impacts and observable signatures of two-fluid effects in the parameter regimes when ion-neutral collisions do not fully couple the neutral and charged fluids. The purpose of this study is to deepen our understanding of the RTI and the effects of the partial ionization on the development of RTI using non-linear two-fluid numerical simulations. Our two-fluid model takes into account neutral viscosity, thermal conductivity, and collisional interaction between neutrals and charges: ionization/recombination, energy and momentum transfer, and frictional heating. In this paper II, the sensitivity of the RTI dynamics to collisional effects for different magnetic field configurations supporting the prominence thread is explored. This is done by artificially varying, or eliminating, effects of both elastic and inelastic collisions by modifying the model equations. We find that ionization and recombination reactions between ionized and neutral fluids, if in equilibrium prior to the onset of the instability, do not substantially impact the development of the primary RTI. However, such reactions can impact development of secondary structures during mixing of the cold prominence and hotter surrounding coronal material. We find that collisionality within and between ionized and neutral particle populations play an important role in both linear and non-linear development of RTI, with ion-neutral collision frequency as the primary determining factor in development or damping of small scale structures. We also observe that degree and signatures of flow decoupling between ion and neutral fluids can depend both on the inter-particle collisionality and the magnetic field configuration of the prominence thread.

This paper presents the results of the analysis of 3D simulations of solar magneto-convection that include the joint action of the ambipolar diffusion and the Hall effect. Three simulation-runs are compared: one including both ambipolar diffusion and Hall effect; one including only ambipolar diffusion; and one without any of these two effects. The magnetic field is amplified from initial field to saturation level by the action of turbulent local dynamo. In each of these cases, we study 2 hours of simulated solar time after the local dynamo reaches the saturation regime. We analyze the power spectra of vorticity, of magnetic field fluctuations and of the different components of the magnetic Poynting flux responsible for the transport of vertical or horizontal perturbations. Our preliminary results show that the ambipolar diffusion produces a strong reduction of vorticity in the upper chromospheric layers and that it dissipates the vortical perturbations converting them into thermal energy. The Hall effect acts in the opposite way, strongly enhancing the vorticity. When the Hall effect is included, the magnetic field in the simulations becomes, on average, more vertical and long-lived flux tube-like structures are produced. We trace a single magnetic structure to study its evolution pattern and the magnetic field intensification, and their possible relation to the Hall effect., Comment: to appear in Philosophical Transactions of the Royal Society A, issue "High resolution wave dynamics in the lower solar atmosphere"

The partial ionization of the solar plasma causes several nonideal effects such as the ambipolar diffusion, the Hall effect, and the Biermann battery effect. Here we report on the first three-dimensional realistic simulations of solar local dynamo where all three effects were taken into account. The simulations started with a snapshot of already saturated battery-seeded dynamo, where two new series were developed: one with solely ambipolar diffusion and another one also taking into account the Hall term in the generalized Ohm's law. The simulations were then run for about 4 hours of solar time to reach the stationary regime and improve the statistics. In parallel, a purely MHD dynamo simulation was also run for the same amount of time. The simulations are compared in a statistical way. The results show that, with the inclusion of the ambipolar diffusion, the amplitudes of the incompressible perturbations related to Alfven waves are reduced, and the Poynting flux is absorbed, with a frequency dependence. The Hall effect causes the opposite action: significant excess of incompressible perturbations is generated and an excess of the Poynting flux is observed in the chromospheric layers. The model with ambipolar diffusion shows, on average, sharper current sheets and slightly more abundant fast magneto-acoustic shocks in the chromosphere. The model with the Hall effect has higher temperatures at the lower chromosphere and stronger and more vertical magnetic field concentrations all over the chromosphere. The study of high-frequency waves reveals that significant power of incompressible perturbations is associated with areas with intense and more vertical magnetic fields and larger temperatures. We find a positive correlation between the magnitude of the ambipolar heating and the temperature increase at the same location after a characteristic time of 10^2 sec., Comment: To appear in Astronomy & Astrophysics

Solar prominences are formed by partially ionized plasma with inter-particle collision frequencies generally warranting magnetohydrodynamic treatment. In this work, we explore the dynamical impacts and observable signatures of two-fluid effects in the parameter regimes when ion-neutral collisions do not fully couple the neutral and charged fluids. We perform 2.5D two-fluid (charges - neutrals) simulations of the Rayleigh-Taylor instability (RTI) at a smoothly changing interface between a solar prominence thread and the corona. The purpose of this study is to deepen our understanding of the RTI and the effects of the partial ionization on the development of RTI using non-linear two-fluid numerical simulations. Our two-fluid model takes into account viscosity, thermal conductivity, and collisional interaction between neutrals and charges: ionization/recombination, energy and momentum transfer, and frictional heating. In this paper I, the sensitivity of the RTI dynamics to the prominence equilibrium configuration, including the impact of the magnetic field strength and shear supporting the prominence thread, and the amount of prominence mass-loading is explored. We show that, at small scales, a realistically smooth prominence-corona interface leads to qualitatively different linear RTI evolution than that expected for a discontinuous interface, while magnetic field shear has the stabilizing effect of reducing the growth rate or eliminating the instability. In the non-linear phase, we observe that in the presence of field shear the development of the instability leads to formation of coherent and interacting 2.5D magnetic structures, which, in turn, can lead to substantial plasma flow across magnetic field lines and associated decoupling of the fluid velocities of charges and neutrals.

There has been tremendous progress in the degree of realism of three-dimensional radiation magneto-hydrodynamic simulations of the solar atmosphere in the past decades. Four of the most frequently used numerical codes are Bifrost, CO5BOLD, MANCHA3D, and MURaM. Here we test and compare the wave propagation characteristics in model runs from these four codes by measuring the dispersion relation of acoustic-gravity waves at various heights. We find considerable differences between the various models. The height dependence of wave power, in particular of high-frequency waves, varies by up to two orders of magnitude between the models, and the phase difference spectra of several models show unexpected features, including $\pm180^\circ$ phase jumps., Comment: 19 pages, 15 figures

The European Solar Telescope (EST) is a research infrastructure for solar physics. It is planned to be an on-axis solar telescope with an aperture of 4 m and equipped with an innovative suite of spectro-polarimetric and imaging post-focus instrumentation. The EST project was initiated and is driven by EAST, the European Association for Solar Telescopes. EAST was founded in 2006 as an association of 14 European countries. Today, as of December 2019, EAST consists of 26 European research institutes from 18 European countries. The Preliminary Design Phase of EST was accomplished between 2008 and 2011. During this phase, in 2010, the first version of the EST Science Requirement Document (SRD) was published. After EST became a project on the ESFRI roadmap 2016, the preparatory phase started. The goal of the preparatory phase is to accomplish a final design for the telescope and the legal governance structure of EST. A major milestone on this path is to revisit and update the Science Requirement Document (SRD). The EST Science Advisory Group (SAG) has been constituted by EAST and the Board of the PRE-EST EU project in November 2017 and has been charged with the task of providing with a final statement on the science requirements for EST. Based on the conceptual design, the SRD update takes into account recent technical and scientific developments, to ensure that EST provides significant advancement beyond the current state-of-the-art. The present update of the EST SRD has been developed and discussed during a series of EST SAG meetings. The SRD develops the top-level science objectives of EST into individual science cases. Identifying critical science requirements is one of its main goals. Those requirements will define the capabilities of EST and the post-focus instrument suite. The technical requirements for the final design of EST will be derived from the SRD., Comment: 2nd edition, December 2019, 138 pages

Waves and shocks traveling through the solar chromospheric plasma are influenced by its partial ionization and weak collisional coupling, and may become susceptible to multi-fluid effects, similar to interstellar shock waves. In this study, we consider fast magneto-acoustic shock wave formation and propagation in a stratified medium, that is permeated by a horizontal magnetic field, with properties similar to that of the solar chromosphere. The evolution of plasma and neutrals is modeled using a two-fluid code that evolves a set of coupled equations for two separate fluids. We observed that waves in neutrals and plasma, initially coupled at the upper photosphere, become uncoupled at higher heights in the chromosphere. This decoupling can be a consequence of either the characteristic spatial scale at the shock front, that becomes similar to the collisional scale, or the change in the relation between the wave frequency, ion cyclotron frequency, and the collisional frequency with height. The decoupling height is a sensitive function of the wave frequency, wave amplitude, and the magnetic field strength. We observed that decoupling causes damping of waves and an increase in the background temperature due to the frictional heating. The comparison between analytical and numerical results allows us to separate the role of the nonlinear effects from the linear ones on the decoupling and damping of waves.

Solar chromosphere consists of a partially ionized plasma, which makes modeling the solar chromosphere a particularly challenging numerical task. Here we numerically model chromospheric waves using a two-fluid approach with a newly developed numerical code. The code solves two-fluid equations of conservation of mass, momentum and energy, together with the induction equation, for the case of the purely hydrogen plasma with collisional coupling between the charged and neutral fluid components. The implementation of a semi-implicit algorithm allows us to overcome the numerical stability constraints due to the stiff collisional terms. We test the code against analytical solutions of acoustic and Alfv\'en wave propagation in uniform medium in several regimes of collisional coupling.The results of our simulations are consistent with the analytical estimates, and with other results described in the literature. In the limit of a large collisional frequency, the waves propagate with a common speed of a single fluid. In the other limit of a vanishingly small collisional frequency, the Alfv\'en waves propagate with an Alfv\'en speed of the charged fluid only, while the perturbation in neutral fluid is very small. The acoustic waves in these limits propagate with the sound speed corresponding to either the charges or the neutrals, while the perturbation in the other fluid component is very small. Otherwise, when the collision frequency is similar to the real part of the wave frequency, the interaction between charges and neutrals through momentum transfer collisions cause alterations of the waves frequencies and damping of the wave amplitudes.

In Part 2 of our guide to collisionless fluid models, we concentrate on Landau fluid closures. These closures were pioneered by Hammett and Perkins and allow for the rigorous incorporation of collisionless Landau damping into a fluid framework. It is Landau damping that sharply separates traditional fluid models and collisionless kinetic theory, and is the main reason why the usual fluid models do not converge to the kinetic description, even in the long-wavelength low-frequency limit. We start with a brief introduction to kinetic theory, where we discuss in detail the plasma dispersion function $Z(\zeta)$, and the associated plasma response function $R(\zeta)=1+\zeta Z(\zeta)=-Z'(\zeta)/2$. We then consider a 1D (electrostatic) geometry and make a significant effort to map all possible Landau fluid closures that can be constructed at the 4th-order moment level. These closures for parallel moments have general validity from the largest astrophysical scales down to the Debye length, and we verify their validity by considering examples of the (proton and electron) Landau damping of the ion-acoustic mode, and the electron Landau damping of the Langmuir mode. We proceed by considering 1D closures at higher-order moments than the 4th-order, and as was concluded in Part 1, this is not possible without Landau fluid closures. We show that it is possible to reproduce linear Landau damping in the fluid framework to any desired precision, thus showing the convergence of the fluid and collisionless kinetic descriptions. We then consider a 3D (electromagnetic) geometry in the gyrotropic (long-wavelength low-frequency) limit and map all closures that are available at the 4th-order moment level. In the Appendix A, we provide comprehensive tables with Pad\'e approximants of $R(\zeta)$ up to the 8th-pole order, with many given in an analytic form., Comment: Improved version, now accepted to JPP Lecture Notes. Some parts were shortened and some parts were expanded. The text now contains Conclusions

We present a detailed guide to advanced collisionless fluid models that incorporate kinetic effects into the fluid framework, and that are much closer to the collisionless kinetic description than traditional magnetohydrodynamics. Such fluid models are directly applicable to modeling turbulent evolution of a vast array of astrophysical plasmas, such as the solar corona and the solar wind, the interstellar medium, as well as accretion disks and galaxy clusters. The text can be viewed as a detailed guide to Landau fluid models and it is divided into two parts. Part 1 is dedicated to fluid models that are obtained by closing the fluid hierarchy with simple (non Landau fluid) closures. Part 2 is dedicated to Landau fluid closures. Here in Part 1, we discuss the CGL fluid model in great detail, together with fluid models that contain dispersive effects introduced by the Hall term and by the finite Larmor radius (FLR) corrections to the pressure tensor. We consider dispersive effects introduced by the non-gyrotropic heat flux vectors. We investigate the parallel and oblique firehose instability, and show that the non-gyrotropic heat flux strongly influences the maximum growth rate of these instabilities. Furthermore, we discuss fluid models that contain evolution equations for the gyrotropic heat flux fluctuations and that are closed at the 4th-moment level by prescribing a specific form for the distribution function. For the bi-Maxwellian distribution, such a closure is known as the "normal" closure. We also discuss a fluid closure for the bi-kappa distribution. Finally, by considering one-dimensional Maxwellian fluid closures at higher-order moments, we show that such fluid models are always unstable. The last possible non Landau fluid closure is therefore the "normal" closure, and beyond the 4th-order moment, Landau fluid closures are required., Comment: Improved version, accepted to JPP Lecture Notes. Some parts were shortened and some parts were expanded. The text now contains Conclusions

Coupling between fast magneto-acoustic and Alfv\'en waves can be observe in fully ionized plasmas mediated by stratification and 3D geometrical effects. In Paper I, Cally & Khomenko (2015) have shown that in a weakly ionized plasma, such as the solar photosphere and chromosphere, the Hall current introduces a new coupling mechanism. The present study extends the results from Paper I to the case of warm plasma. We report on numerical experiments where mode transformation is studied using quasi-realistic stratification in thermodynamic parameters resembling the solar atmosphere. This redresses the limitation of the cold plasma approximation assumed in Paper I, in particular allowing the complete process of coupling between fast and slow magneto-acoustic modes and subsequent coupling of the fast mode to the Alfv\'en mode through the Hall current. Our results confirm the efficacy of the mechanism proposed in Paper I for the solar case. We observe that the efficiency of the transformation is a sensitive function of the angle between the wave propagation direction and the magnetic field, and of the wave frequency. The efficiency increases when the field direction and the wave direction are aligned for increasing wave frequencies. After scaling our results to typical solar values, the maximum amplitude of the transformed Alfv\'en waves, for a frequency of 1 Hz, corresponds to an energy flux (measured above the height of peak Hall coupling) of $\sim10^3$ $\rm W\,m^{-2}$, based on an amplitude of 500 $\rm m\,s^{-1}$ at $\beta=1$, which is sufficient to play a major role in both quiet and active region coronal heating.

Solar active regions show a wide variety of oscillatory phenomena. The presence of the magnetic field leads to the appearance of several wave modes, whose behavior is determined by the sunspot thermal and magnetic structure. We aim to study the relation between the umbral and penumbral waves observed at the high photosphere and the magnetic field topology of the sunspot. Observations of the sunspot in active region NOAA 12662 obtained with the GREGOR telescope (Observatorio del Teide, Spain) were acquired on 2017 June 17. The data set includes a temporal series in the Fe I 5435 \AA\ line obtained with the imaging spectrograph GREGOR Fabry-P\'erot Interferometer (GFPI) and a spectropolarimetric raster map acquired with the GREGOR Infrared Spectrograph (GRIS) in the 10830 \AA\ spectral region. The Doppler velocity deduced from the restored Fe I 5435 \AA\ line has been determined, and the magnetic field vector of the sunspot has been inferred from spectropolarimetric inversions of the Ca I 10839 \AA\ and the Si I 10827 \AA\ lines. A two-armed spiral wavefront has been identified in the evolution of the two-dimensional velocity maps from the Fe I 5435 \AA\ line. The wavefronts initially move counterclockwise in the interior of the umbra, and develop into radially outward propagating running penumbral waves when they reach the umbra-penumbra boundary. The horizontal propagation of the wavefronts approximately follows the direction of the magnetic field, which shows changes in the magnetic twist with height and horizontal position. The spiral wavefronts are interpreted as the visual pattern of slow magnetoacoustic waves which propagate upward along magnetic field lines. Their apparent horizontal propagation is due to their sequential arrival to different horizontal positions at the formation height of the Fe I 5435 \AA\ line, as given by the inclination and orientation of the magnetic field., Comment: Accepted for publication in A&A

Over the last decades, realistic 3D radiative-MHD simulations have become the dominant theoretical tool for understanding the complex interactions between the plasma and the magnetic field on the Sun. Most of such simulations are based on approximations of magnetohydrodynamics, without directly considering the consequences of the very low degree of ionization of the solar plasma in the photosphere and bottom chromosphere. The presence of large amount of neutrals leads to a partial decoupling of the plasma and the magnetic field. As a consequence of that, a series of non-ideal effects (ambipolar diffusion, Hall effect and battery effect) arises. The ambipolar effect is the dominant one in the solar chromosphere. Here we report on the first three-dimensional realistic simulations of magneto-convection including ambipolar diffusion and battery effects. The simulations are done using the newly developed Mancha3D code. Our results reveal that ambipolar diffusion causes measurable effects on the amplitudes of waves excited by convection in the simulations, on the absorption of Poynting flux and heating and on the formation of chromospheric structures. We provide a low limit on the chromospheric temperature increase due to the ambipolar effect using the simulations with battery-excited dynamo fields., Comment: To appear in Astronomy & Astrophysics

The interaction of plasma with magnetic field in the partially ionised solar atmosphere is frequently modelled via a single-fluid approximation, which is valid for the case of a strongly coupled collisional media, such as solar photosphere and low chromosphere. Under the single-fluid formalism the main non-ideal effects are described by a series of extra terms in the generalised induction equation and in the energy conservation equation. These effects are: Ohmic diffusion, ambipolar diffusion, the Hall effect, and the Biermann battery effect. From the point of view of the numerical solution of the single-fluid equations, when ambipolar diffusion or Hall effects dominate can introduce severe restrictions on the integration time step and can compromise the stability of the numerical scheme. In this paper we introduce two numerical schemes to overcome those limitations. The first of them is known as Super Time-Stepping (STS) and it is designed to overcome the limitations imposed when the ambipolar diffusion term is dominant. The second scheme is called the Hall Diffusion Scheme (HDS) and it is used when the Hall term becomes dominant. These two numerical techniques can be used together by applying Strang operator splitting. This paper describes the implementation of the STS and HDS schemes in the single-fluid code Mancha3D. The validation for each of these schemes is provided by comparing the analytical solution with the numerical one for a suite of numerical tests.

We investigate the properties of a sunspot light-bridge, focusing on the changes produced by the impact of a plasma blob ejected from a C-class flare. We observed a sunspot in active region NOAA 12544 using spectropolarimetric raster maps of the four Fe I lines around 15655 \AA\ with the GREGOR Infrared Spectrograph (GRIS), narrow-band intensity images sampling the Fe I 6173 \AA\ line with the GREGOR Fabry-P\'erot Interferometer (GFPI), and intensity broad band images in G-band and Ca II H band with the High-resolution Fast Imager (HiFI). All these instruments are located at the GREGOR telescope at the Observatorio del Teide, Tenerife, Spain. The data cover the time before, during, and after the flare event. The analysis is complemented with Atmospheric Imaging Assembly (AIA) and Helioseismic and Magnetic Imager (HMI) data from the Solar Dynamics Observatory (SDO). The physical parameters of the atmosphere at differents heights were inferred using spectral-line inversion techniques. We identify photospheric and chromospheric brightenings, heating events, and changes in the Stokes profiles associated to the flare eruption and the subsequent arrival of the plasma blob to the light bridge, after traveling along an active region loop. The measurements suggest that these phenomena are the result of reconnection events driven by the interaction of the plasma blob with the magnetic field topology of the light bridge., Comment: Accepted for publication in A&A

The magnetic fields of the quiet Sun cover at any time more than 90\% of its surface and their magnetic energy budget is crucial to explain the thermal structure of the solar atmosphere. One of the possible origins of these fields is due to the action of local dynamo in the upper convection zone of the Sun. Existing simulations of the local solar dynamo require an initial seed field, and sufficiently high spatial resolution, in order to achieve the amplification of the seed field to the observed values in the quiet Sun. Here we report an alternative model of seeding based on the action of the Bierman battery effect. This effect generates a magnetic field due to the local imbalances in electron pressure in the partially ionized solar plasma. We show that the battery effect self-consistently creates from zero an initial seed field of a strength of the order of micro G, and together with dynamo amplification, allows the generation of quiet Sun magnetic fields of a similar strength to those from solar observations., Comment: To appear in Astronomy & Astrophysics

This work aims to understand the behavior of non-linear waves in the vicinity of a coronal null point. In previous works we have showed that high frequency waves are generated in such magnetic configuration. This paper studies those waves in detail in order to provide a plausible explanation of their generation. We demonstrate that slow magneto-acoustic shock waves generated in the chromosphere propagate through the null point and produce a train of secondary shocks that escape along the field lines. A particular combination of the shock wave speeds generates waves at a frequency of 80 mHz. We speculate that this frequency may be sensitive to the atmospheric parameters in the corona and therefore can be used to probe the structure of this solar layer.

Photospheric waves in sunspots moving radially outwards at speeds faster than the characteristic wave velocities have been recently detected. It has been suggested that they are the visual pattern of $p-$modes excited around 5 Mm beneath the sunspot. Using numerical simulations, we have performed a parametric study of the waves observed at the photosphere and higher layers produced by sources located at different depths. The observational measurements are consistent with waves driven between approximately 1 Mm and 5 Mm below the sunspot surface., Comment: Accepted for publication in A&A

Active regions are the most prominent manifestations of solar magnetic fields; their generation and dissipation are fundamental problems in solar physics. Light bridges are commonly present during sunspot decay, but a comprehensive picture of their role in the removal of photospheric magnetic field is still missing. We study the three dimensional configuration of a sunspot and in particular its light bridge during one of the last stages of its decay. We present the magnetic and thermodynamical stratification inferred from full Stokes inversions of the photospheric Si I 10827 \AA\ and Ca I 10839 \AA\ lines obtained with the GREGOR Infrared Spectrograph of the GREGOR telescope at Observatorio del Teide, Tenerife, Spain. The analysis is complemented by a study of continuum images covering the disk passage of the active region, which are provided by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory. The sunspot shows a light bridge with penumbral continuum intensity that separates the central umbra from a smaller umbra. We find that in this region the magnetic field lines form a canopy with lower magnetic field strength in the inner part. The photospheric light bridge is dominated by gas pressure (high-$\beta$), as opposed to the surrounding umbra where the magnetic pressure is higher. A convective flow is observed in the light bridge. This flow is able to bend the magnetic field lines and to produce field reversals. The field lines close above the light bridge and become as vertical and strong as in the surrounding umbra. We conclude that it develops because of two highly magnetized regions which come closer during the sunspot evolution., Comment: Accepted for publication in A&A

In this paper, we show a "proof of concept" of the heating mechanism of the solar chromosphere due to wave dissipation caused by the effects of partial ionization. Numerical modeling of non-linear wave propagation in a magnetic flux tube, embedded in the solar atmosphere, is performed by solving a system of single-fluid quasi-MHD equations, which take into account the ambipolar term from the generalized Ohm's law. It is shown that perturbations caused by magnetic waves can be effectively dissipated due to ambipolar diffusion. The energy input by this mechanism is continuous and shown to be more efficient than dissipation of static currents, ultimately leading to chromospheric temperature increase in magnetic structures., Comment: 7 pages, 5 figures

This paper studies the dependence of the CaIIH line core brightness on the strength and inclination of photospheric magnetic field, and on the parameters of convective and wave motions in a facular region at the solar disc center. We use three simultaneous datasets obtained at the German Vacuum Tower Telescope (Observatorio del Teide, Tenerife): (1) spectra of BaII 4554 A line registered with the instrument TESOS to measure the variations of intensity and velocity through the photosphere up to the temperature minimum; (2) spectropolarimetric data in FeI 1.56 $\mu$m lines (registered with the instrument TIP II) to measure photospheric magnetic fields; (3) filtergrams in CaIIH that give information about brightness fluctuations in the chromosphere. The results show that the CaIIH brightness in the facula strongly depends on the power of waves with periods in the 5-min range, that propagate upwards, and also on the phase shift between velocity oscillations at the bottom photosphere and around the temperature minimum height, measured from BaII line. The CaIIH brightness is maximum at locations where the phase shift between temperature and velocity oscillations lies within 0-100 degrees. There is an indirect influence of convective motions on the CaIIH brightness. Namely, the higher is the amplitude of convective velocities and the larger is the height where they change their direction of motion, the brighter is the facula. Altogether, our results lead to conclusions that facular regions appear bright not only because of the Wilson depression in magnetic structures, but also due to real heating., Comment: to appear in Astronomy & Astrophysics

Large-amplitude longitudinal oscillations (LALOs) in prominences are spectacular manifestations of the solar activity. In such events nearby energetic disturbances induce periodic motions on filaments with displacements comparable to the size of the filaments themselves and with velocities larger than 20 km/s. The pendulum model, in which the gravity projected along a rigid magnetic field is the restoring force, was proposed to explain these events. However, it can be objected that in a realistic situation where the magnetic field reacts to the mass motion of the heavy prominence, the simplified pendulum model could be no longer valid. We have performed non-linear time-dependent numerical simulations of LALOs considering a dipped magnetic field line structure. In this work we demonstrate that for even relatively weak magnetic fields the pendulum model works very well. We therefore validate the pendulum model and show its robustness, with important implications for prominence seismology purposes. With this model it is possible to infer the geometry of the dipped field lines that support the prominence., Comment: Accepted for publication in The Astrophysical Journal

The amplitudes of the Evershed flow are measured using pairs of carefully selected FeI and FeII spectral lines located close in wavelength and registered simultaneously. A sunspot belonging to the NOAA 11582 group was scanned using the spectrograph of the German Vacuum Tower Telescope (Observatorio del Teide, Tenerife). Velocities were extracted from intensity profiles using the lambda-meter technique. The formation heights of the observed spectral lines were calculated using semi-empirical models of a bright and dark penumbral filament taking into account the sunspot location at the limb. Our objective is to compare azimuthally averaged amplitudes of the Evershed flow extracted from neutral and ion lines. We find measurable differences in the radial component of the flow. All five pairs of lines show the same tendency, with a few hundred m/s larger amplitude of the flow measured from FeI lines compared to FeII lines. This tendency is preserved at all photospheric heights and radial distances in the penumbra. We discuss the possible origin of this effect., Comment: to appear in Astronomy and Astrophysics

Coronal waves are an important aspect of the dynamics of the plasma in the corona. Wavefront dislocations are topological features of most waves in nature and also of magnetohydrodynamic waves. Are there dislocations in coronal waves? The finding and explanation of dislocations may shed light on the nature and characteristics of the propagating waves, their interaction in the corona and in general on the plasma dynamics. We positively identify dislocations in coronal waves observed by the Coronal Multi-channel Polarimeter (CoMP) as singularities in the Doppler shifts of emission coronal lines. We study the possible singularities that can be expected in coronal waves and try to reproduce the observed dislocations in terms of localization and frequency of appearance. The observed dislocations can only be explained by the interference of a kink and a sausage wave modes propagating with different frequencies along the coronal magnetic field. In the plane transverse to the propagation, the cross-section of the oscillating plasma must be smaller than the spatial resolution, and the two waves result in net longitudinal and transverse velocity components that are mixed through projection onto the line of sight. Alfv\'en waves can be responsible of the kink mode, but a magnetoacoustic sausage mode is necessary in all cases. Higher (flute) modes are excluded. The kink mode has a pressure amplitude that is smaller than the pressure amplitude of the sausage mode, though its observed velocity is larger. This concentrates dislocations on the top of the loop. To explain dislocations, any model of coronal waves must include the simultaneous propagation and interference of kink and sausage wave modes of comparable but different frequencies, with a sausage wave amplitude much smaller than the kink one., Comment: 11 pages. 5 figures. Accepted for publication in A&A

Spectropolarimetric temporal series from Fe I $\lambda$ 6301.5 \AA\ and Ca II infrared triplet lines are obtained by applying the Stokes synthesis code NICOLE to a numerical simulation of wave propagation in a sunspot umbra from MANCHA code. The analysis of the phase difference between Doppler velocity and intensity core oscillations of the Fe I $\lambda$ 6301.5 \AA\ line reveals that variations in the intensity are produced by opacity fluctuations rather than intrinsic temperature oscillations, except for frequencies between 5 and 6.5 mHz. On the other hand, the photospheric magnetic field retrieved from the weak field approximation provides the intrinsic magnetic field oscillations associated to wave propagation. Our results suggest that this is due to the low magnetic field gradient of our sunspot model. The Stokes parameters of the chromospheric Ca II infrared triplet lines show striking variations as shock waves travel through the formation height of the lines, including emission self-reversals in the line core and highly abnormal Stokes V profiles. Magnetic field oscillations inferred from the Ca II infrared lines using the weak field approximation appear to be related with the magnetic field strength variation between the photosphere and the chromosphere., Comment: Accepted for publication in The Astrophysical Journal

We study the Rayleigh-Taylor instability (RTI) at a prominence-corona transition region in a non-linear regime. Our aim is to understand how the presence of neutral atoms in the prominence plasma influences the instability growth rate, and the evolution of velocity, magnetic field vector and thermodynamic parameters of turbulent drops. We perform 2.5D numerical simulations of the instability initiated by a multi-mode perturbation at the corona-prominence interface using a single-fluid MHD approach including a generalized Ohm's law. The initial equilibrium configuration is purely hydrostatic and contains a homogeneous horizontal magnetic field forming an angle with the direction in which the plasma is perturbed. We analyze simulations with two different orientations of the magnetic field. For each field orientation we compare two simulations, one for the pure MHD case, and one including the ambipolar diffusion in the Ohm's law (AD case). Other than that, both simulations for each field orientation are identical. The numerical results in the initial stage of the instability are compared with the analytical linear calculations. We find that the configuration is always unstable in the AD case. The growth rate of the small-scale modes in the non-linear regime is up to 50% larger in the AD case than in the purely MHD case and the average velocities of flows are a few percent larger. Significant drift momenta are found at the interface between the coronal and the prominence material at all stages of the instability, produced by the faster downward motion of the neutral component with respect to the ionized component. The differences in temperature of the bubbles between the ideal and non-ideal case are also significant, reaching 30%. There is an asymmetry between large rising bubbles and small-scale down flowing fingers, favoring the detection of upward velocities in observations., Comment: Astronomy and Astrophysics, accepted

We study the modification of the classical criterion for the linear onset and growth rate of the Rayleigh-Taylor instability (RTI) in a partially ionized (PI) plasma in the one-fluid description, considering a generalized induction equation. The governing linear equations and appropriate boundary conditions, including gravitational terms, are derived and applied to the case of the RTI in a single interface between two partially ionized plasmas. The boundary conditions lead to an equation for the frequencies in which some of them have positive complex parts, marking the appearance of the RTI. We study the ambipolar term alone first, extending the result to the full induction equation later. We find that the configuration is always unstable because of the presence of a neutral species. In the classical stability regime the growth rate is small, since the collisions prevent the neutral fluid to fully develop the RTI. For parameters in the classical instability regime the growth rate is lowered, but for the considered theoretical values of the collision frequencies and diffusion coefficients for solar prominences the differences with the compressible MHD case are small. We conclude that PI modifies some aspects of the linear RTI instability, since it takes into account that neutrals do not feel the stabilizing effect of the magnetic field. For the set of parameters representative for solar prominences, our model gives the resulting timescale comparable with observed lifetimes of RTI plumes., Comment: Accepted for publication in Astronomy & Astrophysics

We study Rayleigh-Taylor instability (RTI) at the coronal-prominence boundary by means of 2.5D numerical simulations in a single-fluid MHD approach including a generalized Ohm's law. The initial configuration includes a homogeneous magnetic field forming an angle with the direction in which the plasma is perturbed. For each field inclination we compare two simulations, one for the pure MHD case, and one including the ambipolar diffusion in the Ohm's law, otherwise identical. We find that the configuration containing neutral atoms is always unstable. The growth rate of the small-scale modes in the non-linear regime is larger than in the purely MHD case., Comment: Proceeding of IAUS300 "Nature of prominences and their role in Space Weather" Symposium dedicated to Einar Tandberg-Hanssen, Paris, June 10-14, 2013

We describe the presence of wavefront dislocations in magnetohydrodynamic waves in stratified stellar atmospheres. Scalar dislocations such as edges and vortices can appear in Alfv\'en waves, as well as in general magneto-acoustic waves. We detect those dislocations in observations of magnetohydrodynamic waves in sunspots in the solar chromosphere. Through the measured charge of all the dislocations observed, we can give for the first time estimates of the modal contribution in the waves propagating along magnetic fields in solar sunspots., Comment: Accepted for publication in PhysRevLett. 6 pages, 4 figures

We present results of the study of chromospheric and photospheric line-of-sight velocity fields in the young active region NOAA 11024. Multi-layer, multi-wavelength observational data were used for the analysis of the emerging flux in this active region. Spectropolarimetric observations were carried out with the telescope THEMIS on Tenerife (Canary Islands) on 4 July 2009. In addition, space-borne data from SOHO/MDI, STEREO and GOES were also considered. The combination of data from ground- and space-based telescopes allowed us to study the dynamics of the lower atmosphere of the active region with high spatial, spectral, and temporal resolutions. THEMIS spectra show strong temporal variations of the velocity in the chromosphere and photosphere for different activity features: two pores, active and quiet plage regions, and two surges. The range of variations of the chromospheric line-of-sight velocity at the heights of formation of the H-alpha core was extremely large. Both upward and downward motions were observed in these layers. In particular, a surge with upward velocities up to -73 km/s were detected. In the photosphere, predominantly upward motions were found, varying from -3.1 km/s upflows to 1.4 km/s downflows in different structures. The velocity variations at different levels in the lower atmosphere are compatible with magnetic flux emergence., Comment: 17 pages, 8 figures; accepted for publication in Solar Physics

We investigate the impact on Fe abundance determination of including magnetic flux in series of 3D radiation-MHD simulations of solar convection which we used to synthesize spectral intensity profiles corresponding to disc centre. A differential approach is used to quantify the changes in theoretical equivalent width of a set of 28 iron spectral lines spanning a wide range in lambda, excitation potential, oscillator strength, Land\'e factor, and formation height. The lines were computed in LTE using the spectral synthesis code LILIA. We used input magnetoconvection snapshots covering 50 minutes of solar evolution and belonging to series having an average vertical magnetic flux density of 0, 50, 100 and 200 G. For the relevant calculations we used the Copenhagen Stagger code. The presence of magnetic fields causes both a direct (Zeeman-broadening) effect on spectral lines with non-zero Land\'e factor and an indirect effect on temperature-sensitive lines via a change in the photospheric T-tau stratification. The corresponding correction in the estimated atomic abundance ranges from a few hundredths of a dex up to |Delta log(Fe)| ~ 0.15 dex, depending on the spectral line and on the amount of average magnetic flux within the range of values we considered. The Zeeman-broadening effect gains relatively more importance in the IR. The largest modification to previous solar abundance determinations based on visible spectral lines is instead due to the indirect effect, i.e., the line-weakening caused by a warmer stratification on an optical depth scale. Our results indicate that the average solar iron abundance obtained when using magnetoconvection models can be 0.03-0.11 dex higher than when using the simpler HD convection approach. We demonstrate that accounting for magnetic flux is important in state-of-the-art solar photospheric abundance determinations based on 3D simulations., Comment: 12 pages, 7 figures, A&A in press

In this paper, we study the properties of solar granulation in a facular region from the photosphere up to the lower chromosphere. Our aim is to investigate the dependence of granular structure on magnetic field strength. We use observations obtained at the German Vacuum Tower Telescope (Observatorio del Teide, Tenerife) using two different instruments: Triple Etalon SOlar Spectrometer (TESOS), in the BaII 4554 A line to measure velocity and intensity variations along the photosphere; and, simultaneously, Tenerife Infrared Polarimeter (TIP-II), in the FeI 1.56 $\mu$m lines to the measure Stokes parameters and the magnetic field strength at the lower photosphere. We obtain that the convective velocities of granules in the facular area decrease with magnetic field while the convective velocities of intergranular lanes increase with the field strength. Similar to the quiet areas, there is a contrast and velocity sign reversal taking place in the middle photosphere. The reversal heights depend on the magnetic field strength and are, on average, about 100 km higher than in the quiet regions. The correlation between convective velocity and intensity decreases with magnetic field at the bottom photosphere, but increases in the upper photosphere. The contrast of intergranular lanes observed close to the disc center is almost independent of the magnetic field strength. The strong magnetic field of facular area seems to stabilize the convection and to promote more effective energy transfer in the upper layers of the solar atmosphere, since the convective elements reach larger heights., Comment: accepted by Astronomy and Astrophysics