Chromospheric Dynamics and Line Formation

The solar chromosphere is very dynamic, due to the presence of large amplitude hydrodynamic waves. Their propagation is affected by NLTE radiative transport in strong spectral lines, which can in turn be used to diagnose the dynamics of the chromosphere. We give a basic introduction into the equations of NLTE radiation hydrodynamics and describe how they are solved in current numerical simulations. The comparison with observation shows that one-dimensional codes can describe strong brightenings quite well, but the overall chromospheric dynamics appears to be governed by three-dimensional shock propagation.Comment: Lecture notes and review, held at Kodaikanal Winter School on Solar Physics, Dec 2006. This version contains corrected page numbers for some of the reference

Generation of flux tube waves in stellar convection zones. 1: Longitudinal tube waves

The source functions and the energy fluxes are derived for wave generation in magnetic flux tubes embedded in an otherwise magnetic- field free, turbulent, and compressible fluid. Specific results for the generation of longitudinal tube waves are presented

Dynamics and Heating of the Magnetic Network on the Sun: Efficiency of mode transformation

We aim to identify the physical processes which occur in the magnetic network of the chromosphere and which contribute to its dynamics and heating. Specifically, we study the propagation of transverse (kink) MHD waves which are impulsively excited in flux tubes through footpoint motions. When these waves travel upwards, they get partially converted to longitudinal waves through nonlinear effects (mode coupling). By solving the nonlinear, time-dependent MHD equations we find that significant longitudinal wave generation occurs in the photosphere typically for Mach numbers as low as 0.2 and that the onset of shock formation occurs at heights of about 600 km above the photospheric base. We also investigate the compressional heating due to longitudinal waves and the efficiency of mode coupling for various values of the plasma $\beta$, that parameterises the magnetic field strength in the network. We find that this efficiency is maximum for field strengths corresponding to $\beta\approx 0.2$, when the kink and tube wave speeds are almost identical. This can have interesting observational implications. Furthermore, we find that even when the two speeds are different, once shock formation occurs, the longitudinal and transverse shocks exhibit strong mode coupling.Comment: 8 pages, 3 figure

Conformational States of Melittin at a Bilayer Interface

AbstractThe distribution of peptide conformations in the membrane interface is central to partitioning energetics. Molecular-dynamics simulations enable characterization of in-membrane structural dynamics. Here, we describe melittin partitioning into dioleoylphosphatidylcholine lipids using CHARMM and OPLS force fields. Although the OPLS simulation failed to reproduce experimental results, the CHARMM simulation reported was consistent with experiments. The CHARMM simulation showed melittin to be represented by a narrow distribution of folding states in the membrane interface

Small Structures via Thermal Instability of Partially Ionized Plasma. I. Condensation Mode

(Shortened) Thermal instability of partially ionized plasma is investigated by linear perturbation analysis. According to the previous studies under the one fluid approach, the thermal instability is suppressed due to the magnetic pressure. However, the previous studies did not precisely consider the effect of the ion-neutral friction, since they did not treat the flow as two fluid which is composed of ions and neutrals. Then, we revisit the effect of the ion-neutral friction of the two fluid to the growth of the thermal instability. According to our study, (1) The instability which is characterized by the mean molecular weight of neutrals is suppressed via the ion-neutral friction only when the magnetic field and the friction are sufficiently strong. The suppression owing to the friction occurs even along the field line. If the magnetic field and the friction are not so strong, the instability is not stabilized. (2) The effect of the friction and the magnetic field is mainly reduction of the growth rate of the thermal instability of weakly ionized plasma. (3) The effect of friction does not affect the critical wavelength lambdaF for the thermal instability. This yields that lambdaF of the weakly ionized plasma is not enlarged even when the magnetic field exists. We insist that the thermal instability of the weakly ionized plasma in the magnetic field can grow up even at the small length scale where the instability under the assumption of the one fluid plasma can not grow owing to the stabilization by the magnetic field. (4) The wavelength of the maximum growth rate of the instability shifts shortward according to the decrement of the growth rate, because the friction is effective at rather larger scale. Therefore, smaller structures are expected to appear than those without the ion-neutral friction.Comment: To appear in Ap

A New Version of Reimers' law of Mass Loss Based on a Physical Approach

We present a new semi-empirical relation for the mass loss of cool stellar winds, which so far has frequently been described by "Reimers' law". Originally, this relation was based solely on dimensional scaling arguments without any physical interpretation. In our approach, the wind is assumed to result from the spill-over of the extended chromosphere, possibly associated with the action of waves, especially Alfven waves, which are used as guidance in the derivation of the new formula. We obtain a relation akin to the original Reimers law, but which includes two new factors. They reflect how the chromospheric height depends on gravity and how the mechanical energy flux depends, mainly, on effective temperature. The new relation is tested and sensitively calibrated by modelling the blue end of the Horizontal Branch of globular clusters. The most significant difference from mass loss rates predicted by the Reimers relation is an increase by up to a factor of 3 for luminous late-type (super-)giants, in good agreement with observations.Comment: 12 pages, 4 figures, accepted by ApJ Letter

Determining Peptide Partitioning Properties via Computer Simulation

The transfer of polypeptide segments into lipid bilayers to form transmembrane helices represents the crucial first step in cellular membrane protein folding and assembly. This process is driven by complex and poorly understood atomic interactions of peptides with the lipid bilayer environment. The lack of suitable experimental techniques that can resolve these processes both at atomic resolution and nanosecond timescales has spurred the development of computational techniques. In this review, we summarize the significant progress achieved in the last few years in elucidating the partitioning of peptides into lipid bilayer membranes using atomic detail molecular dynamics simulations. Indeed, partitioning simulations can now provide a wealth of structural and dynamic information. Furthermore, we show that peptide-induced bilayer distortions, insertion pathways, transfer free energies, and kinetic insertion barriers are now accurate enough to complement experiments. Further advances in simulation methods and force field parameter accuracy promise to turn molecular dynamics simulations into a powerful tool for investigating a wide range of membrane active peptide phenomena