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

Decoding of Repeated-Root Cyclic Codes up to New Bounds on Their Minimum Distance

The well-known approach of Bose, Ray-Chaudhuri and Hocquenghem and its generalization by Hartmann and Tzeng are lower bounds on the minimum distance of simple-root cyclic codes. We generalize these two bounds to the case of repeated-root cyclic codes and present a syndrome-based burst error decoding algorithm with guaranteed decoding radius based on an associated folded cyclic code. Furthermore, we present a third technique for bounding the minimum Hamming distance based on the embedding of a given repeated-root cyclic code into a repeated-root cyclic product code. A second quadratic-time probabilistic burst error decoding procedure based on the third bound is outlined. Index Terms Bound on the minimum distance, burst error, efficient decoding, folded code, repeated-root cyclic code, repeated-root cyclic product cod

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

Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

The crystal structure of the open conformation of a bacterial voltage-gated sodium channel pore from Magnetococcus sp. (NaVMs) has provided the basis for a molecular dynamics study defining the channel’s full ion translocation pathway and conductance process, selectivity, electrophysiological characteristics, and ion-binding sites. Microsecond molecular dynamics simulations permitted a complete time-course characterization of the protein in a membrane system, capturing the plethora of conductance events and revealing a complex mixture of single and multi-ion phenomena with decoupled rapid bidirectional water transport. The simulations suggest specific localization sites for the sodium ions, which correspond with experimentally determined electron density found in the selectivity filter of the crystal structure. These studies have also allowed us to identify the ion conductance mechanism and its relation to water movement for the NavMs channel pore and to make realistic predictions of its conductance properties. The calculated single-channel conductance and selectivity ratio correspond closely with the electrophysiology measurements of the NavMs channel expressed in HEK 293 cells. The ion translocation process seen in this voltage-gated sodium channel is clearly different from that exhibited by members of the closely related family of voltage-gated potassium channels and also differs considerably from existing proposals for the conductance process in sodium channels. These studies simulate sodium channel conductance based on an experimentally determined structure of a sodium channel pore that has a completely open transmembrane pathway and activation gate

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

Paul Piccone’s Providential Moment: Phenomenology, Subjectivity, and 20th Century Marxism in Telos

This thesis explores the intellectual history of editor, writer, and philosopher, Paul Piccone and Telos, an independent journal of contemporary critical theory, which he founded in 1968. Born in Italy, Piccone lived most of his life in the United States, earning his Ph.D. in philosophy at SUNY-Buffalo in 1970. Piccone served as Telos’ editor and a major contributor from 1968 to 2004. This thesis follows the trajectory of his thought by contextualizing his writing within the broader world of Marxist, and eventually post-Marxist, political philosophy. Telos also concerned itself with modern interpretations of historical dialectics and early 20th-century Marxist philosophy. Piccone himself predicated much of his philosophy on Husserlian phenomenology, which stresses concrete experiences, and his writing therefore stands at a unique confluence of Husserl and Marx. Piccone ultimately became a leading exponent of anti-Liberal philosophy and the theory of artificial negativity, which examines capitalist hegemony in both material and socio-historical terms

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