Numerical simulations of a siphon mechanism for quiescent prominence formation

Quiescent prominences represent a significant challenge to our understanding of the flow of mass and energy in the outer layers of the solar atmosphere. A small number of quiescent prominences contain as much mass as the entire corona (Athay, 1976). The problem then is how to get that much material into the relatively small volume of a prominence and maintain it at a temperature of 10,000 K in close proximity to material at one million K. The thermal insulation to conduction provided by the magnetic field explains the disparate temperatures. The mass source problem is less well understood. One method for supplying mass to the prominence is to siphon it from the chromosphere. The siphon mechanism begins with a magnetic loop that evolves into a configuration with a gravitational well, such as that described by Kippenhahn and Schluter (1957). This could be formed, for example, by a twist in the magnetic field. A gravitational well could also be formed by a condensation induced sag in the field. This could further enhance the condensation process. Once this well has formed, or as it is forming, the material in the well area of the loop must cool and condense to the point where radiative losses exceed any heat input. Additional material must also flow into the well from the underlying chromosphere to supply the mass required to form the prominence. One example from a series of numerical simulations that were performed to study the formation of quiescent prominences is presented

Ephemeral active regions and coronal bright points: A solar maximum Mission 2 guest investigator study

A dominate association of coronal bright points (as seen in He wavelength 10830) was confirmed with the approach and subsequent disappearance of opposite polarity magnetic network. While coronal bright points do occur with ephemeral regions, this association is a factor of 2 to 4 less than with sites of disappearing magnetic flux. The intensity variations seen in He I wavelength 10830 are intermittent and often rapid, varying over the 3 minute time resolution of the data; their bright point counterparts in the C IV wavelength 1548 and 20 cm wavelength show similar, though not always coincident time variations. Ejecta are associated with about 1/3 of the dark points and are evident in the C IV and H alpha data. These results support the idea that the anti-correlation of X-ray bright points with the solar cycle can be explained by the correlation of these coronal emission structures with sites of cancelling flux, indicating that, in some cases, the process of magnetic flux removal results in the release of energy. That the intensity variations are rapid and variable suggests that this process works intermittently

Constraints on filament models deduced from dynamical analysis

The conclusions deduced from simultaneous observations with the Ultra-Violet Spectrometer and Polarimeter (UVSP) on the Solar Maximum Mission satellite, and the Multichannel Subtractive Double Pass (MSPD) spectrographs at Meudon and Pic du Midi observatories are presented. The observations were obtained in 1980 and 1984. All instruments have almost the same field of view and provide intensity and velocity maps at two temperatures. The resolution is approx. 0.5 to 1.5" for H alpha line and 3" for C IV. The high resolution and simultaneity of the two types of observations allows a more accurate description of the flows in prominences as functions of temperature and position. The results put some contraints on the models and show that dynamical aspects must be taken into account

Phase diagram for unzipping DNA with long-range interactions

We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and double-stranded DNA, and we focus on the case in which quenched disorder in the sequence of monomers is unimportant for the statistical mechanics. We show how including excluded volume interactions in the model affects the phase diagram for the critical pulling force, and we predict a re-entrancy phase at low temperatures which has not been previously discussed. We also consider the case of non-equilibrium pulling, in which the external force probes the local, rather than the global structure of the dsDNA or adsorbed polymer. The dynamics of the pulling transition in such experiments could illuminate the polymer's loop structure, which depends on the nature of excluded volume interactions.Comment: 4 pages, 2 figures; this version clarifies Eq. 8, and corrects errors in Fig.

SUMER: Solar Ultraviolet Measurements of Emitted Radiation

The SUMER (solar ultraviolet measurements of emitted radiation) experiment is described. It will study flows, turbulent motions, waves, temperatures and densities of the plasma in the upper atmosphere of the Sun. Structures and events associated with solar magnetic activity will be observed on various spatial and temporal scales. This will contribute to the understanding of coronal heating processes and the solar wind expansion. The instrument will take images of the Sun in EUV (extreme ultra violet) light with high resolution in space, wavelength and time. The spatial resolution and spectral resolving power of the instrument are described. Spectral shifts can be determined with subpixel accuracy. The wavelength range extends from 500 to 1600 angstroms. The integration time can be as short as one second. Line profiles, shifts and broadenings are studied. Ratios of temperature and density sensitive EUV emission lines are established

Dynamics of DNA-breathing: Weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem

We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We show that long time distributions for the survival of DNA bubbles and the size autocorrelation function can be derived from an asymptotic weak noise approach. In particular, below the melting temperature the bubble closure corresponds to a noisy finite time singularity. We demonstrate that the associated Fokker-Planck equation is equivalent to a quantum Coulomb problem. Below the melting temperature the bubble lifetime is associated with the continuum of scattering states of the repulsive Coulomb potential; at the melting temperature the Coulomb potential vanishes and the underlying first exit dynamics exhibits a long time power law tail; above the melting temperature, corresponding to an attractive Coulomb potential, the long time dynamics is controlled by the lowest bound state. Correlations and finite size effects are discussed.Comment: 12 pages, 10 figures, revte

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent $c$ for which we find the new value $c=4\nu-1/2$ such that the transition is second order with $c=1.85<2$ in $d=3$. We show that a finite stretching force $F$ destabilizes DNA, corresponding to a lower melting temperature $T(F)$, in agreement with single-molecule DNA stretching experiments.Comment: 5 pages, 3 figure

Ab initio theory of helix-coil phase transition

In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).Comment: 24 pages, 3 figure

Spinning Conformal Correlators

We develop the embedding formalism for conformal field theories, aimed at doing computations with symmetric traceless operators of arbitrary spin. We use an index-free notation where tensors are encoded by polynomials in auxiliary polarization vectors. The efficiency of the formalism is demonstrated by computing the tensor structures allowed in n-point conformal correlation functions of tensors operators. Constraints due to tensor conservation also take a simple form in this formalism. Finally, we obtain a perfect match between the number of independent tensor structures of conformal correlators in d dimensions and the number of independent structures in scattering amplitudes of spinning particles in (d+1)-dimensional Minkowski space.Comment: 46 pages, 3 figures; V2: references added; V3: tiny misprint corrected in (A.9

Comparative analysis of homology models of the Ah receptor ligand binding domain: Verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates the biological and toxic effects of a wide variety of structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While significant interspecies differences in AHR ligand binding specificity, selectivity, and response have been observed, the structural determinants responsible for those differences have not been determined, and homology models of the AHR ligand-binding domain (LBD) are available for only a few species. Here we describe the development and comparative analysis of homology models of the LBD of 16 AHRs from 12 mammalian and nonmammalian species and identify the specific residues contained within their ligand binding cavities. The ligand-binding cavity of the fish AHR exhibits differences from those of mammalian and avian AHRs, suggesting a slightly different TCDD binding mode. Comparison of the internal cavity in the LBD model of zebrafish (zf) AHR2, which binds TCDD with high affinity, to that of zfAHR1a, which does not bind TCDD, revealed that the latter has a dramatically shortened binding cavity due to the side chains of three residues (Tyr296, Thr386, and His388) that reduce the amount of internal space available to TCDD. Mutagenesis of two of these residues in zfAHR1a to those present in zfAHR2 (Y296H and T386A) restored the ability of zfAHR1a to bind TCDD and to exhibit TCDD-dependent binding to DNA. These results demonstrate the importance of these two amino acids and highlight the predictive potential of comparative analysis of homology models from diverse species. The availability of these AHR LBD homology models will facilitate in-depth comparative studies of AHR ligand binding and ligand-dependent AHR activation and provide a novel avenue for examining species-specific differences in AHR responsiveness. © 2013 American Chemical Society