MHD Simulations of Core Collapse Supernovae with Cosmos++

We performed 2D, axisymmetric, MHD simulations with Cosmos++ in order to examine the growth of the magnetorotational instability (MRI) in core--collapse supernovae. We have initialized a non--rotating 15 solar mass progenitor, infused with differential rotation and poloidal magnetic fields. The collapse of the iron core is simulated with the Shen EOS, and the parametric Ye and entropy evolution. The wavelength of the unstable mode in the post--collapse environment is expected to be only ~ 200 m. In order to achieve the fine spatial resolution requirement, we employed remapping technique after the iron core has collapsed and bounced. The MRI unstable region appears near the equator and angular momentum and entropy are transported outward. Higher resolution remap run display more vigorous overturns and stronger transport of angular momentum and entropy. Our results are in agreement with the earlier work by Akiyama et al. (2003) and Obergaulinger et al. (2009).Comment: 3 pages, 2 figures. To appear in the proceedings of the "Deciphering the Ancient Universe with Gamma-Ray Bursts", April 2010, Kyoto, Japan, eds. N. Kawai and S. Nagataki (AIP

The telomerase essential N-terminal domain promotes DNA synthesis by stabilizing short RNA-DNA hybrids.

Telomerase is an enzyme that adds repetitive DNA sequences to the ends of chromosomes and consists of two main subunits: the telomerase reverse transcriptase (TERT) protein and an associated telomerase RNA (TER). The telomerase essential N-terminal (TEN) domain is a conserved region of TERT proposed to mediate DNA substrate interactions. Here, we have employed single molecule telomerase binding assays to investigate the function of the TEN domain. Our results reveal telomeric DNA substrates bound to telomerase exhibit a dynamic equilibrium between two states: a docked conformation and an alternative conformation. The relative stabilities of the docked and alternative states correlate with the number of basepairs that can be formed between the DNA substrate and the RNA template, with more basepairing favoring the docked state. The docked state is further buttressed by the TEN domain and mutations within the TEN domain substantially alter the DNA substrate structural equilibrium. We propose a model in which the TEN domain stabilizes short RNA-DNA duplexes in the active site of the enzyme, promoting the docked state to augment telomerase processivity

Discretized rotation has infinitely many periodic orbits

For a fixed k in (-2,2), the discretized rotation on Z^2 is defined by (x,y)->(y,-[x+ky]). We prove that this dynamics has infinitely many periodic orbits.Comment: Revised after referee reports, and added a quantitative statemen

Structural basis of template-boundary definition in Tetrahymena telomerase.

Telomerase is required to maintain repetitive G-rich telomeric DNA sequences at chromosome ends. To do so, the telomerase reverse transcriptase (TERT) subunit reiteratively uses a small region of the integral telomerase RNA (TER) as a template. An essential feature of telomerase catalysis is the strict definition of the template boundary to determine the precise TER nucleotides to be reverse transcribed by TERT. We report the 3-Å crystal structure of the Tetrahymena TERT RNA-binding domain (tTRBD) bound to the template boundary element (TBE) of TER. tTRBD is wedged into the base of the TBE RNA stem-loop, and each of the flanking RNA strands wraps around opposite sides of the protein domain. The structure illustrates how the tTRBD establishes the template boundary by positioning the TBE at the correct distance from the TERT active site to prohibit copying of nontemplate nucleotides

The aggregation of cytochrome C may be linked to its flexibility during refolding

Large-scale expression of biopharmaceutical proteins in cellular hosts results in production of large insoluble mass aggregates. In order to generate functional product, these aggregates require further processing through refolding with denaturant, a process in itself that can result in aggregation. Using a model folding protein, cytochrome C, we show how an increase in final denaturant concentration decreases the propensity of the protein to aggregate during refolding. Using polarised fluorescence anisotropy, we show how reduced levels of aggregation can be achieved by increasing the period of time the protein remains flexible during refolding, mediated through dilution ratios. This highlights the relationship between the flexibility of a protein and its propensity to aggregate. We attribute this behaviour to the preferential urea-residue interaction, over self-association between molecules

Dynamics of Alpha-Helix Formation in the CSAW Model

We study the folding dynamics of polyalanine (Ala$_{20}$), a protein fragment with 20 residues whose native state is a single alpha helix. We use the CSAW model (conditioned self-avoiding walk), which treats the protein molecule as a chain in Brownian motion, with interactions that include hydrophobic forces and internal hydrogen bonding. We find that large scale structures form before small scale structures, and obtain the relevant relaxation times. We find that helix nucleation occurs at two separate points on the protein chain. The evolution of small and large scale structures involve different mechanisms. While the former can be describe by rate equations governing the growth of helical content, the latter is akin to the relaxation of an elastic solid.Comment: 18 pages, 10 figure

Modeling Seven Years of Event Horizon Telescope Observations with Radiatively Inefficient Accretion Flow Models

An initial three-station version of the Event Horizon Telescope, a millimeter-wavelength very-long baseline interferometer, has observed Sagittarius A* (Sgr A*) repeatedly from 2007 to 2013, resulting in the measurement of a variety of interferometric quantities. Of particular importance, there is now a large set of closure phases, measured over a number of independent observing epochs. We analyze these observations within the context of a realization of semi-analytic radiatively inefficient disk models, implicated by the low luminosity of Sgr A*. We find a broad consistency among the various observing epochs and between different interferometric data types, with the latter providing significant support for this class of models of Sgr A*. The new data significantly tighten existing constraints on the spin magnitude and its orientation within this model context, finding a spin magnitude of $a=0.10^{+0.30+0.56}_{-0.10-0.10}$, an inclination with respect to the line of sight of $\theta={60^\circ}^{+5^\circ+10^\circ}_{-8^\circ-13^\circ}$, and a position angle of $\xi={156^\circ}^{+10^\circ+14^\circ}_{-17^\circ-27^\circ}$ east of north. These are in good agreement with previous analyses. Notably, the previous $180^\circ$ degeneracy in the position angle has now been conclusively broken by the inclusion of the closure phase measurements. A reflection degeneracy in the inclination remains, permitting two localizations of the spin vector orientation, one of which is in agreement with the orbital angular momentum of the infrared gas cloud G2 and the clockwise disk of young stars. This possibly supports a relationship between Sgr A*'s accretion flow and these larger-scale features.Comment: 16 pages, 11 figures, accepted to Ap

Spatial Relationship between Solar Flares and Coronal Mass Ejections

We report on the spatial relationship between solar flares and coronal mass ejections (CMEs) observed during 1996-2005 inclusive. We identified 496 flare-CME pairs considering limb flares (distance from central meridian > 45 deg) with soft X-ray flare size > C3 level. The CMEs were detected by the Large Angle and Spectrometric Coronagraph (LASCO) on board the Solar and Heliospheric Observatory (SOHO). We investigated the flare positions with respect to the CME span for the events with X-class, M-class, and C-class flares separately. It is found that the most frequent flare site is at the center of the CME span for all the three classes, but that frequency is different for the different classes. Many X-class flares often lie at the center of the associated CME, while C-class flares widely spread to the outside of the CME span. The former is different from previous studies, which concluded that no preferred flare site exists. We compared our result with the previous studies and conclude that the long-term LASCO observation enabled us to obtain the detailed spatial relation between flares and CMEs. Our finding calls for a closer flare-CME relationship and supports eruption models typified by the CSHKP magnetic reconnection model.Comment: 7 pages; 4 figures; Accepted by the Astrophysical Journa