6,963 research outputs found
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-Ã… 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), 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 , an inclination with respect to
the line of sight of
, and a position
angle of east of
north. These are in good agreement with previous analyses. Notably, the
previous 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
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