280 research outputs found
Building large phylogenetic trees on coarse-grained parallel machines
Phylogenetic analysis is an area of computational biology concerned
with the reconstruction of evolutionary relationships between organisms, genes,
and gene families. Maximum likelihood evaluation has proven to be one of the
most reliable methods for constructing phylogenetic trees. The huge computa-
tional requirements associated with maximum likelihood analysis means that it is
not feasible to produce large phylogenetic trees using a single processor. We have
completed a fully cross platform coarse grained distributed application, DPRml,
which overcomes many of the limitations imposed by the current set of parallel
phylogenetic programs. We have completed a set of efï¬ciency tests that show how
to maximise efï¬ciency while using the program to build large phylogenetic trees.
The software is publicly available under the terms of the GNU general public li-
cence from the system webpage at http://www.cs.nuim.ie/distribute
Black holes as mirrors: quantum information in random subsystems
We study information retrieval from evaporating black holes, assuming that
the internal dynamics of a black hole is unitary and rapidly mixing, and
assuming that the retriever has unlimited control over the emitted Hawking
radiation. If the evaporation of the black hole has already proceeded past the
"half-way" point, where half of the initial entropy has been radiated away,
then additional quantum information deposited in the black hole is revealed in
the Hawking radiation very rapidly. Information deposited prior to the half-way
point remains concealed until the half-way point, and then emerges quickly.
These conclusions hold because typical local quantum circuits are efficient
encoders for quantum error-correcting codes that nearly achieve the capacity of
the quantum erasure channel. Our estimate of a black hole's information
retention time, based on speculative dynamical assumptions, is just barely
compatible with the black hole complementarity hypothesis.Comment: 18 pages, 2 figures. (v2): discussion of decoding complexity
clarifie
RX J1856.5-3754 as a possible Strange Star candidate
RX J1856.5-3754 has been proposed as a strange star candidate due to its very
small apparent radius measured from its X-ray thermal spectrum. However, its
optical emission requires a much larger radius and thus most of the stellar
surface must be cold and undetectable in X-rays. In the case the star is a
neutron star such a surface temperature distribution can be explained by the
presence of a strong toroidal field in the crust (Perez-Azorin et al. 2006,
Geppert et al. 2006). We consider a similar scenario for a strange star with a
thin baryonic crust to determine if such a magnetic field induced effect is
still possible.Comment: 4 pages, 4 figures; to appear in proceedings of the conference
"Isolated Neutron Stars: From the Interior to the Surface", eds. S. Zane, R.
Turolla, D. Page; Astrophysics & Space Science in pres
Cell wall organic matrix composition and biomineralization across reef-building coralline algae under global change.
OnlinePublCrustose coralline algae (CCA) are one of the most important benthic substrate consolidators on coral reefs through their ability to deposit calcium carbonate on an organic matrix in their cell walls. Discrete polysaccharides have been recognized for their role in biomineralization, yet little is known about the carbohydrate composition of organic matrices across CCA taxa and whether they have the capacity to modulate their organic matrix constituents amidst environmental change, particularly the threats of ocean acidification (OA) and warming. We simulated elevated pCOâ‚‚ and temperature (IPCC RCP 8.5) and subjected four mid-shelf Great Barrier Reef species of CCA to two months of experimentation. To assess the variability in surficial monosaccharide composition and biomineralization across species and treatments, we determined the monosaccharide composition of the polysaccharides present in the cell walls of surficial algal tissue and quantified calcification. Our results revealed dissimilarity among species' monosaccharide constituents, which suggests that organic matrices are composed of different polysaccharides across CCA taxa. We also found that species differentially modulate composition in response to ocean acidification and warming. Our findings suggest that both variability in composition and ability to modulate monosaccharide abundance may play a crucial role in surficial biomineralization dynamics under the stress of OA and global warming.Ellie Bergstrom, Jelle Lahnstein, Helen Collins, Tessa M. Page, Vincent Bulone, and Guillermo Diaz-Pulid
Tunneling into fuzzball states
String theory suggests that black hole microstates are quantum, horizon sized
`fuzzballs', rather than smooth geometries with horizon. Radiation from
fuzzballs can carry information and does not lead to information loss. But if
we let a shell of matter collapse then it creates a horizon, and it seems that
subsequent radiation will lead to information loss. We argue that the
resolution to this problem is that the shell can tunnel to the fuzzball
configurations. The amplitude for tunneling is small because we are relating
two macroscopically different configurations, but the number of states that we
can tunnel to, given through the Bekenstein entropy, is very large. These small
and large numbers can cancel each other, making it possible for the shell to
tunnel into fuzzball states before a significant amount of radiation has been
emitted. This offers a way to resolve the information paradox.Comment: 7 pages, 2 figures, Late
The Seyfert-LINER Galaxy NGC 7213: An XMM-Newton Observation
We examine the XMM X-ray spectrum of the LINER-AGN NGC 7213, which is best
fit with a power law, K-alpha emission lines from Fe I, Fe XXV and Fe XXVI and
a soft X-ray collisionally ionised thermal plasma with kT=0.18 +0.03/-0.01 keV.
We find a luminosity of 7x10^(-4) L_Edd, and a lack of soft X-ray excess
emission, suggesting a truncated accretion disc. NGC 7213 has intermediate
X-ray spectral properties, between those of the weak AGN found in the LINER M81
and higher luminosity Seyfert galaxies. This supports the notion of a
continuous sequence of X-ray properties from the Galactic Centre through LINER
galaxies to Seyferts, likely determined by the amount of material available for
accretion in the central regions.Comment: 7 pages, 2 figures. To appear in From X-ray Binaries to Quasars:
Black Hole Accretion on All Mass Scales, ed. T. J. Maccarone, R. P. Fender,
and L. C. Ho (Dordrecht: Kluwer
Parity nonconserving cold neutron-parahydrogen interactions
Three pion dominated observables of the parity nonconserving interactions
between the cold neutrons and parahydrogen are calculated. The transversely
polarized neutron spin rotation, unpolarized neutron longitudinal polarization,
and photon-asymmetry of the radiative polarized neutron capture are considered.
For the numerical evaluation of the observables, the strong interactions are
taken into account by the Reid93 potential and the parity nonconserving
interactions by the DDH model along with the two-pion exchange.Comment: 17 pages, 2 figure
The Magnificent Seven: Magnetic fields and surface temperature distributions
Presently seven nearby radio-quiet isolated neutron stars discovered in ROSAT
data and characterized by thermal X-ray spectra are known. They exhibit very
similar properties and despite intensive searches their number remained
constant since 2001 which led to their name ``The Magnificent Seven''. Five of
the stars exhibit pulsations in their X-ray flux with periods in the range of
3.4 s to 11.4 s. XMM-Newton observations revealed broad absorption lines in the
X-ray spectra which are interpreted as cyclotron resonance absorption lines by
protons or heavy ions and / or atomic transitions shifted to X-ray energies by
strong magnetic fields of the order of 10^13 G. New XMM-Newton observations
indicate more complex X-ray spectra with multiple absorption lines. Pulse-phase
spectroscopy of the best studied pulsars RX J0720.4-3125 and RBS 1223 reveals
variations in derived emission temperature and absorption line depth with pulse
phase. Moreover, RX J0720.4-3125 shows long-term spectral changes which are
interpreted as due to free precession of the neutron star. Modeling of the
pulse profiles of RX J0720.4-3125 and RBS 1223 provides information about the
surface temperature distribution of the neutron stars indicating hot polar caps
which have different temperatures, different sizes and are probably not located
in antipodal positions.Comment: 10 pages, 8 figures, to appear in Astrophysics and Space Science, in
the proceedings of "Isolated Neutron Stars: from the Interior to the
Surface", edited by D. Page, R. Turolla and S. Zan
Two-dimensional Quantum-Corrected Eternal Black Hole
The one-loop quantum corrections to geometry and thermodynamics of black hole
are studied for the two-dimensional RST model. We chose boundary conditions
corresponding to the eternal black hole being in the thermal equilibrium with
the Hawking radiation. The equations of motion are exactly integrated. The one
of the solutions obtained is the constant curvature space-time with dilaton
being a constant function. Such a solution is absent in the classical theory.
On the other hand, we derive the quantum-corrected metric (\ref{solution})
written in the Schwarzschild like form which is a deformation of the classical
black hole solution \cite{5d}. The space-time singularity occurs to be milder
than in classics and the solution admits two asymptotically flat black hole
space-times lying at "different sides" of the singularity. The thermodynamics
of the classical black hole and its quantum counterpart is formulated. The
thermodynamical quantities (energy, temperature, entropy) are calculated and
occur to be the same for both the classical and quantum-corrected black holes.
So, no quantum corrections to thermodynamics are observed. The possible
relevance of the results obtained to the four-dimensional case is discussed.Comment: Latex, 28 pges; minor corrections in text and abstract made and new
references adde
An action for the exact string black hole
A local action is constructed describing the exact string black hole
discovered by Dijkgraaf, Verlinde and Verlinde in 1992. It turns out to be a
special 2D Maxwell-dilaton gravity theory, linear in curvature and field
strength. Two constants of motion exist: mass M>1, determined by the level k,
and U(1)-charge Q>0, determined by the value of the dilaton at the origin. ADM
mass, Hawking temperature T_H \propto \sqrt{1-1/M} and Bekenstein-Hawking
entropy are derived and studied in detail. Winding/momentum mode duality
implies the existence of a similar action, arising from a branch ambiguity,
which describes the exact string naked singularity. In the strong coupling
limit the solution dual to AdS_2 is found to be the 5D Schwarzschild black
hole. Some applications to black hole thermodynamics and 2D string theory are
discussed and generalizations - supersymmetric extension, coupling to matter
and critical collapse, quantization - are pointed out.Comment: 41 pages, 2 eps figures, dedicated to Wolfgang Kummer on occasion of
his Emeritierung; v2: added ref; v3: extended discussion in sections 3.2, 3.3
and at the end of 5.3 by adding 2 pages of clarifying text; updated refs;
corrected typo
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