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 pCO₂ 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