Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Rotating Black Holes in Higher Dimensions with a Cosmological Constant

We present the metric for a rotating black hole with a cosmological constant and with arbitrary angular momenta in all higher dimensions. The metric is given in both Kerr-Schild and Boyer-Lindquist form. In the Euclidean-signature case, we also obtain smooth compact Einstein spaces on associated S^{D-2} bundles over S^2, infinitely many for each odd D\ge 5. Applications to string theory and M-theory are indicated.Comment: 8 pages, Latex. Short version, with more compact notation, of hep-th/0404008. To appear in Phys. Rev. Let

Proof of the Generalized Second Law for Quasistationary Semiclassical Black Holes

A simple direct explicit proof of the generalized second law of black hole thermodynamics is given for a quasistationary semiclassical black hole.Comment: 12 pages, LaTeX, report Alberta-Thy-10-93 (revision of paper in response to Phys. Rev. Lett. referees' comments, which suffered a series of long delays

Entropy bounds for charged and rotating systems

It was shown in a previous work that, for systems in which the entropy is an extensive function of the energy and volume, the Bekenstein and the holographic entropy bounds predict new results. In this paper, we go further and derive improved upper bounds to the entropy of {\it extensive} charged and rotating systems. Furthermore, it is shown that for charged and rotating systems (including non-extensive ones), the total energy that appear in both the Bekenstein entropy bound (BEB) and the causal entropy bound (CEB) can be replaced by the {\it internal} energy of the system. In addition, we propose possible corrections to the BEB and the CEB.Comment: 12 pages, revte

Entanglement, recoherence and information flow in an accelerated detector - quantum field system: Implications for black hole information issue

We study an exactly solvable model where an uniformly accelerated detector is linearly coupled to a massless scalar field initially in the Minkowski vacuum. Using the exact correlation functions we show that as soon as the coupling is switched on one can see information flowing from the detector to the field and propagating with the radiation into null infinity. By expressing the reduced density matrix of the detector in terms of the two-point functions, we calculate the purity function in the detector and study the evolution of quantum entanglement between the detector and the field. Only in the ultraweak coupling regime could some degree of recoherence in the detector appear at late times, but never in full restoration. We explicitly show that under the most general conditions the detector never recovers its quantum coherence and the entanglement between the detector and the field remains large at late times. To the extent this model can be used as an analog to the system of a black hole interacting with a quantum field, our result seems to suggest in the prevalent non-Markovian regime, assuming unitarity for the combined system, that black hole information is not lost but transferred to the quantum field degrees of freedom. Our combined system will evolve into a highly entangled state between a remnant of large area (in Bekenstein's black hole atom analog) without any information of its initial state, and the quantum field, now imbued with complex information content not-so-easily retrievable by a local observer.Comment: 16 pages, 12 figures; minor change

Spinning Down a Black Hole With Scalar Fields

We study the evolution of a Kerr black hole emitting scalar radiation via the Hawking process. We show that the rate at which mass and angular momentum are lost by the black hole leads to a final evolutionary state with nonzero angular momentum, namely $a/M \approx 0.555$.Comment: 4 pages (including 3 postscript figures), Revtex, uses epsf.tex, twocolumn.sty and header.sty (included). Submitted to Physical Review Letter

Do Evaporating Black Holes Form Photospheres?

Several authors, most notably Heckler, have claimed that the observable Hawking emission from a microscopic black hole is significantly modified by the formation of a photosphere around the black hole due to QED or QCD interactions between the emitted particles. In this paper we analyze these claims and identify a number of physical and geometrical effects which invalidate these scenarios. We point out two key problems. First, the interacting particles must be causally connected to interact, and this condition is satisfied by only a small fraction of the emitted particles close to the black hole. Second, a scattered particle requires a distance ~ E/m_e^2 for completing each bremsstrahlung interaction, with the consequence that it is improbable for there to be more than one complete bremsstrahlung interaction per particle near the black hole. These two effects have not been included in previous analyses. We conclude that the emitted particles do not interact sufficiently to form a QED photosphere. Similar arguments apply in the QCD case and prevent a QCD photosphere (chromosphere) from developing when the black hole temperature is much greater than Lambda_QCD, the threshold for QCD particle emission. Additional QCD phenomenological arguments rule out the development of a chromosphere around black hole temperatures of order Lambda_QCD. In all cases, the observational signatures of a cosmic or Galactic halo background of primordial black holes or an individual black hole remain essentially those of the standard Hawking model, with little change to the detection probability. We also consider the possibility, as proposed by Belyanin et al. and D. Cline et al., that plasma interactions between the emitted particles form a photosphere, and we conclude that this scenario too is not supported.Comment: version published in Phys Rev D 78, 064043; 25 pages, 3 figures; includes discussion on extending our analysis to TeV-scale, higher-dimensional black hole

Green function Retrieval and Time-reversal in a Disordered World

We apply the theory of multiple wave scattering to two contemporary, related topics: imaging with diffuse correlations and stability of time-reversal of diffuse waves, using equipartition, coherent backscattering and frequency speckles as fundamental concepts.Comment: 1 figur

Nonthermal radiation of rotating black holes

Nonthermal radiation of a Kerr black hole is considered as tunneling of created particles through an effective Dirac gap. In the leading semiclassical approximation this approach is applicable to bosons as well. Our semiclassical results for photons and gravitons do not contradict those obtained previously. For neutrinos the result of our accurate quantum mechanical calculation is about two times larger than the previous one.Comment: 10 pages, 2 figures; 2 references added, few typos correcte

No-Bang Quantum State of the Cosmos

A quantum state of the entire cosmos (universe or multiverse) is proposed which is the equal mixture of the Giddings-Marolf states that are asymptotically single de Sitter spacetimes in both past and future and are regular on the throat or neck of minimal three-volume. That is, states are excluded that have a big bang or big crunch or which split into multiple asymptotic de Sitter spacetimes. (For simplicity, transitions between different values of the cosmological constant are assumed not to occur, though different positive values are allowed.) The entropy of this mixed state appears to be of the order of the three-fourths power of the Bekenstein-Hawking A/4 entropy of de Sitter spacetime. Most of the component pure states do not have rapid inflation, but when an inflaton is present and the states are weighted by the volume at the end of inflation, a much smaller number of states may dominate and give a large amount of inflation and hence may agree with observations.Comment: 18 pages, LaTeX, updated with a few new qualifications and reference