Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Conformally Flat Smoothed Particle Hydrodynamics: Application to Neutron Star Mergers

We present a new 3D SPH code which solves the general relativistic field + hydrodynamics equations in the conformally flat approximation. Several test cases are considered to test different aspects of the code. We finally apply then the code to the coalescence of a neutron star binary system. The neutron stars are modeled by a polytropic equation of state (EoS) with adiabatic indices $\Gamma=2.0$, $\Gamma=2.6$ and $\Gamma=3.0$. We calculate the gravitational wave signals, luminosities and frequency spectra by employing the quadrupole approximation for emission and back reaction in the slow motion limit. In addition, we consider the amount of ejected mass.Comment: 23 pages, 12 figures. Accepted for publication in Phys. Rev. D. v3: Final Versio

MeerKAT uncovers the physics of an odd radio circle

Odd radio circles (ORCs) are recently-discovered faint diffuse circles of radio emission, of unknown cause, surrounding galaxies at moderate redshift (z ∼0.2-0.6). Here, we present detailed new MeerKAT radio images at 1284 MHz of the first ORC, originally discovered with the Australian Square Kilometre Array Pathfinder, with higher resolution (6 arcsec) and sensitivity (∼2.4 μJy/beam). In addition to the new images, which reveal a complex internal structure consisting of multiple arcs, we also present polarization and spectral index maps. Based on these new data, we consider potential mechanisms that may generate the ORCs

Search for gravitational wave bursts in LIGO's third science run

We report on a search for gravitational wave bursts in data from the three LIGO interferometric detectors during their third science run. The search targets subsecond bursts in the frequency range 100-1100 Hz for which no waveform model is assumed, and has a sensitivity in terms of the root-sum-square (rss) strain amplitude of hrss ~ 10^{-20} / sqrt(Hz). No gravitational wave signals were detected in the 8 days of analyzed data.Comment: 12 pages, 6 figures. Amaldi-6 conference proceedings to be published in Classical and Quantum Gravit

Quantum state preparation and macroscopic entanglement in gravitational-wave detectors

Long-baseline laser-interferometer gravitational-wave detectors are operating at a factor of 10 (in amplitude) above the standard quantum limit (SQL) within a broad frequency band. Such a low classical noise budget has already allowed the creation of a controlled 2.7 kg macroscopic oscillator with an effective eigenfrequency of 150 Hz and an occupation number of 200. This result, along with the prospect for further improvements, heralds the new possibility of experimentally probing macroscopic quantum mechanics (MQM) - quantum mechanical behavior of objects in the realm of everyday experience - using gravitational-wave detectors. In this paper, we provide the mathematical foundation for the first step of a MQM experiment: the preparation of a macroscopic test mass into a nearly minimum-Heisenberg-limited Gaussian quantum state, which is possible if the interferometer's classical noise beats the SQL in a broad frequency band. Our formalism, based on Wiener filtering, allows a straightforward conversion from the classical noise budget of a laser interferometer, in terms of noise spectra, into the strategy for quantum state preparation, and the quality of the prepared state. Using this formalism, we consider how Gaussian entanglement can be built among two macroscopic test masses, and the performance of the planned Advanced LIGO interferometers in quantum-state preparation

Searching for a Stochastic Background of Gravitational Waves with LIGO

The Laser Interferometer Gravitational-wave Observatory (LIGO) has performed the fourth science run, S4, with significantly improved interferometer sensitivities with respect to previous runs. Using data acquired during this science run, we place a limit on the amplitude of a stochastic background of gravitational waves. For a frequency independent spectrum, the new limit is $\Omega_{\rm GW} < 6.5 \times 10^{-5}$. This is currently the most sensitive result in the frequency range 51-150 Hz, with a factor of 13 improvement over the previous LIGO result. We discuss complementarity of the new result with other constraints on a stochastic background of gravitational waves, and we investigate implications of the new result for different models of this background.Comment: 37 pages, 16 figure

Upper limits on the strength of periodic gravitational waves from PSR J1939+2134

The first science run of the LIGO and GEO gravitational wave detectors presented the opportunity to test methods of searching for gravitational waves from known pulsars. Here we present new direct upper limits on the strength of waves from the pulsar PSR J1939+2134 using two independent analysis methods, one in the frequency domain using frequentist statistics and one in the time domain using Bayesian inference. Both methods show that the strain amplitude at Earth from this pulsar is less than a few times $10^{-22}$.Comment: 7 pages, 1 figure, to appear in the Proceedings of the 5th Edoardo Amaldi Conference on Gravitational Waves, Tirrenia, Pisa, Italy, 6-11 July 200

Improving the sensitivity to gravitational-wave sources by modifying the input-output optics of advanced interferometers

We study frequency dependent (FD) input-output schemes for signal-recycling interferometers, the baseline design of Advanced LIGO and the current configuration of GEO 600. Complementary to a recent proposal by Harms et al. to use FD input squeezing and ordinary homodyne detection, we explore a scheme which uses ordinary squeezed vacuum, but FD readout. Both schemes, which are sub-optimal among all possible input-output schemes, provide a global noise suppression by the power squeeze factor, while being realizable by using detuned Fabry-Perot cavities as input/output filters. At high frequencies, the two schemes are shown to be equivalent, while at low frequencies our scheme gives better performance than that of Harms et al., and is nearly fully optimal. We then study the sensitivity improvement achievable by these schemes in Advanced LIGO era (with 30-m filter cavities and current estimates of filter-mirror losses and thermal noise), for neutron star binary inspirals, and for narrowband GW sources such as low-mass X-ray binaries and known radio pulsars. Optical losses are shown to be a major obstacle for the actual implementation of these techniques in Advanced LIGO. On time scales of third-generation interferometers, like EURO/LIGO-III (~2012), with kilometer-scale filter cavities, a signal-recycling interferometer with the FD readout scheme explored in this paper can have performances comparable to existing proposals. [abridged]Comment: Figs. 9 and 12 corrected; Appendix added for narrowband data analysi

Modified Kolmogorov Wave Turbulence in QCD matched onto "Bottom-up" Thermalization

We investigate modification of Kolmogorov wave turbulence in QCD calculating gluon spectra as functions of time in the presence of a low energy source which feeds in energy density in the infrared region at a time-dependent rate. Then considering the picture of saturation constraints as has been constructed in the "bottom-up" thermalization approach we revisit that picture for RHIC center-mass energy, $W = 130 {GeV}$, and also extend it to LHC center-mass energy, $W = 5500 {GeV}$, thus for two cases having an opportunity to calculate the equilibration time, $tau_{eq|therm}$, of the gluon system produced in a central heavy ion collision at mid-rapidity region. Thereby, at RHIC and LHC energies we can match the equilibration time, obtained from the late stage gluon spectrum of the modified Kolmogorov wave turbulence, onto that of the "bottom-up" thermalization and other evolutional approaches as well. In addition, from the revised "bottom-up" approach we find the gluon liberation coefficient to be on the average, $c = 0.81 - 1.06$ at RHIC and $c = 0.50 - 0.56$ at LHC. We also present other phenomenological estimates of $tau_{therm}$ which, at QCD realistic couplings, yield $0.45fm - 0.65fm < tau_{therm} < 0.97fm - 2.72fm$ at RHIC and $0.31fm - 0.40fm < tau_{therm} < 0.86fm - 2.04fm$ at LHC, both reflecting the original and modified Kolmogorov wave turbulent scenarios. In the latter case, at certain conditions, taking also into account both very small and realistic couplings we give estimates - $0.65fm < tau_{therm} < 1.29fm$ at RHIC and $0.52fm < tau_{therm} < 1.16fm$ at LHC, as well as at realistic couplings we find $0.53 < tau_{therm} < 0.7fm$ at RHIC and $0.41 < tau_{therm} < 0.65fm$ at LHC.Comment: 37 pages, 8 figures and 5 tables: typos were corrected, content changed in Abstract and Conclusions, 2 tables were added in Conclusion

Information-Seeking Behavior of Clergy: The Research, the Results, and the Future

This article reviews the information seeking behaviors of clergy