The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC.

Positive selection is widely estimated from protein coding sequence alignments by the nonsynonymous-to-synonymous ratio ω. Increasingly elaborate codon models are used in a likelihood framework for this estimation. Although there is widespread concern about the robustness of the estimation of the ω ratio, more efforts are needed to estimate this robustness, especially in the context of complex models. Here, we focused on the branch-site codon model. We investigated its robustness on a large set of simulated data. First, we investigated the impact of sequence divergence. We found evidence of underestimation of the synonymous substitution rate for values as small as 0.5, with a slight increase in false positives for the branch-site test. When dS increases further, underestimation of dS is worse, but false positives decrease. Interestingly, the detection of true positives follows a similar distribution, with a maximum for intermediary values of dS. Thus, high dS is more of a concern for a loss of power (false negatives) than for false positives of the test. Second, we investigated the impact of GC content. We showed that there is no significant difference of false positives between high GC (up to ∼80%) and low GC (∼30%) genes. Moreover, neither shifts of GC content on a specific branch nor major shifts in GC along the gene sequence generate many false positives. Our results confirm that the branch-site is a very conservative test

Breakdown of correspondence in chaotic systems: Ehrenfest versus localization times

Breakdown of quantum-classical correspondence is studied on an experimentally realizable example of one-dimensional periodically driven system. Two relevant time scales are identified in this system: the short Ehrenfest time t_h and the typically much longer localization time scale T_L. It is shown that surprisingly weak modification of the Hamiltonian may eliminate the more dramatic symptoms of localization without effecting the more subtle but ubiquitous and rapid loss of correspondence at t_h.Comment: 4 pages, 5 figures, replaced with a version submitted to PR

Gaia, White Dwarfs, and the Age of the Galaxy

The Milky Way is composed of four major stellar populations: the thin disk, thick disk, bulge, and halo. At present, we do not know the age of any of these populations to better than one or two billion years. This lack of knowledge keeps us from answering fundamental questions about the Galaxy: When did the thin disk, thick disk, and halo form? Did they form over an extended period, and if so, how long? Was star formation continuous across these populations or instead occur in distinct episodes? The Gaia satellite is providing precise trigonometric parallaxes for a plethora of white dwarfs in each of these populations. We combine these parallaxes (and hence, distances) with photometry and analyze them using a modeling technique that relies on Bayesian statistics. This allows us to derive precise ages for individual white dwarfs and determine the age distribution and star formation history for each of the constituents of our Galaxy. Here we will present current progress in this endeavor, with emphasis on the ages of individual white dwarfs in the Hyades. Measuring the ages of individual white dwarfs in well-studied clusters provides proof of concept for our technique, as well exploration of any systematic offsets caused from timescales from main sequence models, as well as the initial-final mass relation

Academics perception towards various water reuse options: University of Trás-os-Montes e Alto Douro - UTAD Campus (Portugal) as a case study

Any strategy of water reuse has to achieve social acceptance to be successful. This paper presents the results of a multiple choice survey that attempted to establish the general attitude toward water reuse by asking academics in UTAD (Portugal) a wide range of questions. The survey included 20 reuse options, which were clustered into three reuse categories, specifically: low, medium and high contact levels. Correlation analysis between the level of support of low, medium and high contact options and demographic characteristics, personal and environmental beliefs was performed. Results show that a high proportion of the participants supported low and medium contact reuse options. Correlation was found to exist between the income classes and to the level of support of medium and high reuse options and between education level and the support for high contact reuse options. The responses to the survey suggested that some beliefs influence the level of support

Population Dynamics and Non-Hermitian Localization

We review localization with non-Hermitian time evolution as applied to simple models of population biology with spatially varying growth profiles and convection. Convection leads to a constant imaginary vector potential in the Schroedinger-like operator which appears in linearized growth models. We illustrate the basic ideas by reviewing how convection affects the evolution of a population influenced by a simple square well growth profile. Results from discrete lattice growth models in both one and two dimensions are presented. A set of similarity transformations which lead to exact results for the spectrum and winding numbers of eigenfunctions for random growth rates in one dimension is described in detail. We discuss the influence of boundary conditions, and argue that periodic boundary conditions lead to results which are in fact typical of a broad class of growth problems with convection.Comment: 19 pages, 11 figure

Probing Primordial Non-Gaussianity with Large-Scale Structure

We consider primordial non-Gaussianity due to quadratic corrections in the gravitational potential parametrized by a non-linear coupling parameter fnl. We study constraints on fnl from measurements of the galaxy bispectrum in redshift surveys. Using estimates for idealized survey geometries of the 2dF and SDSS surveys and realistic ones from SDSS mock catalogs, we show that it is possible to probe |fnl|~100, after marginalization over bias parameters. We apply our methods to the galaxy bispectrum measured from the PSCz survey, and obtain a 2sigma-constraint |fnl|< 1800. We estimate that an all sky redshift survey up to z~1 can probe |fnl|~1. We also consider the use of cluster abundance to constrain fnl and find that in order to be sensitive to |fnl|~100, cluster masses need to be determined with an accuracy of a few percent, assuming perfect knowledge of the mass function and cosmological parameters.Comment: 15 pages, 7 figure

Driving the resonant quantum kicked rotor via extended initial conditions

We study the resonances of the quantum kicked rotor subjected to an extended initial distribution. For the primary resonances we obtain the dispersion relation for the map of this system. We find an analytical dependence of the statistical moments on the shape of the initial distribution. For the secondary resonances we obtain numerically a similar dependence. This allows us to devise an extended initial condition which produces an average angular momentum pointing in a preset direction which increases with time with a preset ratio.Comment: 6 pages, 5 figures, send to EPJ

Detection Limits for Super-Hubble Suppression of Causal Fluctuations

We investigate to what extent future microwave background experiments might be able to detect a suppression of fluctuation power on large scales in flat and open universe models. Such suppression would arise if fluctuations are generated by causal processes, and a measurement of a small suppression scale would be problematic for inflation models, but consistent with many defect models. More speculatively, a measurement of a suppression scale of the order of the present Hubble radius could provide independent evidence for a fine-tuned inflation model leading to a low-density universe. We find that, depending on the primordial power spectrum, a suppression scale modestly larger than the visible Horizon can be detected, but that the detectability drops very rapidly with increasing scale. For models with two periods of inflation, there is essentially no possibility of detecting a causal suppression scale.Comment: 8 pages, 4 figures, revtex, In Press Physical Review D 200

Performance of 20:1 multiplexer for large area charge readouts in directional dark matter TPC detectors

More target mass is required in current TPC based directional dark matter detectors for improved detector sensitivity. This can be achieved by scaling up the detector volumes, but this results in the need for more analogue signal channels. A possible solution to reducing the overall cost of the charge readout electronics is to multiplex the signal readout channels. Here, we present work on an expanded LMH6574 multiplexer system with a capability of reducing the number of readouts in such TPC detectors by a factor of 20. Results indicate that the important charge distribution asymmetry along an ionization track is retained after multiplexed signals are demultiplexed