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

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

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

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

Maximal Neutrino Mixing from a Minimal Flavor Symmetry

We study a number of models, based on a non-Abelian discrete group, that successfully reproduce the simple and predictive Yukawa textures usually associated with U(2) theories of flavor. These models allow for solutions to the solar and atmospheric neutrino problems that do not require altering successful predictions for the charged fermions or introducing sterile neutrinos. Although Yukawa matrices are hierarchical in the models we consider, the mixing between second- and third-generation neutrinos is naturally large. We first present a quantitative analysis of a minimal model proposed in earlier work, consisting of a global fit to fermion masses and mixing angles, including the most important renormalization group effects. We then propose two new variant models: The first reproduces all important features of the SU(5)xU(2) unified theory with neither SU(5) nor U(2). The second demonstrates that discrete subgroups of SU(2) can be used in constructing viable supersymmetric theories of flavor without scalar universality even though SU(2) by itself cannot.Comment: 34 pages LaTeX, 1 eps figure, minor revisions and references adde

Chaos in a double driven dissipative nonlinear oscillator

We propose an anharmonic oscillator driven by two periodic forces of different frequencies as a new time-dependent model for investigating quantum dissipative chaos. Our analysis is done in the frame of statistical ensemble of quantum trajectories in quantum state diffusion approach. Quantum dynamical manifestation of chaotic behavior, including the emergence of chaos, properties of strange attractors, and quantum entanglement are studied by numerical simulation of ensemble averaged Wigner function and von Neumann entropy.Comment: 9 pages, 18 figure

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

Atmospheric Heating and Wind Acceleration: Results for Cool Evolved Stars based on Proposed Processes

A chromosphere is a universal attribute of stars of spectral type later than ~F5. Evolved (K and M) giants and supergiants (including the zeta Aurigae binaries) show extended and highly turbulent chromospheres, which develop into slow massive winds. The associated continuous mass loss has a significant impact on stellar evolution, and thence on the chemical evolution of galaxies. Yet despite the fundamental importance of those winds in astrophysics, the question of their origin(s) remains unsolved. What sources heat a chromosphere? What is the role of the chromosphere in the formation of stellar winds? This chapter provides a review of the observational requirements and theoretical approaches for modeling chromospheric heating and the acceleration of winds in single cool, evolved stars and in eclipsing binary stars, including physical models that have recently been proposed. It describes the successes that have been achieved so far by invoking acoustic and MHD waves to provide a physical description of plasma heating and wind acceleration, and discusses the challenges that still remain.Comment: 46 pages, 9 figures, 1 table; modified and unedited manuscript; accepted version to appear in: Giants of Eclipse, eds. E. Griffin and T. Ake (Berlin: Springer

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