SWEEPFINDER2: Increased sensitivity, robustness, and flexibility

SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection, as well as increased flexibility that enables the user to examine genomic regions in greater detail and to specify a fixed distance between test sites. Moreover, SweepFinder2 enables the use of invariant sites for sweep detection, increasing both its power and precision relative to SweepFinder

Hyperons and massive neutron stars: vector repulsion and SU(3) symmetry

With the discovery of massive neutron stars such as PSR J1614-2230, the question has arisen whether exotic matter such as hyperons can exist in the neutron star core. We examine the conditions under which hyperons can exist in massive neutron stars. We consistently investigate the vector meson-hyperon coupling, going from SU(6) quark model to a broader SU(3) symmetry. We propose that the maximum neutron star mass decreases linearly with the strangeness content f_s of the neutron star core as M_max(f_s) = M_max(0) - 0.6 M_solar (f_s/0.1), which seems to be independent of the underlying nuclear equation of state and the vector baryon-meson coupling scheme. Thus, pulsar mass measurements can be used to constrain the hyperon fraction in neutron stars.Comment: 13 pages, 10 figure

Gravitational waves from the sound of a first order phase transition

We report on the first three-dimensional numerical simulations of first-order phase transitions in the early Universe to include the cosmic fluid as well as the scalar field order parameter. We calculate the gravitational wave (GW) spectrum resulting from the nucleation, expansion, and collision of bubbles of the low-temperature phase, for phase transition strengths and bubble wall velocities covering many cases of interest. We find that the compression waves in the fluid continue to be a source of GWs long after the bubbles have merged, a new effect not taken properly into account in previous modeling of the GW source. For a wide range of models, the main source of the GWs produced by a phase transition is, therefore, the sound the bubbles make

First-order restoration of SU(Nf) x SU(Nf) chiral symmetry with large Nf and Electroweak phase transition

It has been argued by Pisarski and Wilczek that finite temperature restoration of the chiral symmetry SU(Nf) x SU(Nf) is first-order for Nf >=3. This type of chiral symmetry with a large Nf may appear in the Higgs sector if one considers models such as walking technicolor theories. We examine the first-order restoration of the chiral symmetry from the point of view of the electroweak phase transition. The strength of the transition is estimated in SU(2) x U(1) gauged linear sigma model by means of the finite temperature effective potential at one-loop with the ring improvement. Even if the mass of the neutral scalar boson corresponding to the Higgs boson is larger than 114 GeV, the first-order transition can be strong enough for the electroweak baryogenesis, as long as the extra massive scalar bosons (required for the linear realization) are kept heavier than the neutral scalar boson. Explicit symmetry breaking terms reduce the strength of the first-order transition, but the transition can remain strongly first-order even when the masses of pseudo Nambu-Goldstone bosons become as large as the current lower bound of direct search experiments.Comment: 18 pages, 18 figures, minor corrections, references adde

High temperature thermal conductivity of 2-leg spin-1/2 ladders

Based on numerical simulations, a study of the high temperature, finite frequency, thermal conductivity $\kappa(\omega)$ of spin-1/2 ladders is presented. The exact diagonalization and a novel Lanczos technique are employed.The conductivity spectra, analyzed as a function of rung coupling, point to a non-diverging $dc-$limit but to an unconventional low frequency behavior. The results are discussed with perspective recent experiments indicating a significant magnetic contribution to the energy transport in quasi-one dimensional compounds.Comment: 4 pages, 4 figure

Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X, and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3^{|X|} poly(|X|)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted 1 phylogenetic networks

On the determination of anti-neutrino spectra from nuclear reactors

In this paper we study the effect of, well-known, higher order corrections to the allowed beta decay spectrum on the determination of anti-neutrino spectra resulting from the decays of fission fragments. In particular, we try to estimate the associated theory errors and find that induced currents like weak magnetism may ultimately limit our ability to improve the current accuracy and under certain circumstance could even largely increase the theoretical errors. We also perform a critical evaluation of the errors associated with our method to extract the anti-neutrino spectrum using synthetic beta spectra. It turns out, that a fit using only virtual beta branches with a judicious choice of the effective nuclear charge provides results with a minimal bias. We apply this method to actual data for U235, Pu239 and Pu241 and confirm, within errors, recent results, which indicate a net 3% upward shift in energy averaged anti-neutrino fluxes. However, we also find significant shape differences which can in principle be tested by high statistics anti-neutrino data samples.Comment: 20 pages, 5 figures, 9 tables, added references, version accepted for publication in Phys. Rev. C. Corrected errors in tab. 1 and eqs. 18 and 19. Results and conclusion unchange