LP-VIcode: a program to compute a suite of variational chaos indicators

An important point in analysing the dynamics of a given stellar or planetary system is the reliable identification of the chaotic or regular behaviour of its orbits. We introduce here the program LP-VIcode, a fully operational code which efficiently computes a suite of ten variational chaos indicators for dynamical systems in any number of dimensions. The user may choose to simultaneously compute any number of chaos indicators among the following: the Lyapunov Exponents, the Mean Exponential Growth factor of Nearby Orbits, the Slope Estimation of the largest Lyapunov Characteristic Exponent, the Smaller ALignment Index, the Generalized ALignment Index, the Fast Lyapunov Indicator, the Othogonal Fast Lyapunov Indicator, the dynamical Spectra of Stretching Numbers, the Spectral Distance, and the Relative Lyapunov Indicator. They are combined in an efficient way, allowing the sharing of differential equations whenever this is possible, and the individual stopping of their computation when any of them saturates.Comment: 26 pages, 9 black-and-white figures. Accepted for publication in Astronomy and Computing (Elsevier

Forming first-ranked early-type galaxies through hierarchical dissipationless merging

We have developed a computationally competitive N-body model of a previrialized aggregation of galaxies in a flat LambdaCDM universe to assess the role of the multiple mergers that take place during the formation stage of such systems in the configuration of the remnants assembled at their centres. An analysis of a suite of 48 simulations of low-mass forming groups (of about 1E13 solar masses) demonstrates that the gravitational dynamics involved in their hierarchical collapse is capable of creating realistic first-ranked galaxies without the aid of dissipative processes. Our simulations indicate that the brightest group galaxies (BGGs) constitute a distinct population from other group members, sketching a scenario in which the assembly path of these objects is dictated largely by the formation of their host system. We detect significant differences in the distribution of Sersic indices and total magnitudes, as well as a luminosity gap between BGGs and the next brightest galaxy that is positively correlated with the total luminosity of the parent group. Such gaps arise from both the grow of BGGs at the expense of lesser companions and the decrease in the relevance of second-ranked objects in equal measure. This results in a dearth of intermediate-mass galaxies which explains the characteristic central dip detected in their luminosity functions in dynamically young galaxy aggregations. The fact that the basic global properties of our BGGs define a thin mass fundamental plane strikingly similar to that followed giant early-type galaxies in the local universe reinforces confidence in the results obtained.Comment: 25 pages, 14 figures, 3 tables. Accepted to MNRA

Electric-Field Gradient at Cd Impurities in In2o3. A FLAPW Study

We report an ab initio study of the electric-field gradient tensor (EFG) at Cd impurities located at both inequivalent cationic sites in the semiconductor In2O3. Calculations were performed with the FLAPW method, that allows us to treat the electronic structure of the doped system and the atomic relaxations introduced by the impurities in the host lattice in a fully self-consistent way. From our results for the EFG (in excellent agreement with the experiments), it is clear that the problem of the EFG at impurities in In2O3 cannot be described by the point-charge model and antishielding factors.Comment: 4 pages, 2 figures, and 2 table

Fitting functions for a disk-galaxy model with different LCDM-halo profiles

We present an adaptation of the standard scenario of disk-galaxy formation to the concordant LCDM cosmology aimed to derive analytical expressions for the scale length and rotation speed of present-day disks that form within four different, cosmologically motivated protogalactic dark matter halo-density profiles. We invoke a standard galaxy-formation model that includes virial equilibrium of spherical dark halos, specific angular momentum conservation during gas cooling, and adiabatic halo response to the gas inflow. The mean mass-fraction and mass-to-light ratio of the central stellar disk are treated as free parameters whose values are tuned to match the zero points of the observed size-luminosity and circular speed-luminosity relations of galaxies. We supply analytical formulas for the characteristic size and rotation speed of disks built inside Einasto r^{1/6}, Hernquist, Burkert, and Navarro-Frenk-White dark matter halos. These expressions match simultaneously the observed zero points and slopes of the different correlations that can be built in the RVL space of disk galaxies from plausible values of the galaxy- and star-formation efficiencies

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACER, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Herein, we present EPA-NG, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER. EPA-NG can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-NG, we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3748 taxa in just under 7 h, using 2048 cores. Our performance assessment shows that EPA-NG outperforms RAxML-EPA and PPLACER by up to a factor of 30 in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-NG scales well up to 2048 cores. EPA-NG is available under the AGPLv3 license

Substitutions near the hemagglutinin receptor-binding site determine the antigenic evolution of influenza A H3N2 viruses in U.S. swine

Swine influenza A virus is an endemic and economically important pathogen in pigs, with the potential to infect other host species. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major component in swine influenza A vaccines. However, as a result of antigenic drift, vaccine strains must be regularly updated to reflect currently circulating strains. Characterizing the cross-reactivity between strains in pigs and seasonal influenza virus strains in humans is also important in assessing the relative risk of interspecies transmission of viruses from one host population to the other. Hemagglutination inhibition (HI) assay data for swine and human H3N2 viruses were used with antigenic cartography to quantify the antigenic differences among H3N2 viruses isolated from pigs in the United States from 1998 to 2013 and the relative cross-reactivity between these viruses and current human seasonal influenza A virus strains. Two primary antigenic clusters were found circulating in the pig population, but with enough diversity within and between the clusters to suggest updates in vaccine strains are needed. We identified single amino acid substitutions that are likely responsible for antigenic differences between the two primary antigenic clusters and between each antigenic cluster and outliers. The antigenic distance between current seasonal influenza virus H3 strains in humans and those endemic in swine suggests that population immunity may not prevent the introduction of human viruses into pigs, and possibly vice versa, reinforcing the need to monitor and prepare for potential incursions

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACER, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Herein, we present EPA-NG, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER. EPA-NG can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-NG, we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3748 taxa in just under 7 h, using 2048 cores. Our performance assessment shows that EPA-NG outperforms RAxML-EPA and PPLACER by up to a factor of 30 in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-NG scales well up to 2048 cores