Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

ρ\rho - nucleus bound states in Walecka model

Possible formation of $\rho$ nucleus bound state is studied in the framework of Walecka model. The bound states are found in different nuclei ranging from $^3He$ to $^{208}Pb$. These bound states may have a direct bearing on the recent experiments on the photoproduction of $\rho$ meson in the nuclear medium.Comment: RevTeX fil

First measurements of the ^16O(e,e'pn)^14N reaction

This paper reports on the first measurement of the ^16O(e,e'pn)^14N reaction. Data were measured in kinematics centred on a super-parallel geometry at energy and momentum transfers of 215 MeV and 316 MeV/c. The experimental resolution was sufficient to distinguish groups of states in the residual nucleus but not good enough to separate individual states. The data show a strong dependence on missing momentum and this dependence appears to be different for two groups of states in the residual nucleus. Theoretical calculations of the reaction using the Pavia code do not reproduce the shape or the magnitude of the data.Comment: 10 pages, 11 figures, 2 tables, Accepted for publication in EPJ

Why Are Male Social Relationships Complex in the Doubtful Sound Bottlenose Dolphin Population?

Copyright 2008 Elsevier B.V., All rights reserved.Peer reviewedPublisher PD

Knockout of proton-neutron pairs from 16^{16}O with electromagnetic probes

After recent improvements to the Pavia model of two-nucleon knockout from $^{16}$O with electromagnetic probes the calculated cross sections are compared to experimental data from such reactions. Comparison with data from a measurement of the $^{16}$O(e,e$'$pn) reaction show much better agreement between experiment and theory than was previously observed. In a comparison with recent data from a measurement of the $^{16}$O($\gamma$,pn) reaction the model over-predicts the measured cross section at low missing momentum.Comment: 6 pages, 5 figure

A new measurement of the neutron detection efficiency for the NaI Crystal Ball detector

We report on a measurement of the neutron detection efficiency in NaI crystals in the Crystal Ball detector obtained from a study of single p0 photoproduction on deuterium using the tagged photon beam at the Mainz Microtron. The results were obtained up to a neutron energy of 400 MeV. They are compared to previous measurements made more than 15 years ago at the pion beam at the BNL AGS

T and F asymmetries in π0 photoproduction on the proton

The γp→π0p reaction was studied at laboratory photon energies from 425 to 1445 MeV with a transversely polarized target and a longitudinally polarized beam. The beam-target asymmetry F was measured for the first time and new high precision data for the target asymmetry T were obtained. The experiment was performed at the photon tagging facility of the Mainz Microtron (MAMI) using the Crystal Ball and TAPS photon spectrometers. The polarized cross sections were expanded in terms of associated Legendre functions and compared to recent predictions from several partial-wave analyses. The impact of the new data on our understanding of the underlying partial-wave amplitudes and baryon resonance contributions is discussed

Photoproduction of π0-pairs off protons and off neutrons

Total cross sections, angular distributions, and invariant-mass distributions have been measured for the photoproduction of π0π0 pairs off free protons and off nucleons bound in the deuteron. The experiments were performed at the MAMI accelerator facility in Mainz using the Glasgow photon tagging spectrometer and the Crystal Ball/TAPS detector. The accelerator delivered electron beams of 1508 and 1557MeV, which produced bremsstrahlung in thin radiator foils. The tagged photon beam covered energies up to 1400MeV. The data from the free proton target are in good agreement with previous measurements and were only used to test the analysis procedures. The results for differential cross sections (angular distributions and invariant-mass distributions) for free and quasi-free protons are almost identical in shape, but differ in absolute magnitude up to 15%. Thus, moderate final-state interaction effects are present. The data for quasi-free neutrons are similar to the proton data in the second resonance region (final-state invariant masses up to ≈1550 MeV), where both reactions are dominated by the N(1520)3/2−→Δ(1232)3/2+π decay. At higher energies, angular and invariant-mass distributions are different. A simple analysis of the shapes of the invariant-mass distributions in the third resonance region is consistent with strong contributions of an N⋆→Nσ decay for the proton, while the reaction is dominated by a sequential decay via a Δπ intermediate state for the neutron. The data are compared to predictions from the Two-Pion-MAID model and the Bonn-Gatchina coupled-channel analysis

Measurement of the transverse target and beam-target asymmetries in η\eta meson photoproduction at MAMI

We present new data for the transverse target asymmetry T and the very first data for the beam-target asymmetry F in the $\vec \gamma \vec p\to\eta p$ reaction up to a center-of-mass energy of W=1.9 GeV. The data were obtained with the Crystal-Ball/TAPS detector setup at the Glasgow tagged photon facility of the Mainz Microtron MAMI. All existing model predictions fail to reproduce the new data indicating a significant impact on our understanding of the underlying dynamics of $\eta$ meson photoproduction. The peculiar nodal structure observed in existing T data close to threshold is not confirmed.Comment: 5 pages, 3 figures, accepted for publication in PR