Generalized harmonic formulation in spherical symmetry

In this pedagogically structured article, we describe a generalized harmonic formulation of the Einstein equations in spherical symmetry which is regular at the origin. The generalized harmonic approach has attracted significant attention in numerical relativity over the past few years, especially as applied to the problem of binary inspiral and merger. A key issue when using the technique is the choice of the gauge source functions, and recent work has provided several prescriptions for gauge drivers designed to evolve these functions in a controlled way. We numerically investigate the parameter spaces of some of these drivers in the context of fully non-linear collapse of a real, massless scalar field, and determine nearly optimal parameter settings for specific situations. Surprisingly, we find that many of the drivers that perform well in 3+1 calculations that use Cartesian coordinates, are considerably less effective in spherical symmetry, where some of them are, in fact, unstable.Comment: 47 pages, 15 figures. v2: Minor corrections, including 2 added references; journal version

Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle

Citation: Dickey, A. M., Loy, J. D., Bono, J. L., Smith, T. P. L., Apley, M. D., Lubbers, B. V., . . . Clawson, M. L. (2016). Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle. Veterinary Research, 47, 11. doi:10.1186/s13567-016-0316-2Moraxella bovoculi is a recently described bacterium that is associated with infectious bovine keratoconjunctivitis (IBK) or "pinkeye" in cattle. In this study, closed circularized genomes were generated for seven M. bovoculi isolates: three that originated from the eyes of clinical IBK bovine cases and four from the deep nasopharynx of asymptomatic cattle. Isolates that originated from the eyes of IBK cases profoundly differed from those that originated from the nasopharynx of asymptomatic cattle in genome structure, gene content and polymorphism diversity and consequently placed into two distinct phylogenetic groups. These results suggest that there are genetically distinct strains of M. bovoculi that may not associate with IBK

An Invitation to Higher Gauge Theory

In this easy introduction to higher gauge theory, we describe parallel transport for particles and strings in terms of 2-connections on 2-bundles. Just as ordinary gauge theory involves a gauge group, this generalization involves a gauge '2-group'. We focus on 6 examples. First, every abelian Lie group gives a Lie 2-group; the case of U(1) yields the theory of U(1) gerbes, which play an important role in string theory and multisymplectic geometry. Second, every group representation gives a Lie 2-group; the representation of the Lorentz group on 4d Minkowski spacetime gives the Poincar\'e 2-group, which leads to a spin foam model for Minkowski spacetime. Third, taking the adjoint representation of any Lie group on its own Lie algebra gives a 'tangent 2-group', which serves as a gauge 2-group in 4d BF theory, which has topological gravity as a special case. Fourth, every Lie group has an 'inner automorphism 2-group', which serves as the gauge group in 4d BF theory with cosmological constant term. Fifth, every Lie group has an 'automorphism 2-group', which plays an important role in the theory of nonabelian gerbes. And sixth, every compact simple Lie group gives a 'string 2-group'. We also touch upon higher structures such as the 'gravity 3-group' and the Lie 3-superalgebra that governs 11-dimensional supergravity.Comment: 60 pages, based on lectures at the 2nd School and Workshop on Quantum Gravity and Quantum Geometry at the 2009 Corfu Summer Institut

Excited States of Proton-bound DNA/RNA Base Homo-dimers: Pyrimidines

We are presenting the electronic photo fragment spectra of the protonated pyrimidine DNA bases homo-dimers. Only the thymine dimer exhibits a well structured vibrational progression, while protonated monomer shows broad vibrational bands. This shows that proton bonding can block some non radiative processes present in the monomer.Comment: We acknowledge the use of the computing facility cluster GMPCS of the LUMAT federation (FR LUMAT 2764

Analysis of the X(1835) and related baryonium states with Bethe-Salpeter equation

In this article, we study the mass spectrum of the baryon-antibaryon bound states $p\bar{p}$, $\Sigma\bar{\Sigma}$, $\Xi\bar{\Xi}$, $\Lambda\bar{\Lambda}$, $p\bar{N}(1440)$, $\Sigma\bar{\Sigma}(1660)$, $\Xi\bar{\Xi}^\prime$ and $\Lambda\bar{\Lambda}(1600)$ with the Bethe-Salpeter equation. The numerical results indicate that the $p\bar{p}$, $\Sigma\bar{\Sigma}$, $\Xi\bar{\Xi}$, $p\bar{N}(1440)$, $\Sigma\bar{\Sigma}(1660)$, $\Xi\bar{\Xi}^\prime$ bound states maybe exist, and the new resonances X(1835) and X(2370) can be tentatively identified as the $p\bar{p}$ and $p\bar{N}(1440)$ (or $N(1400)\bar{p}$) bound states respectively with some gluon constituents, and the new resonance X(2120) may be a pseudoscalar glueball. On the other hand, the Regge trajectory favors identifying the X(1835), X(2120) and X(2370) as the excited $\eta^\prime(958)$ mesons with the radial quantum numbers $n=3$, 4 and 5, respectively.Comment: 13 pages, 2 figures, revise a numbe

Roadmap on dynamics of molecules and clusters in the gas phase

This roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty order of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity from the smallest (diatomic) molecules to clusters and nanoparticles. Combining some of these techniques opens up new avenues to unravel hitherto unexplored reaction pathways and mechanisms, and to establish their significance in, e.g. radiotherapy and radiation damage on the nanoscale, astrophysics, astrochemistry and atmospheric science

Signal transduction pathway controlling synthesis of a class of degradative enzymes in Bacillus subtilis: expression of the regulatory genes and analysis of mutations in degS and degU.

The rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis are controlled by a signal transduction pathway defined by at least four regulatory genes: degS, degU, degQ (formerly sacQ), and degR (formerly prtR). The DegS-DegU proteins show amino acid similarities with two-component procaryotic modulator-effector pairs such as NtrB-NtrC, CheA-CheY, and EnvZ-OmpR. By analogy with these systems, it is possible that DegS is a protein kinase which could catalyze the transfer of a phosphoryl moiety to DegU, which acts as a positive regulator. DegR and DegQ correspond to polypeptides of 60 and 46 amino acids, respectively, which also activate the synthesis of degradative enzymes. We show that the degS and degU genes are organized in an operon. The putative sigma A promoter of the operon was mapped upstream from degS. Mutations in degS and degU were characterized at the molecular level, and their effects on transformability and cell motility were studied. The expression of degQ was shown to be subject both to catabolite repression and DegS-DegU-mediated control, allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation. These results are consistent with the hypothesis that this control system responds to an environmental signal such as limitations of nitrogen, carbon, or phosphate sources

Modeling Electromagnetic Form Factors of Light and Heavy Pseudoscalar Mesons

The electromagnetic form factors of light and heavy pseudoscalar mesons are calculated within two covariant constituent-quark models, viz., a light-front and a dispersion relation approach. We investigate the details and physical origins of the model dependence of various hadronic observables: the weak decay constant, the charge radius and the elastic electromagnetic form factor