Strange Cepheids and RR Lyrae

Strange modes can occur in radiative classical Cepheids and RR Lyrae models. These are vibrational modes that are trapped near the surface as a result of a 'potential barrier' caused by the sharp hydrogen partial ionization region. Typically the modal number of the strange mode falls between the 7th and 12th overtone, depending on the astrophysical parameters of the equilibrium stellar models (L, M, \Teff, X, Z). Interestingly these modes can be linearly unstable outside the usual instability strip, in which case they should be observable as new kinds of variable stars, 'strange Cepheids' or 'strange RR Lyrae' stars. The present paper reexamines the linear stability properties of the strange modes by taking into account the effects of an isothermal atmosphere, and of turbulent convection. It is found that the linear vibrational instability of the strange modes is resistant to both of these effects. Nonlinear hydrodynamic calculations indicate that the pulsation amplitude of these modes is likely to saturate at the millimagnitude level. These modes should therefore be detectable albeit not without effort.Comment: 6 pages, 7 figures, submitted to Ap

Towards a new generation of multi-dimensional stellar evolution models: development of an implicit hydrodynamic code

This paper describes the first steps of development of a new multidimensional time implicit code devoted to the study of hydrodynamical processes in stellar interiors. The code solves the hydrodynamical equations in spherical geometry and is based on the finite volume method. Radiation transport is taken into account within the diffusion approximation. Realistic equation of state and opacities are implemented, allowing the study of a wide range of problems characteristic of stellar interiors. We describe in details the numerical method and various standard tests performed to validate the method. We present preliminary results devoted to the description of stellar convection. We first perform a local simulation of convection in the surface layers of a A-type star model. This simulation is used to test the ability of the code to address stellar conditions and to validate our results, since they can be compared to similar previous simulations based on explicit codes. We then present a global simulation of turbulent convective motions in a cold giant envelope, covering 80% in radius of the stellar structure. Although our implicit scheme is unconditionally stable, we show that in practice there is a limitation on the time step which prevent the flow to move over several cells during a time step. Nevertheless, in the cold giant model we reach a hydro CFL number of 100. We also show that we are able to address flows with a wide range of Mach numbers (10^-3 < Ms< 0.5), which is impossible with an anelastic approach. Our first developments are meant to demonstrate that the use of an implicit scheme applied to a stellar evolution context is perfectly thinkable and to provide useful guidelines to optimise the development of an implicit multi-D hydrodynamical code.Comment: 21 pages, 18 figures, accepted for publication in A&

Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens

<p>Abstract</p> <p>Background</p> <p>The Enteropathogen Resource Integration Center (ERIC; <url>http://www.ericbrc.org</url>) has a goal of providing bioinformatics support for the scientific community researching enteropathogenic bacteria such as <it>Escherichia coli </it>and <it>Salmonella </it>spp. Rapid and accurate identification of experimental conclusions from the scientific literature is critical to support research in this field. Natural Language Processing (NLP), and in particular Information Extraction (IE) technology, can be a significant aid to this process.</p> <p>Description</p> <p>We have trained a powerful, state-of-the-art IE technology on a corpus of abstracts from the microbial literature in PubMed to automatically identify and categorize biologically relevant entities and predicative relations. These relations include: Genes/Gene Products and their Roles; Gene Mutations and the resulting Phenotypes; and Organisms and their associated Pathogenicity. Evaluations on blind datasets show an F-measure average of greater than 90% for entities (genes, operons, etc.) and over 70% for relations (gene/gene product to role, etc). This IE capability, combined with text indexing and relational database technologies, constitute the core of our recently deployed text mining application.</p> <p>Conclusion</p> <p>Our Text Mining application is available online on the ERIC website <url>http://www.ericbrc.org/portal/eric/articles</url>. The information retrieval interface displays a list of recently published enteropathogen literature abstracts, and also provides a search interface to execute custom queries by keyword, date range, etc. Upon selection, processed abstracts and the entities and relations extracted from them are retrieved from a relational database and marked up to highlight the entities and relations. The abstract also provides links from extracted genes and gene products to the ERIC Annotations database, thus providing access to comprehensive genomic annotations and adding value to both the text-mining and annotations systems.</p

Period doubling bifurcation and high-order resonances in RR Lyrae hydrodynamical models

We investigated period doubling, a well-known phenomenon in dynamical systems, for the first time in RR Lyrae models. These studies provide theoretical background for the recent discovery of period doubling in some Blazhko RR Lyrae stars with the Kepler space telescope. Since period doubling was observed only in Blazhko-modulated stars so far, the phenomenon can help in the understanding of the modulation as well. Utilising the Florida-Budapest turbulent convective hydrodynamical code, we identified the phenomenon in radiative and convective models as well. A period-doubling cascade was also followed up to an eight-period solution confirming that the destabilisation of the limit cycle is indeed the underlying phenomenon. Floquet stability roots were calculated to investigate the possible causes and occurrences of the phenomenon. A two-dimensional diagnostic diagram was constructed to display the various resonances between the fundamental mode and the different overtones. Combining the two tools, we confirmed that the period-doubling instability is caused by a 9:2 resonance between the 9th overtone and the fundamental mode. Destabilisation of the limit cycle by a resonance of a high-order mode is possible because the overtone is a strange mode. The resonance is found to be sufficiently strong enough to shift the period of overtone with up to 10 percent. Our investigations suggest that a more complex interplay of radial (and presumably non-radial) modes could happen in RR Lyrae stars that might have connections with the Blazhko effect as well.Comment: 9 pages, 9 figures, accepted for publication in MNRA

Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli

The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with less changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: 1) subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation, and 2) subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.Comment: 14 pages, 8 figures, to be published in PLoS Computational Biolog

Phase Transitions on Nonamenable Graphs

We survey known results about phase transitions in various models of statistical physics when the underlying space is a nonamenable graph. Most attention is devoted to transitive graphs and trees

Passing to the Limit in a Wasserstein Gradient Flow: From Diffusion to Reaction

We study a singular-limit problem arising in the modelling of chemical reactions. At finite {\epsilon} > 0, the system is described by a Fokker-Planck convection-diffusion equation with a double-well convection potential. This potential is scaled by 1/{\epsilon}, and in the limit {\epsilon} -> 0, the solution concentrates onto the two wells, resulting into a limiting system that is a pair of ordinary differential equations for the density at the two wells. This convergence has been proved in Peletier, Savar\'e, and Veneroni, SIAM Journal on Mathematical Analysis, 42(4):1805-1825, 2010, using the linear structure of the equation. In this paper we re-prove the result by using solely the Wasserstein gradient-flow structure of the system. In particular we make no use of the linearity, nor of the fact that it is a second-order system. The first key step in this approach is a reformulation of the equation as the minimization of an action functional that captures the property of being a curve of maximal slope in an integrated form. The second important step is a rescaling of space. Using only the Wasserstein gradient-flow structure, we prove that the sequence of rescaled solutions is pre-compact in an appropriate topology. We then prove a Gamma-convergence result for the functional in this topology, and we identify the limiting functional and the differential equation that it represents. A consequence of these results is that solutions of the {\epsilon}-problem converge to a solution of the limiting problem.Comment: Added two sections, corrected minor typos, updated reference

Novae Ejecta as Colliding Shells

Following on our initial absorption-line analysis of fifteen novae spectra we present additional evidence for the existence of two distinct components of novae ejecta having different origins. As argued in Paper I one component is the rapidly expanding gas ejected from the outer layers of the white dwarf by the outburst. The second component is pre-existing outer, more slowly expanding circumbinary gas that represents ejecta from the secondary star or accretion disk. We present measurements of the emission-line widths that show them to be significantly narrower than the broad P Cygni profiles that immediately precede them. The emission profiles of novae in the nebular phase are distinctly rectangular, i.e., strongly suggestive of emission from a relatively thin, roughly spherical shell. We thus interpret novae spectral evolution in terms of the collision between the two components of ejecta, which converts the early absorption spectrum to an emission-line spectrum within weeks of the outburst. The narrow emission widths require the outer circumbinary gas to be much more massive than the white dwarf ejecta, thereby slowing the latter's expansion upon collision. The presence of a large reservoir of circumbinary gas at the time of outburst is suggestive that novae outbursts may sometime be triggered by collapse of gas onto the white dwarf, as occurs for dwarf novae, rather than steady mass transfer through the inner Lagrangian point.Comment: 12 pages, 3 figures; Revised manuscript; Accepted for publication in Astrophysics & Space Scienc

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

To study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common TIM barrel fold and catalyze a wide range of chemical reactions. Here, we describe a collaboration between the Enzyme Specificity Consortium (ENSPEC) and the New York SGX Research Center for Structural Genomics (NYSGXRC) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. Using sequence- and structure-based protein comparisons, we first selected 535 target proteins from a variety of genomes for high-throughput structure determination by X-ray crystallography; 63 of these targets were not previously annotated as superfamily members. To date, 20 unique amidohydrolase and 41 unique enolase structures have been determined, increasing the fraction of sequences in the two superfamilies that can be modeled based on at least 30% sequence identity from 45% to 73%. We present case studies of proteins related to uronate isomerase (an amidohydrolase superfamily member) and mandelate racemase (an enolase superfamily member), to illustrate how this structure-focused approach can be used to generate hypotheses about sequence–structure–function relationships