Intrinsic Differences in the Inner Jets of High- and Low-Optically Polarized Radio Quasars

A significant fraction of compact radio-loud quasars display most of the characteristics of relativistically beamed, high-optical polarization blazars, yet are weakly polarized in the optical regime. We have used the VLBA at 22 and 43 GHz to look for differences in the parsec-scale magnetic field structures of 18 high- and low-optically polarized, compact radio-loud quasars (HPQs and LPRQs, respectively). We find a strong correlation between the polarization level of the unresolved parsec-scale radio core at 43 GHz and overall optical polarization of the source, which suggests a common (possibly co-spatial) origin for the emission at these two wavelengths. The magnetic fields of the polarized 43 GHz radio cores are aligned roughly transverse to the jet axis. Similar orientations are seen in the optical, suggesting that the polarized flux at both wavelengths is due to one or more strong transverse shocks located very close to the base of the jet. In LPRQs, these shocks appear to be weak near the core, and gradually increase in strength down the jet. The LPRQs in our sample tend to have less luminous radio cores than the HPQs, and jet components with magnetic fields predominantly parallel to the flow. The components in HPQ jets, on the other hand, tend to have transverse alignments. These differences cannot be accounted for by a simple model in which HPQs and LPRQs are the same type of object, seen at different angles to the line of sight. A more likely scenario is that LPRQs represent a quiescent phase of blazar activity, in which the inner jet flow does not undergo strong shocks.Comment: 29 pages, includes 25 figures and 6 tables. Uses emulateapj5.sty. Accepted for publication in the Astrophysical Journal. A version with better quality figures (785Kb, gzipped) can be found at http://sgra.jpl.nasa.gov/html_lister/LPQ

Annotation of SBML Models Through Rule-Based Semantic Integration

*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides richly modelled biological knowledge suitable for annotation of SBML models.
*Results:* We demonstrate proof-of-principle for this rule-based mediation with two use cases for SBML model annotation. This was implemented with existing tools, decreasing development time and increasing reusability. This initial work establishes the feasibility of this approach as part of an automated SBML model annotation system.
*Availability:* Detailed information including download and mapping of the ontologies as well as integration results is available from "http://www.cisban.ac.uk/RBM":http://www.cisban.ac.uk/RB

The Relation between Radio Polarization and Gamma-ray Emission in AGN Jets

We have compared the parsec-scale jet linear polarization properties of the Fermi LAT-detected and non-detected sources in the complete flux-density-limited (MOJAVE-1) sample of highly beamed AGN. Of the 123 MOJAVE sources, 30 were detected by the LAT during its first three months of operation. We find that during the era since the launch of Fermi, the unresolved core components of the LAT-detected jets have significantly higher median fractional polarization at 15 GHz. This complements our previous findings that these LAT sources have higher apparent jet speeds, brightness temperatures and Doppler factors, and are preferentially found in higher activity states.Comment: 6 pages, 3 figures, to appear in the proceedings of "High Energy Phenomena In Relativistic Outflows II" (Buenos Aires, Argentina, October 26-30, 2009) International Journal of Modern Physics

Relativistic Beaming and Flux Variability in Active Galactic Nuclei

We discuss the impact of special relativistic effects on the observed light curves and variability duty cycles of AGNs. We model the properties of AGN light curves at radio wavelengths using a simulated shot noise process in which the occurrence of major flaring events in a relativistic jet is governed by Poisson statistics. We show that flaring sources whose radiation is highly beamed toward us are able to reach very high flux levels, but will in fact spend most of their time in relatively low flaring states due to relativistic contraction of flare time scales in the observer frame. The fact that highly beamed AGNs do not return to a steady-state quiescent level between flares implies that their weakly beamed counterparts should have highly stable flux densities that result from a superposition of many long-term, low-amplitude flares. The ``apparent'' quiescent flux levels of these weakly beamed AGNs (identified in many unified models as radio galaxies) will be significantly higher than their ''true'' quiescent (i.e., non-flaring) levels. We use Monte Carlo simulations to investigate flux variability bias in the selection statistics of flat-spectrum AGN samples. In the case of the Caltech-Jodrell Flat-spectrum survey, the predicted orientation bias towards jets seen end-on is weakened if the parent population is variable, since the highly beamed sources have a stronger tendency to be found in low flaring states. This effect is small, however, since highly beamed sources are relatively rare, and their fluxes tend to be boosted sufficiently above the survey limit such that they are selected regardless of their flaring level. We find that for larger flat-spectrum AGN surveys with fainter flux cutoffs, variability should not be an appreciable source of selection bias.Comment: Accepted for publication in the Astrophysical Journa