Conceptual model of E. coli transcriptional machinery

At the moment one type of analysis of transcription regulatory networks (TRNs) in prokaryotes is topological analysis of graph structure of possible regulatory interaction links (see for example [1]). That type of analysis takes into account possibility links that designate the fact that one gene product in some conditions can modulate transcription of the other. The benefit of such approach is that it is allow analyzing TRN at the whole cell level. At the same type it is known that at least some responses are regulated by abundance of elements of transcription machinery [2-3]. We have developed conceptual model of whole cell E. coli TRN with SBGN ER, SBGN PD and SBGN AF languages [4]. That model is the first step towards incorporation of some quantitative information into whole cell TRN modeling.

1.	Freyre-González et al. Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach. Genome Biol (2008) vol. 9 (10) pp. R154
2.	Klumpp and Hwa. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc Natl Acad Sci USA (2008) vol. 105 (51) pp. 20245-50
3.	Barker et al. Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J Mol Biol (2001) vol. 305 (4) pp. 689-702
4.	Le Novère et al. The systems biology graphical notation. Nature biotechnology (2009) vol. 27 (8) pp. 735-41
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High-resolution polarization imaging of the Fermi blazar 3C 279

Ever since the discovery by the Fermi mission that active galactic nuclei (AGN) produce copious amounts of high-energy emission, its origin has remained elusive. Using high-frequency radio interferometry (VLBI) polarization imaging, we could probe the magnetic field topology of the compact high-energy emission regions in blazars. A case study for the blazar 3C 279 reveals the presence of multiple g -ray emission regions. Pass 8 Fermi-Large Area Telescope (LAT) data are used to investigate the flux variations in the GeV regime; six g -ray flares were observed in the source during November 2013 to August 2014. We use the 43 GHz VLBI data to study the morphological changes in the jet. Ejection of a new component (NC2) during the first three g -ray flares suggests the VLBI core as the possible site of the high-energy emission. A delay between the last three flares and the ejection of a new component (NC3) indicates that highenergy emission in this case is located upstream of the 43 GHz core (closer to the black hole).Accepted manuscrip

Modeling the time-dependent polarization of blazars

Linear polarization is an extremely valuable observational tool for probing the dynamic physical conditions of blazar jets. Some patterns are seen in the data, suggestive of order that can be explained by shock waves and helical magnetic field components. However, much disorder is apparent, which implies that turbulence plays a major role as well, especially in the fluctuations of flux and polarization, and perhaps particle acceleration. Here, we present some actual flux and polarization versus time data, plus simulations of model jets. We analyze the output of the simulations in a manner that can be compared with observational data. The results suggest that the ratio of turbulent to ordered magnetic fields varies with time.AST-1615796 - National Science Foundation; NASA; NNX14AQ58G; NNX15AR45

"Orphan" γ\gamma-ray Flares and Stationary Sheaths of Blazar Jets

Blazars exhibit flares across the entire electromagnetic spectrum. Many $\gamma$-ray flares are highly correlated with flares detected at longer wavelengths; however, a small subset appears to occur in isolation, with little or no correlated variability at longer wavelengths. These "orphan" $\gamma$-ray flares challenge current models of blazar variability, most of which are unable to reproduce this type of behavior. Macdonald et al. have developed the Ring of Fire model to explain the origin of orphan $\gamma$-ray flares from within blazar jets. In this model, electrons contained within a blob of plasma moving relativistically along the spine of the jet inverse-Compton scatter synchrotron photons emanating off of a ring of shocked sheath plasma that enshrouds the jet spine. As the blob propagates through the ring, the scattering of the ring photons by the blob electrons creates an orphan $\gamma$-ray flare. This model was successfully applied to modeling a prominent orphan $\gamma$-ray flare observed in the blazar PKS 1510$-$089. To further support the plausibility of this model, Macdonald et al. presented a stacked radio map of PKS 1510$-$089 containing the polarimetric signature of a sheath of plasma surrounding the spine of the jet. In this paper, we extend our modeling and stacking techniques to a larger sample of blazars: 3C 273, 4C 71$.$01, 3C 279, 1055$+$018, CTA 102, and 3C 345, the majority of which have exhibited orphan $\gamma$-ray flares. We find that the model can successfully reproduce these flares, while our stacked maps reveal the existence of jet sheaths within these blazars.Comment: 19 pages, 27 figures, accepted for publication in ApJ. arXiv admin note: text overlap with arXiv:1505.0123

Anisotropy induced Feshbach resonances in a quantum dipolar gas of magnetic atoms

We explore the anisotropic nature of Feshbach resonances in the collision between ultracold magnetic submerged-shell dysprosium atoms, which can only occur due to couplings to rotating bound states. This is in contrast to well-studied alkali-metal atom collisions, where most Feshbach resonances are hyperfine induced and due to rotation-less bound states. Our novel first-principle coupled-channel calculation of the collisions between open-4f-shell spin-polarized bosonic dysprosium reveals a striking correlation between the anisotropy due to magnetic dipole-dipole and electrostatic interactions and the Feshbach spectrum as a function of an external magnetic field. Over a 20 mT magnetic field range we predict about a dozen Feshbach resonances and show that the resonance locations are exquisitely sensitive to the dysprosium isotope.Comment: 5 pages, 4 figure

Singular continuous spectrum is generic

In a variety of contexts, we prove that singular continuous spectrum is generic in the sense that for certain natural complete metric spaces of operators, those with singular spectrum are a dense $G_\delta$.Comment: 5 page