A Simple Nested Simulation for SED-ML

This document describes a simple nested Simulation Experiment for SED-ML [1] that is easy to implement and will help to broaden what SED-ML is able to encode

Longitudinal Atomic Beam Spin Echo Experiments: A possible way to study Parity Violation in Hydrogen

We discuss the propagation of hydrogen atoms in static electric and magnetic fields in a longitudinal atomic beam spin echo (lABSE) apparatus. Depending on the choice of the external fields the atoms may acquire both dynamical and geometrical quantum mechanical phases. As an example of the former, we show first in-beam spin rotation measurements on atomic hydrogen, which are in excellent agreement with theory. Additional calculations of the behaviour of the metastable 2S states of hydrogen reveal that the geometrical phases may exhibit the signature of parity-(P-)violation. This invites for possible future lABSE experiments, focusing on P-violating geometrical phases in the lightest of all atoms.Comment: 6 pages, 4 figure

TinkerCell: Modular CAD Tool for Synthetic Biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.Comment: 23 pages, 20 figure

Metastable states, the adiabatic theorem and parity violating geometric phases II

We discuss and calculate parity conserving (PC) and parity violating (PV) geometric phases for the metastable 2S states of hydrogen and deuterium. The atoms are supposed to be subjected to slowly varying electric and magnetic fields which act as external parameters for the atoms. Geometric flux density fields are introduced which allow for an easy overview how to choose the paths in parameter space in order to obtain only PC or only PV geometric phases. The PV phases are calculated in the Standard Model of particle physics. Even if numerically they come out small they have interest of principle as a new manifestation of parity violation in atomic physics.Comment: 63 pages, 8 figures, 10 table

Photoionization Suppression by Continuum Coherence: Experiment and Theory

We present experimental and theoretical results of a detailed study of laser-induced continuum structures (LICS) in the photoionization continuum of helium out of the metastable state 2s $^1S_0$. The continuum dressing with a 1064 nm laser, couples the same region of the continuum to the {4s $^1S_0$} state. The experimental data, presented for a range of intensities, show pronounced ionization suppression (by as much as 70% with respect to the far-from-resonance value) as well as enhancement, in a Beutler-Fano resonance profile. This ionization suppression is a clear indication of population trapping mediated by coupling to a contiuum. We present experimental results demonstrating the effect of pulse delay upon the LICS, and for the behavior of LICS for both weak and strong probe pulses. Simulations based upon numerical solution of the Schr\"{o}dinger equation model the experimental results. The atomic parameters (Rabi frequencies and Stark shifts) are calculated using a simple model-potential method for the computation of the needed wavefunctions. The simulations of the LICS profiles are in excellent agreement with experiment. We also present an analytic formulation of pulsed LICS. We show that in the case of a probe pulse shorter than the dressing one the LICS profile is the convolution of the power spectra of the probe pulse with the usual Fano profile of stationary LICS. We discuss some consequences of deviation from steady-state theory.Comment: 29 pages, 17 figures, accepted to PR

Extended Gas in Seyfert Galaxies: Near Infrared Observations of NGC 2110 and Circinus

We present results of near--IR long-slit spectroscopy in the J and K bands of the Seyfert 2 galaxies NGC 2110 and Circinus, investigating the gaseous distribution, excitation, reddening and kinematics. In NGC 2110, the emission line ratio [FeII]/Pa beta increases towards the nucleus (to ~ 7). The nuclear [Fe II]1.257 (microns) and Pa beta lines are broader (FWHM ~ 500 km/s) than the H2 (2.121) line (FWHM ~ 300 km/s). Both these results suggest that shocks, driven by the radio jet, are an important source of excitation of [Fe II]. The H2 excitation appears to be dominated by X-rays from the nucleus. In Circinus, both [FeII]/Pa beta and H2/Br gamma decrease from ~ 2 at 4 arcsec from the nucleus to nuclear values of ~ 0.6 and ~ 1, respectively, suggesting that the starburst dominates the nuclear excitation, while the AGN dominates the excitation further out (r > 2 arcsec). For both galaxies, the gaseous kinematics are consistent with circular rotation in the plane of the disk. Our rotation curves suggest that the nucleus (identified with the peak of the IR continuum) is displaced from the kinematic centre of the galaxies. This effect has been observed previously in NGC 2110 based on the kinematics of optical emission lines, but the displacement is smaller in the infrared, suggesting the effect is related to obscuration. The continuum J-K colours of the nuclear region indicate a red stellar population in NGC 2110 and a reddened young stellar population in Circinus. Right at the nucleus of both galaxies, the colours are redder, apparently a result of hot dust emission from the inner edge of a circumnuclear torus.Comment: 11 pages, 14 figures, accepted for publication in MNRA

The Spectral Energy Distribution of Normal, Starburst and Active Galaxies

We present the results of an extensive literature search of multiwavelength data for a sample of 59 galaxies, consisting of 26 Starbursts, 15 Seyfert 2's, 5 LINER's, 6 normal spirals and 7 normal elliptical galaxies. The data include soft X-ray fluxes, ultraviolet and optical spectra, near, mid/far infrared photometry and radio measurements, selected to match as closely as possible the IUE aperture (10" X 20"). The galaxies are separated into 6 groups with similar characteristics, namely, Ellipticals, Spirals, LINER's, Seyfert 2's, Starbursts of Low and High reddening, for which we create average spectral energy distributions (SED). The individual groups SED's are normalized to the $\lambda$7000\AA flux and compared, looking for similarities and differences among them.The bolometric fluxes of different types of galaxies were calculated integrating their SED's. These values are compared with individual waveband flux densities, in order to determine the wavebands which contribute most to the bolometric flux. Linear regressions were performed between the bolometric and individual band fluxes for each kind of galaxy. These fits can be used in the calculation of the bolometric flux for other objects of similar activity type, but with reduced waveband information. We have also collected multiwavelength data for 4 HII regions, a thermal supernova remnant, and a non-thermal supernova remnant (SNR), which are compared with the Starburst SED's.Comment: 29 pages, 13 postscript figures and 10 tables. To appear in The Astronomical Journa

Long-Term Profile Variability of Double-Peaked Emmission Lines in AGNs

An increasing number of AGNs exhibit broad, double-peaked Balmer emission lines, which arise from the outer regions of the accretion disk which fuels the AGN. The line profiles vary on timescales of 5--10 years. Our group has monitored a set of 20 double-peaked emitters for the past 8 years (longer for some objects). Here we describe a project to characterize the variability patterns of the double-peaked H alpha line profiles and compare with those of two simple models: a circular disk with a spiral arm and an elliptical disk.Comment: 2 pages, 1 figure, to appear in the proceedings of "The Interplay among Black Holes, Stars and ISM in Galactic Nuclei", IAU 222, eds. T. Storchi Bergmann, L.C. Ho, and H.R. Schmit