Multi-phase Nature of a Radiation-Driven Fountain with Nuclear Starburst in a Low-mass Active Galactic Nucleus

The structures and dynamics of molecular, atomic, and ionized gases are studied around a low-luminosity active galactic nucleus (AGN) with a small ($2\times 10^6 M_\odot$) black hole using 3D radiation hydrodynamic simulations. We studied, for the first time, the non-equilibrium chemistry for the X-ray dominated region in the "radiation-driven fountain" (Wada 2012) with supernova feedback. A double hollow cone structure is naturally formed without postulating a thick "torus" around a central source. The cone is occupied with an inhomogeneous, diffuse ionized gas and surrounded by a geometrically thick ($h/r \gtrsim 1$) atomic gas. Dense molecular gases are distributed near the equatorial plane, and energy feedback from supernovae enhances their scale height. Molecular hydrogen exists in a hot phase ( > 1000 K) as well as in a cold ( $10^3$ cm$^{-3}$) phase. The velocity dispersion of H$_2$ in the vertical direction is comparable to the rotational velocity, which is consistent with near infrared observations of nearby Seyfert galaxies. Using 3D radiation transfer calculations for the dust emission, we find polar emission in the mid-infrared band (12$\mu m$), which is associated with bipolar outflows, as suggested in recent interferometric observations of nearby AGNs. If the viewing angle for the nucleus is larger than 75 deg, the spectral energy distribution (~ 2 -- 60 $\mu m$) of this model is consistent with that of the Circinus galaxy. The multi-phase interstellar medium observed in optical/infrared and X-ray observations is also discussed.Comment: 9 pages, 5 figures. Accepted for ApJL. A movie file for Fig.5b can be downloaded from http://astrophysics.jp/Circinus

The Collegian (1964-11)

https://scholarworks.utrgv.edu/collegian/1277/thumbnail.jp

Replisome-mediated homeostasis of DNA/RNA hybrids in eukaryotic genomes is critical for cell fates and chromatin stability

During DNA replication, forks often stall upon encountering obstacles blocking their progression. Cells will act to speedily remove or overcome such barriers, thus allowing complete synthesis of chromosomes. This is the case for R-loops, DNA/RNA hybrids that arise during transcription. One mechanism to remove such R-loops involve DNA/RNA helicases. Here, I have shown that one such helicase, Sen1, associates with replisome components during S phase in the model organism S. cerevisiae. I demonstrate that the N-terminal domain of Sen1 is both sufficient and necessary for the interaction of the protein with the replisome. I also identified Ctf4 as one of at least two replisome interactors of Sen1. By mutational analysis, a mutant of Sen1 (Sen1-3) that cannot interact with the replisome was created. This mutant is healthy on its own but is lethal in the absence of both RNase H1 and H2. Overexpression of the sen1-3 allele from the constitutive ACT1 promoter is able to suppress this synthetic lethality, suggesting that Sen1 travels with replisomes in order to be quickly recruited at sites of R-loops that impair fork progression so as to remove those R-loops. In some cases, cells exploit fork stalling for biologically important processes. This is the case in Sz. pombe, where an imprint prevents complete DNA replication, triggering cell-type switching. This imprint is dependent on Pol1, a component of the replisome. Importantly, a single imprinting-defective allele of pol1 has been identified to date. Using in vitro assays, I have shown that this Pol1 mutant has reduced affinity for its substrates and is a correspondingly poor polymerase. By generating novel alleles of pol1, I have also demonstrated that switching-deficiency correlates with the affinity of Pol1 for its substrates in vivo. Finally, two interactors of Pol1 (Mcl1Ctf4 and Spp1Pri1 ) have been shown to have switching defects. S. cerevisiae and Sz. pombe have similar yet distinct genetic nomenclature conventions. Given that both model organisms were used in this study, it is important to highlight the conventions for both organisms to prevent confusion. In S. cerevisiae, wildtype gene names are expressed as a three letter, uppercase and italic name followed by a number (e.g. SEN1). The three letter name often corresponds to the screen through which the gene in question was originally identified. Mutants are generally designated with the same three letter but in lower case (unless the mutant is dominant) and with an allele designation (e.g. sen1∆, sen1-1 and sen1-2). Because of historical context, the allele designations vary in format (e.g. leu2-3,112 is a mutant of LEU2). Protein names are given as a three letter name with the first letter in uppercase (e.g. Sen1). This is also true for mutant proteins, with the added allele designation (e.g Sen1-1 and Sen1-2). In this study, I have generated constructs of the SEN1 gene and these constructs are referred to as SEN1 (X-Y), where X and Y refer to the first and last residues being encoded for. The corresponding proteins are referred to as Sen1 (X-Y). Different promoters have been used and, where appropriate, the promoters are expressed similarly to their wildtype gene names (e.g. GAL1, SEN1 and ACT1). In Sz. pombe, wildtype gene names are expressed as a three letter, lowercase and italic name followed by a number (e.g. pol1). Mutants are generally designated in the same format but with an allele designation. Like in S. cerevisiae, the allele designation varies widely (e.g. pol1-1, pol1-H4 and pol1-ts13). Additionally, because of the historical context, some (but not all) alleles of pol1 are referred to as swi7 to reflect the fact that they are defective for cell-type switching. Similar to the situation in S. cerevisiae, proteins names are given as a three letter name with the first letter in uppercase for both wildtype and mutants (e.g. Pol1 and Swi7-1). Sometimes, for the sake of comparison, genes or proteins are referred to their S. cerevisiae orthologues (e.g. swi1TOF1 and Swi1Tof1 , respectively). Several protein tags have been used in this study. When written in gene form, they were written in capital letters and italicized, irrespective of the host (e.g. 5FLAG) and when in protein form, they were written in capital, irrespective of the host (e.g. 5FLAG)

Songlines from Direct Collapse Seed Black Holes: Effects of X-rays on Black Hole Growth and Stellar Populations

In the last decade, the growth of supermassive black holes (SMBHs) has been intricately linked to galaxy formation and evolution and is a key ingredient in the assembly of galaxies. To investigate the origin of SMBHs, we perform cosmological simulations that target the direct collapse black hole (DCBH) seed formation scenario in the presence of two different strong Lyman-Werner (LW) background fields. These simulations include the X-ray irradiation from a central massive black hole (MBH), $\rm{H}_2$ self-shielding and stellar feedback from metal-free and metal-enriched stars. We find in both simulations that local X-ray feedback induces metal-free star formation $\sim 0.5$ Myr after the MBH forms. The MBH accretion rate reaches a maximum of $10^{-3}$ $M_{\odot}$ yr$^{-1}$ in both simulations. However, the duty cycle differs which is derived to be $6\%$ and $50\%$ for high and low LW cases, respectively. The MBH in the high LW case grows only $\sim 6\%$ in 100 Myr compared to $16\%$ in the low LW case. We find that the maximum accretion rate is determined by the local gas thermodynamics whereas the duty cycle is determined by the large scale gas dynamics and gas reservoir. We conclude that radiative feedback from the central MBH plays an important role in star formation in the nuclear regions and stifling initial MBH growth, relative to the typical Eddington rate argument, and that initial MBH growth might be affected by the local LW radiation field.Comment: 8 pages, 6 figures. Accepted for publication in ApJ, with minor changes to submitted versio

Tracing the Physical Conditions in Active Galactic Nuclei with Time-Dependent Chemistry

We present an extension of the code ProDiMo that allows for a modeling of processes pertinent to active galactic nuclei and to an ambient chemistry that is time dependent. We present a proof-of-concept and focus on a few astrophysically relevant species, e.g., H+, H2+ and H3+; C+ and N+; C and O; CO and H2O; OH+, H2O+ and H3O+; HCN and HCO+. We find that the freeze-out of water is strongly suppressed and that this affects the bulk of the oxygen and carbon chemistry occurring in AGN. The commonly used AGN tracer HCN/HCO+ is strongly time-dependent, with ratios that vary over orders of magnitude for times longer than 10^4 years. Through ALMA observations this ratio can be used to probe how the narrow-line region evolves under large fluctuations in the SMBH accretion rate. Strong evolutionary trends, on time scales of 10^4-10^8 years, are also found in species such as H3O+, CO, and H2O. These reflect, respectively, time dependent effects in the ionization balance, the transient nature of the production of molecular gas, and the freeze-out/sublimation of water.Comment: Accepted for publication at the Journal of Physical Chemistry A "Oka Festschrift: Celebrating 45 Years of Astrochemistry

X-ray Ionization of Heavy Elements Applied to Protoplanetary Disks

The consequences of the Auger effect on the population of heavy-element ions are analyzed for the case of relatively cool gas irradiated by keV X-rays with intended applications to the accretion disks of young stellar objects. Highly charged ions are rapidly reduced to the doubly charged state in neutral gas, so the aim here is to derive the production rates for these singly and doubly charged ions and to specify their transformation by recombination, charge transfer, and molecular reactions. The theory is illustrated by calculations of the abundance

Models of the ISM in galaxy centers

Part I: M51 is observed at a wavelength of 850 mum, where most radiation is emitted by dust. We find prominent spiral arms and an underlying exponential disk. The properties of the disk and the arms are studied. Part II and III: Gas in Galaxy Centers is exposed to intense radiation from a starburst region, an Active Galactic Nucleus (AGN), or both. The OB stars in starforming regions mostly radiate in the far-ultraviolet (FUV) and accreting black holes mostly in the X-ray regime. FUV and X-ray photons lead to a totally different chemical composition of gas clouds. Therefore, molecules such as H2, CO, HCN and HCO+ emit different line intensities. In the thesis, we model the line emission of the molecules in these gas clouds with Photon Dominated Regions models (FUV: PDR) and X-ray Dominated Region models (X-rays: XDR). These models are applied to nearby active galaxies such as NGC 253 and NGC 1068.Leiden Observatory LKBFUBL - phd migration 201