ALBERT

Description: Using hydrodynamical simulations, we show for the first time that an episode of star formation in the centre of the Milky Way, with a star formation rate (SFR) ~0.5 M  yr –1 for ~30 Myr, can produce bubbles that resemble the Fermi bubbles (FBs), when viewed from the solar position. The morphology, extent and multiwavelength observations of FBs, especially X-rays, constrain various physical parameters such as SFR, age, and the circumgalactic medium (CGM) density. We show that the interaction of the CGM with the Galactic wind driven by star formation in the central region can explain the observed surface brightness and morphological features of X-rays associated with the FBs. Furthermore, assuming that cosmic ray electrons are accelerated in situ by shocks and/or turbulence, the brightness and morphology of -ray emission and the microwave haze can be explained. The kinematics of the cold and warm clumps in our model also matches with recent observations of absorption lines through the bubbles.

Description: Bondi accretion assumes that there is a sink of mass at the centre – which in the case of a black hole (BH) corresponds to the advection of matter across the event horizon. Other stars, such as a neutron star (NS), have surfaces and hence the infalling matter has to slow down at the surface. We study the initial value problem in which the matter distribution is uniform and at rest at t = 0. We consider different inner boundary conditions for BHs and NSs: outflow boundary condition (mimicking mass sink at the centre) valid for BHs; and reflective and steady-shock (allowing gas to cross the inner boundary at subsonic speeds) boundary conditions for NSs. We also obtain a similarity solution for cold accretion on to BHs and NSs. 1D simulations show the formation of an outward-propagating and a standing shock in NSs for reflective and steady-shock boundary conditions, respectively. Entropy is the highest at the bottom of the subsonic region for reflective boundary conditions. In 2D this profile is convectively unstable. Using steady-shock inner boundary conditions, the flow is unstable to the standing accretion shock instability in 2D, which leads to global shock oscillations and may be responsible for quasi-periodic oscillations seen in the light curves of accreting systems. For steady accretion in the quiescent state, spherical accretion rate on to an NS can be suppressed by orders of magnitude compared to that on to a BH.

Description: Computational modeling is employed to provide a plausible structural explanation for the experimentally-observed differential global genome repair (GGR) propensity of the ALII-N 2 -dG and ALII-N 6 -dA DNA adducts of aristolochic acid II. Our modeling studies suggest that an intrinsic twist at the carcinogen–purine linkage of ALII-N 2 -dG induces lesion site structural perturbations and conformational heterogeneity of damaged DNA. These structural characteristics correlate with the relative repair propensities of AA-adducts, where GGR recognition occurs for ALII-N 2 -dG, but is evaded for intrinsically planar ALII-N 6 -dA that minimally distorts DNA and restricts the conformational flexibility of the damaged duplex. The present analysis on the ALII adduct model systems will inspire future experimental studies on these adducts, and thereby may extend the list of structural factors that directly correlate with the propensity for GGR recognition.

Description: Traditionally the thermodynamic profiles (gas density, temperature, etc.) of galaxy clusters are obtained by assuming spherical symmetry and modelling projected X-ray spectra in each annulus. The outer annuli contribute to the inner ones and their contribution needs to be subtracted to obtain the temperature and density of spherical shells. The usual deprojection methods lead to propagation of errors from outside to in and typically do not model the covariance of parameters in different radial shells. In this paper we describe a method based on a free-form model of clusters with cluster parameters (density, temperature) given in spherical shells, which we jointly forward fit to the X-ray data by constructing a Bayesian posterior probability distribution that we sample using the MCMC technique. By systematically marginalizing over the nuisance outer shells, we estimate the inner entropy profiles of clusters and fit them to various models for a sample of Chandra X-ray observations of 17 clusters. We show that the entropy profiles in almost all of our clusters are best described as cored power laws. A small subsample is found to be either consistent with a power law, or alternatively their cores are not fully resolved (smaller than, or about few kpc). We find marginal evidence for bimodality in the central values of entropy (and cooling time) corresponding to cool-core and non cool-core clusters. The minimum value of the ratio of the cooling time and the free-fall time (min[ t cool / t ff ]; correlation is much weaker with core entropy) is anti-correlated with H α and radio luminosity. H α emitting cold gas is absent in our clusters with min( t cool / t ff ) 10. Our lowest core entropies are systematically and substantially lower than the values quoted by the ACCEPT sample.

Description: In this paper we calculate the escape fraction ( f esc ) of ionizing photons from starburst galaxies. Using 2D axisymmetric hydrodynamic simulations, we study superbubbles created by overlapping supernovae in OB associations. We calculate the escape fraction of ionizing photons from the centre of the disc along different angles through the superbubble and the gas disc. After convolving with the luminosity function of OB associations, we show that the ionizing photons escape within a cone of ~40°, consistent with observations of nearby galaxies. The evolution of the escape fraction with time shows that it falls initially as cold gas is accumulated in a dense shell. After the shell crosses a few scaleheights and fragments, the escape fraction through the polar regions rises again. The angle-averaged escape fraction cannot exceed ~[1 – cos (1 rad)] = 0.5 from geometrical considerations (using the emission cone opening angle). We calculate the dependence of the time- and angle-averaged escape fraction on the mid-plane disc gas density (in the range n 0 = 0.15–50 cm –3 ) and the disc scaleheight (between z 0 = 10 and 600 pc). We find that the escape fraction is related to the disc parameters (the mid-plane disc density and scaleheight) roughly so that $f_{\rm esc}^\alpha n_0^2 z_0^3$ (with α 2.2) is a constant. For discs with a given warm neutral medium temperature, massive discs have lower escape fraction than low-mass galaxies. For Milky Way ISM parameters, we find f esc ~ 5 per cent, and it increases to 10 per cent for a galaxy 10 times less massive. We discuss the possible effects of clumpiness of the ISM on the estimate of the escape fraction and the implications of our results for the reionization of the Universe.

Description: Using hydrodynamic simulations, we study the mass-loss due to supernova-driven outflows from Milky Way type disc galaxies, paying particular attention to the effect of the extended hot halo gas. We find that the total mass-loss at inner radii scales roughly linearly with total mass of stars formed, and that the mass loading factor at the virial radius can be several times its value at inner radii because of the swept up hot halo gas. The temperature distribution of the outflowing material in the inner region (~10 kpc) is bimodal in nature, peaking at 10 5  K and 10 6.5  K, responsible for optical and X-ray emission, respectively. The contribution of cold/warm gas with temperature ≤10 5.5 K to the outflow rate within 10 kpc is 0.3–0.5. The warm mass loading factor, 3 e 5 ( T  ≤ 3 10 5  K) is related to the mass loading factor at the virial radius ( v ) as v   25 3 e 5 (SFR/M yr –1 ) –0.15 for a baryon fraction of 0.1 and a starburst period of 50 Myr. We also discuss the effect of multiple bursts that are separated by both short and long periods. The outflow speed at the virial radius is close to the sound speed in the hot halo,  200 km s –1 . We identify two ‘sequences’ of outflowing cold gas at small scales: a fast (500 km s –1 ) sequence, driven by the unshocked free-wind; and a slow sequence (± 100 km s –1 ) at the conical interface of the superwind and the hot halo.

Description: Expression of viral proteins frequently includes non-canonical decoding events (‘recoding’) during translation. ‘2A’ oligopeptides drive one such event, termed ‘stop-carry on’ recoding. Nascent 2A peptides interact with the ribosomal exit tunnel to dictate an unusual stop codon-independent termination of translation at the final Pro codon of 2A. Subsequently, translation ‘reinitiates’ on the same codon, two individual proteins being generated from one open reading frame. Many 2A peptides have been identified, and they have a conserved C-terminal motif. Little similarity is present in the N-terminal portions of these peptides, which might suggest that these amino acids are not important in the 2A reaction. However, mutagenesis indicates that identity of the amino acid at nearly all positions of a single 2A peptide is important for activity. Each 2A may then represent a specific solution for positioning the conserved C-terminus within the peptidyl-transferase centre to promote recoding. Nascent 2A peptide:ribosome interactions are suggested to alter ribosomal fine structure to discriminate against prolyl-tRNA Pro and promote termination in the absence of a stop codon. Such structural modifications may account for our observation that replacement of the final Pro codon of 2A with any stop codon both stalls ribosome processivity and inhibits nascent chain release.

Description: Using hydrodynamical simulations, we show for the first time that an episode of star formation in the centre of the Milky Way, with a star formation rate (SFR) ~0.5 M  yr –1 for ~30 Myr, can produce bubbles that resemble the Fermi bubbles (FBs), when viewed from the solar position. The morphology, extent and multiwavelength observations of FBs, especially X-rays, constrain various physical parameters such as SFR, age, and the circumgalactic medium (CGM) density. We show that the interaction of the CGM with the Galactic wind driven by star formation in the central region can explain the observed surface brightness and morphological features of X-rays associated with the FBs. Furthermore, assuming that cosmic ray electrons are accelerated in situ by shocks and/or turbulence, the brightness and morphology of -ray emission and the microwave haze can be explained. The kinematics of the cold and warm clumps in our model also matches with recent observations of absorption lines through the bubbles.

Description: We study the effects of optically thin radiative cooling on the structure of radiatively inefficient accretion flows (RIAFs). The flow structure is geometrically thick, and independent of the gas density and cooling, if the cooling time is longer than the viscous time-scale (i.e. t cool    t visc ). For higher densities, the gas can cool before it can accrete and forms the standard geometrically thin, optically thick Shakura–Sunyaev disc. For usual cooling processes (such as bremsstrahlung), we expect an inner hot flow and an outer thin disc. For a short cooling time the accretion flow separates into two phases: a radiatively inefficient hot coronal phase and a cold thin disc. We argue that there is an upper limit on the density of the hot corona corresponding to a critical value of t cool / t ff ( ~ 10–100), the ratio of the cooling time and the free-fall time. Based on our simulations, we have developed a model for transients observed in black hole X-ray binaries (XRBs). An XRB in a quiescent hot RIAF state can transition to a cold blackbody-dominated state because of an increase in the mass accretion rate. The transition from a thin disc to a RIAF happens because of mass exhaustion due to accretion; the transition happens when the cooling time becomes longer than the viscous time at inner radii. Since the viscous time-scale for a geometrically thin disc is quite long, the high-soft state is expected to be long-lived. The different time-scales in black hole transients correspond to different physical processes such as viscous evolution, cooling and free fall. Our model captures the overall features of observed state transitions in XRBs.

Description: We examine the role of thermal conduction and magnetic fields in cores of galaxy clusters through global simulations of the intracluster medium (ICM). In particular, we study the influence of thermal conduction, both isotropic and anisotropic, on the condensation of multiphase gas in cluster cores. Previous hydrodynamic simulations have shown that cold gas condenses out of the hot ICM in thermal balance only when the ratio of the cooling time ( t cool ) and the free-fall time ( t ff ) is less than 10. Since thermal conduction is significant in the ICM and it suppresses local cooling at small scales, it is imperative to include thermal conduction in such studies. We find that anisotropic (along local magnetic field lines) thermal conduction does not influence the condensation criterion for a general magnetic geometry, even if thermal conductivity is large. However, with isotropic thermal conduction cold gas condenses only if conduction is suppressed (by a factor 0.3) with respect to the Spitzer value.