Modeling the HeII Transverse Proximity Effect: Constraints on Quasar Lifetime and Obscuration

The HeII transverse proximity effect - enhanced HeII Ly{\alpha} transmission in a background sightline caused by the ionizing radiation of a foreground quasar - offers a unique opportunity to probe the emission properties of quasars, in particular the emission geometry (obscuration, beaming) and the quasar lifetime. Building on the foreground quasar survey published in Schmidt+2017, we present a detailed model of the HeII transverse proximity effect, specifically designed to include light travel time effects, finite quasar ages, and quasar obscuration. We post-process outputs from a cosmological hydrodynamical simulation with a fluctuating HeII UV background model, plus the added effect of the radiation from a single bright foreground quasar. We vary the age $t_\mathrm{age}$ and obscured sky fractions $\Omega_\mathrm{obsc}$ of the foreground quasar, and explore the resulting effect on the HeII transverse proximity effect signal. Fluctuations in IGM density and the UV background, as well as the unknown orientation of the foreground quasar, result in a large variance of the HeII Ly{\alpha} transmission along the background sightline. We develop a fully Bayesian statistical formalism to compare far UV HeII Ly{\alpha} transmission spectra of the background quasars to our models, and extract joint constraints on $t_\mathrm{age}$ and $\Omega_\mathrm{obsc}$ for the six Schmidt+2017 foreground quasars with the highest implied HeII photoionization rates. Our analysis suggests a bimodal distribution of quasar emission properties, whereby one foreground quasar, associated with a strong HeII transmission spike, is relatively old $(22\,\mathrm{Myr})$ and unobscured $\Omega_\mathrm{obsc}<35\%$, whereas three others are either younger than $(10\,\mathrm{Myr})$ or highly obscured $(\Omega_\mathrm{obsc}>70\%)$.Comment: 19 pages, 6 figures, submitted to Ap

A stringent yeast two-hybrid matrix screening approach for protein-protein interaction discovery

The yeast two-hybrid (Y2H) system is currently one of the most important techniques for protein-protein interaction (PPI) discovery. Here, we describe a stringent three-step Y2H matrix interaction approach that is suitable for systematic PPI screening on a proteome scale. We start with the identification and elimination of autoactivating strains that would lead to false-positive signals and prevent the identification of interactions. Nonautoactivating strains are used for the primary PPI screen that is carried out in quadruplicate with arrayed preys. Interacting pairs of baits and preys are identified in a pairwise retest step. Only PPI pairs that pass the retest step are regarded as potentially biologically relevant interactions and are considered for further analysis

A Definitive Survey for Lyman Limit Systems at z~3.5 with the Sloan Digital Sky Survey

We perform a semi-automated survey for tau>=2 Lyman Limit systems (LLSs) in quasar spectra from the Sloan Digital Sky Survey, Data Release 7. From a starting sample of 2473 quasars with zem=3.6-4.4, we analyze 469 spectra meeting strict seletion criteria for a total redshift path Dz=93.8 and identify 192 intervening systems at z>3.3. The incidence of tau>=2 LLSs per unit redshift, l(z), is well described by a single-power law at these redshifts: l(z) = C_LLS [(1+z)/(1+z_*)]^gamma, with z_*=3.7, C_LLS = 1.9+/-0.2, and gamma = 5.2+/-1.5 (68% c.l.). These values are systematically lower than previous estimates (especially at z<4) but are consistent with recent measurements of the mean free path to ionizing radiation. Extrapolations of this power-law to z=0 are inconsistent with previous estimations of l(z) at z<1 and suggest a break at z~2, similar to that observed for the Lya forest. Our results also indicate that the systems giving rise to LLS absorption decrease by ~50% in comoving number density and/or physical size from z=4 to 3.3, perhaps due to an enhanced extragalactic ultraviolet background. The observations place an integral constraint on the HI frequency distribution f(N_HI,X) and indicate that the power-law slope beta= dln[f(N,X)]/dln[N] is likely shallower than beta = -1 at N_HI=10^18 cm^-2. Including other constraints on f(N_HI,X) from the literature, we infer that beta is steeper than beta = -1.7 at N_HI~10^15 cm^-2, implying at least two inflections in f(N_HI,X). We also perform a survey for proximate LLSs (PLLSs) and find that l(z)_PLLS is systematically lower ~25% than intervening systems. Finally, we estimate that systematic effects impose an uncertainty of 10-20% in the l(z) measurements; these effects may limit the precision of all future surveys.Comment: 26 pages, 17 figures (most in color). Submitted to Ap

Chemical abundances of damped Lyman alpha systems in the XQ-100 survey

The XQ-100 survey has provided high signal-noise spectra of 100 redshift 3-4.5 quasars with the X-Shooter spectrograph. The metal abundances for 13 elements in the 41 damped Lyman alpha systems (DLAs) identified in the XQ-100 sample are presented, and an investigation into abundances of a variety of DLA classes is conducted. The XQ-100 DLA sample contains five DLAs within 5000 km/s of their host quasar (proximate DLAs; PDLAs) as well as three sightlines which contain two DLAs within 10,000 km/s of each other along the same line-of-sight (multiple DLAs; MDLAs). Combined with previous observations in the literature, we demonstrate that PDLAs with logN(HI)<21.0 show lower [S/H] and [Fe/H] (relative to intervening systems with similar redshift and N(HI)), whilst higher [S/H] and [Si/H] are seen in PDLAs with logN(HI)>21.0. These abundance discrepancies are independent of their line-of-sight velocity separation from the host quasar, and the velocity width of the metal lines (v90). Contrary to previous studies, MDLAs show no difference in [alpha/Fe] relative to single DLAs matched in metallicity and redshift. In addition, we present follow-up UVES data of J0034+1639, a sightline containing three DLAs, including a metal-poor DLA with [Fe/H]=-2.82 (the third lowest [Fe/H] in DLAs identified to date) at z=4.25. Lastly we study the dust-corrected [Zn/Fe], emphasizing that near-IR coverage of X-Shooter provides unprecedented access to MgII, CaII and TiII lines (at redshifts 3-4) to provide additional evidence for subsolar [Zn/Fe] ratio in DLAs.Comment: Accepted to MNRAS. 19 pages plus Appendix material (102 pages total

The HST/ACS+WFC3 Survey for Lyman Limit Systems II: Science

We present the first science results from our Hubble Space Telescope Survey for Lyman limit absorption systems (LLS) using the low dispersion spectroscopic modes of the Advanced Camera for Surveys and the Wide Field Camera 3. Through an analysis of 71 quasars, we determine the incidence frequency of LLS per unit redshift and per unit path length, l(z) and l(x) respectively, over the redshift range 1 < z< 2.6, and find a weighted mean of l(x)=0.29 +/-0.05 for 2.0 < z < 2.5 through a joint analysis of our sample and that of Ribaudo et al. (2011). Through stacked spectrum analysis, we determine a median (mean) value of the mean free path to ionizing radiation at z=2.4 of lambda_mfp = 243(252)h^(-1) Mpc, with an error on the mean value of +/- 43h^(-1) Mpc. We also re-evaluate the estimates of lambda_mfp from Prochaska et al. (2009) and place constraints on the evolution of lambda_mfp with redshift, including an estimate of the "breakthrough" redshift of z = 1.6. Consistent with results at higher z, we find that a significant fraction of the opacity for absorption of ionizing photons comes from systems with N_HI <= 10^{17.5} cm^(-2) with a value for the total Lyman opacity of tau_lyman = 0.40 +/- 0.15. Finally, we determine that at minimum, a 5-parameter (4 power-law) model is needed to describe the column density distribution function f(N_HI, X) at z \sim 2.4, find that f(N_HI,X) undergoes no significant change in shape between z \sim 2.4 and z \sim 3.7, and provide our best fit model for f(N_HI,X).Comment: 36 pages, 20 figures, 10 tables, revision to match accepted ApJ versio

A Direct Measurement of the IGM Opacity to HI Ionizing Photons

We present a new method to directly measure the opacity from HI Lyman limit (LL) absorption k_LL along quasar sightlines by the intergalactic medium (IGM). The approach analyzes the average (``stacked'') spectrum of an ensemble of quasars at a common redshift to infer the mean free path (MFP) to ionizing radiation. We apply this technique to 1800 quasars at z=3.50-4.34 drawn from the Sloan Digital Sky Survey (SDSS), giving the most precise measurements on k_LL at any redshift. From z=3.6 to 4.3, the opacity increases steadily as expected and is well parameterized by MFP = (48.4 +/- 2.1) - (38.0 +/- 5.3)*(z-3.6) h^-1 Mpc (proper distance). The relatively high MFP values indicate that the incidence of systems which dominate k_LL evolves less strongly at z>3 than that of the Lya forest. We infer a mean free path three times higher than some previous estimates, a result which has important implications for the photo-ionization rate derived from the emissivity of star forming galaxies and quasars. Finally, our analysis reveals a previously unreported, systematic bias in the SDSS quasar sample related to the survey's color targeting criteria. This bias potentially affects all z~3 IGM studies using the SDSS database.Comment: 7 pages, 4 figures; Accepted to ApJ

Nature and statistical properties of quasar associated absorption systems in the XQ-100 Legacy Survey

We statistically study the physical properties of a sample of narrow absorption line (NAL) systems looking for empirical evidences to distinguish between intrinsic and intervening NALs without taking into account any a priori definition or velocity cut-off. We analyze the spectra of 100 quasars with 3.5 < z$\rm_{em}$ < 4.5, observed with X-shooter/VLT in the context of the XQ-100 Legacy Survey. We detect a $\sim$ 8 $\sigma$ excess in the number density of absorbers within 10,000 km/s of the quasar emission redshift with respect to the random occurrence of NALs. This excess does not show a dependence on the quasar bolometric luminosity and it is not due to the redshift evolution of NALs. It extends far beyond the standard 5000 km/s cut-off traditionally defined for associated absorption lines. We propose to modify this definition, extending the threshold to 10,000 km/s when also weak absorbers (equivalent width < 0.2 \AA) are considered. We infer NV is the ion that better traces the effects of the quasar ionization field, offering the best statistical tool to identify intrinsic systems. Following this criterion we estimate that the fraction of quasars in our sample hosting an intrinsic NAL system is 33 percent. Lastly, we compare the properties of the material along the quasar line of sight, derived from our sample, with results based on close quasar pairs investigating the transverse direction. We find a deficiency of cool gas (traced by CII) along the line of sight associated with the quasar host galaxy, in contrast with what is observed in the transverse direction.Comment: 18 pages, 13 figures, 5 table