We obtained high-resolution Far Ultraviolet Spectroscopic Explorer (FUSE; R ∼ 20,000) and Very Large Telescope (VLT; R ∼ 45,000) spectra of the quasar HE 2347-4342 in order to study the properties of the intergalactic medium between redshifts z = 2.0 and 2.9. The high-quality optical spectrum allows us to identify approximately 850 H I absorption lines with column densities between N ∼ 5×1011 and 1018 cm-2. The reprocessed FUSE spectrum extends the wavelength coverage of the He II absorption down to an observed wavelength of 920 Å. Source flux is detected to rest-frame wavelengths as short as ∼237 Å. Approximately 1400 He II absorption lines are identified, including 917 He II Lyα systems and some of their He II Lyβ, Lyγ, and Lyδ counterparts. The ionization structure of He II is complex, with approximately 90 absorption lines that are not detected in the hydrogen spectrum. These features may represent the effect of soft ionizing sources. The ratio η = N(He II)/N(H I) varies approximately from unity to more than a thousand, with a median value of 62 and a distribution consistent with the intrinsic spectral indexes of quasars. This provides evidence that the dominant ionizing field is from the accumulated quasar radiation, with contributions from other soft sources such as star-forming regions and obscured active galactic nuclei, which do not ionize helium. We find an evolution in η toward smaller values at lower redshift, with the gradual disappearance of soft components. At redshifts z > 2.7, the large but finite increase in the He II opacity, τ = 5 ± 1, suggests that we are viewing the end stages of a reionization process that began at an earlier epoch. Fits of the absorption profiles of unblended lines indicate comparable velocities between hydrogen and He+ ions. For line widths bHe+He+ = ξbH, we find ξ = 0.95 ± 0.12, indicating a velocity field in the intergalactic medium dominated by turbulence. At hydrogen column densities N < 3 × 1012 cm-2, the number of forest lines shows a significant deficit relative to a power law and becomes negligible below N = 1011 cm-2.

I present spectroscopic measurements for 260 sources from the Gemini Near Infrared Spectrograph–Distant Quasar Survey (GNIRS-DQS). Being the largest uniform, homogeneous survey of its kind, it represents a flux-limited sample of Sloan Digital Sky Survey (SDSS) quasars at 1.5 < z < 3.5. A combination of the GNIRS and SDSS spectra covers principal quasar diagnostic features, chiefly the C IV λ1549, Mg II λλ2798, 2803, Hβ λ4861, and [O III] λλ4959, 5007 emission lines, in each source. The spectral inventory is utilized primarily to develop prescriptions for obtaining more accurate and precise redshifts, black hole masses, and accretion rates for all quasars. Additionally, the measurements facilitate an understanding of the dependence of rest-frame ultraviolet–optical spectral properties of quasars on redshift, luminosity, and Eddington ratio, and test whether the physical properties of the quasar central engine evolve over cosmic time.

The diffuse interstellar bands (DIBs) probably arise from complex organic molecules whose strength in local galaxies correlates with neutral hydrogen column density, N(H I), and dust reddening, E(B−V). Because Damped Lyman-α systems are known to have high N(H I), and Ca II absorbers in quasar (QSO) spectra are posited to have high N(H I) and reddening, both represent promising sites for the detection of DIBs at cosmological distances. I present the results of a search for diffuse bands in seven DLAs and nine Ca II absorbers. I announce the detection of the first narrow DIBs at z>0 towards one DLA and one Ca II system. I further investigate the relative strengths of the DIBs as well as their correlations with N(H I) and E(B−V). Finally, I discuss the prospects for using DIBs to better understand the properties of quasar absorption systems, and for using DIB searches in absorption systems to better understand the properties of DIBs.

The diffuse interstellar bands (DIBs) probably arise from complex organic molecules whose strength in local galaxies correlates with neutral hydrogen column density, N(H I), and dust reddening, E(B−V). Because Damped Lyman-α systems are known to have high N(H I), and Ca II absorbers in quasar (QSO) spectra are posited to have high N(H I) and reddening, both represent promising sites for the detection of DIBs at cosmological distances. I present the results of a search for diffuse bands in seven DLAs and nine Ca II absorbers. I announce the detection of the first narrow DIBs at z>0 towards one DLA and one Ca II system. I further investigate the relative strengths of the DIBs as well as their correlations with N(H I) and E(B−V). Finally, I discuss the prospects for using DIBs to better understand the properties of quasar absorption systems, and for using DIB searches in absorption systems to better understand the properties of DIBs.

We present Hubble Space Telescope far-UV spectra of four QSOs whose sightlines pass through the halo of NGC 1097 at impact parameters of rho = 48-165 kpc. NGC 1097 is a nearby spiral galaxy that has undergone at least two minor merger events, but no apparent major mergers, and is relatively isolated with respect to other nearby bright galaxies. This makes NGC 1097 a good case study for exploring baryons in a paradigmatic bright-galaxy halo. Ly alpha absorption is detected along all sightlines and Si III lambda 1206 is found along the three sightlines with the smallest.; metal lines of C II, Si II, and Si IV are only found with certainty toward the innermost sightline. The kinematics of the absorption lines are best replicated by a model with a disk-like distribution of gas approximately planar to the observed 21 cm H I disk, which is rotating more slowly than the inner disk, and into which gas is infalling from the intergalactic medium. Some part of the absorption toward the innermost sightline may arise either from a small-scale outflow or from tidal debris associated with the minor merger that gives rise to the well known "dog-leg" stellar stream that projects from NGC 1097. When compared to other studies, NGC 1097 appears to be a "typical" absorber, although the large dispersion in absorption line column density and equivalent width in a single halo goes perhaps some way toward explaining the wide range of these values seen in higher-z studies.

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 analyse the spectra of 100 quasars with 3.5 < z(em) < 4.5, observed with X-shooter/Very Large Telescope in the context of the XQ-100 Legacy Survey. We detect an similar to 8 sigma excess in the CIV number density within 10 000 km s(-1) 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(-1) cutoff traditionally defined for associated absorption lines. We propose to modify this definition, extending the threshold to 10 000 km s(-1) when weak absorbers (equivalent width < 0.2 angstrom) are also 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 per cent. 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 C II) along the line of sight connected to the quasar host galaxy, in contrast with what is observed in the transverse direction.

Context. Over the past few years, on several occasions, large, continuous rotations of the electric vector position angle (EVPA) of linearly polarized optical emission from blazars have been reported. These events are often coincident with high energy gamma-ray flares and they have attracted considerable attention, since they could allow us to probe the magnetic field structure in the gamma-ray emitting region of the jet. The flat-spectrum radio quasar 3C 279 is one of the most prominent examples showing this behaviour. Aims. Our goal is to study the observed EVPA rotations and to distinguish between a stochastic and a deterministic origin of the polarization variability. Methods. We have combined multiple data sets of R-band photometry and optical polarimetry measurements of 3C 279, yielding exceptionally well-sampled flux density and polarization curves that cover a period of 2008-2012. Several large EVPA rotations are identified in the data. We introduce a quantitative measure for the EVPA curve smoothness, which is then used to test a set of simple random walk polarization variability models against the data. Results. 3C 279 shows different polarization variation characteristics during an optical low-flux state and a flaring state. The polarization variation during the flaring state, especially the smooth similar to 360 degrees rotation of the EVPA in mid-2011, is not consistent with the tested stochastic processes. Conclusions. We conclude that, during the two different optical flux states, two different processes govern polarization variation, which is possibly a stochastic process during the low-brightness state and a deterministic process during the flaring activity.

Modern cosmology predicts that a galaxy overdensity (e.g., protocluster) will be associated with a large intergalactic medium gas reservoir, which can be traced by Ly alpha forest absorption. We have undertaken a systematic study of the relation between Coherently Strong intergalactic Lya Absorption systems (CoSLAs), which have the highest optical depth (tau) in the tau distribution, and mass overdensities on the scales of similar to 10-20 h(-1) comoving Mpc. On such large scales, our cosmological simulations show a strong correlation between the effective optical depth (tau(eff)) of the CoSLAs and the three-dimensional mass overdensity. In spectra with moderate signal-to-noise ratio, however, the profiles of CoSLAs can be confused with individual high column density absorbers. For z > 2.6, where the corresponding Ly beta is redshifted to the optical, we have developed a selection technique to distinguish between these two alternatives. We have applied this technique to similar to 6000 sight lines provided by Sloan Digital Sky Survey III quasar survey at z = 2.6-3.3 with a continuum-to-noise ratio greater than 8, and we present a sample of five CoSLA candidates with tau(eff) on 15 h(-1) Mpc greater than 4.5x the mean optical depth. At lower redshifts of z < 2.6, where the background quasar density is higher, the overdensity can be traced by intergalactic absorption groups using multiple sight lines with small angular separations. Our overdensity searches fully use the current and next generation of Ly alpha forest surveys, which cover a survey volume of > 1 (h(-1) Gpc)(3). Systems traced by CoSLAs will yield a uniform sample of the most massive overdensities at z > 2 to provide stringent constraints to models of structure formation.

Angular differential imaging provides a novel way of probing high contrast regions of our universe. Until now, its applications have been primarily localized to searching for exoplanets around nearby stars. This work presents a suite of applications of angular differential imaging from the theoretical underpinning of data reduction, to its use characterizing substellar objects, to a new application looking for the host galaxies of damped Lyman α systems which are usually lost in the glare of ultra-bright quasars along the line of sight. The search for exoplanets utilizes angular differential imaging and relies on complex algorithms to remove residual speckles and artifacts in the images. One such algorithm, the Template Locally Optimized Combination of Images (TLOCI), uses a least-squares method to maximize the signal-to-noise ratio and can be used with variable parameters, such as an input spectral template, matrix inversion method, aggressivity and unsharp mask size. Given the large volume of image sequences that need to be processed in any exoplanet survey, it is important to find a small set of parameters that can maximize detections for any conditions. Rigorous testing of these parameters were done with on-sky images and simulated inserted planets to find the optimal combination of parameters. Overall, a standard matrix inversion, along with two to three input templates, a modest aggressivity of 0.7 and the smallest unsharp mask was found to be the best choice to balance optimal detection. Beyond optimizations, TLOCI has been used in conjunction with angular differential imaging to characterize substellar objects in our local solar neighbourhood. In particular, the star HD 984 was imaged as a part of the Gemini Planet Imager Exoplanet Survey. Although previously known to have a substellar companion, new imaging presented here in the H and J bands help further characterize this object. Comparisons with a library of brown dwarf spectral types found a best match to HD 984 B of a type M7±2. Orbital fitting suggests an 18 AU (70 year) orbit, with a 68% confidence interval between 12 and 27 AU. Object magnitude was used to find the luminosity, mass and temperature using DUSTY models. Although angular differential imaging has proven its value in high contrast imaging, it has largely remained in the field of substellar object detection, despite other high contrast regimes in which it could be applied. One potential application is outside the local solar neighbourhood with studies of damped Lyman α systems, which have struggled to identify host galaxies thought to be caused by systems seen in the spectra of bright quasars. Work herein presents the first application of angular differential imaging to finding the host galaxies to damped Lyman α systems. Using ADI we identified three potential systems within 30kpc of the sightline of the quasar and demonstrate the potential for future imaging of galaxies at close separations. In summary, this thesis presents a comprehensive look at multiple aspects of high contrast angular differential imaging. It explores optimizations with a data reduction algorithm, implementations characterizing substellar objects, and new applications imaging galaxies. / Graduate

This thesis presents the discovery of the first luminous z & 6.5 quasars in the VISTA kilo-degree Infrared Galaxy Survey (VIKING). After some basic quality control, quasar selection is investigated via use of initial data supplementedwith detailed modelling of the photometric and spatial distributions of stars of spectral type M, L and T, which are known to be the cause of significant contamination in quasar colour selection spaces. Optimised selection constraints are placed on detection significance and morphology and the performance of a traditional colour selection technique is compared to a Bayesian model comparison technique. The latter is found to offer a ∼10 per cent gain in completeness over traditional colour selection. Quasar candidates are ranked via Bayesian model comparison and a subset of the highest ranked objects are put forward for follow-up imaging. In June 2011, 44 high-z quasar candidates underwent deep optical i- and z- band imaging on the ESO NTT. Just 6 of these candidates were found to have optical colours consistent z & 6.5 quasars. Spectroscopic follow-up of these objects is ongoing, but thus far three new quasars have been discovered at redshifts of z=6.5, 6.7, 6.9. This discovery rate is consistentwith zero evolution in the rate of decline in quasar space density from z & 6.4. This differs fromthe latest results from UKIDSS. Further results expected from these and other surveys will begin to constrain the true nature of quasar space density evolution in the near future. The discovery of three z ≥ 6.5 quasars in VIKING is a significant highlight in the first year of VISTA science operations. These quasars will remain important probes of the high-z universe throughout the next decade.