This thesis presents the results of a study into modelling the ionisation of heavy elements in the intergalactic medium (IGM) by solving the time-dependent ionisation rate equations. An algorithm has been developed which calculates ionisation fractions of the first 30 elements (hydrogen to zinc) as a function of time, given the gas density and temperature, and the ultra-violet radiation intensity. The results from this algorithm are compared against the standard assumption of ionisation equilibrium used in previous models of IGM metals. Firstly, the new time-dependent algorithm is used to model the ionisation in uniform volumes of gas, with constant temperature, density and background radiation. Four models are performed, with different values of the ionisation parameter. The models demonstrate the timescales over which different metals in the IGM can be out of ionisation equilibrium, to investigate the conditions under which the time-dependent algorithm should be used in future modelling of metals in the IGM. The models show that for ionisation parameters U = 0.01-0.3 many metals observed in quasar absorption spectra could be out of equilibrium for up to 107 or a few times 108 years when subject to a new hard quasar spectrum. The metals' equilibrium ionisation fractions found in these time-dependent results are compared against the time-independent solutions found by Cloudy (Ferland et al., 1998, PASP, 110, 761) for the same models. Comparing to this well-established programme shows the algorithm is accurate for the most common elements, but disagreement is found for the rarer elements with incomplete atomic data. An application of the new time-dependent ionisation algorithm to a full cosmolog- ical N-body simulation is then presented. The algorithm is used to study the effects of a young quasar on the ionisation structure of metals in the surrounding IGM. An independent simulation of a quasar turning on during the Epoch of Reionisation, performed with a joint particle-mesh and radiative-transfer code (Tittley & Meiksin, 2007, MNRAS, 380, 1369), is used to provide the density, temperature and UV intensity inputs for the time-dependent algorithm. Non-equilibrium effects in the metal ionisation are seen to last for significant lengths of time, as the IGM reacts slowly to the rapid change in UV radiation. Mock quasar absorption line spectra are then generated by passing lines of sight through the simulation volume. Using the ionisation fraction results from the new algorithm, transmission functions with metal absorption features are produced, and the effect of non-equilibrium ionisation on the CII and CIV column densities and their ratio are presented.

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We study the cluster of H I and O VI absorption systems and the claimed detection of O vin absorption from the intergalactic medium at z ≈ 0.0567, associated with a group of galaxies toward the BL Lac object PKS 2155-304. As measured by spectrographs on the Hubble Space Telescope, Far Ultraviolet Spectroscopic Explorer, and Chandra, this system appears to contain gas at a variety of temperatures. We analyze this multiphase gas in a clumpy-infall model. From the absence of C IV and Si in absorption in the Lyα clouds, we infer metallicities less than 2.5%-10% of solar values. The only metals are detected in two O VI absorption components, offset by ±400 km s -1 from the group barycenter (cz ≈ 16,600 km s-1)- The O VI components may signify "nearside" and "backside" infall into the group potential well, which coincides with the claimed O VIII absorption. If the claimed O VIII detection is real, our analysis suggests that clusters of strong Lyα and O VI absorbers, associated with groups of galaxies, may be the "signposts" of shock-heated metal-enriched baryons. Through combined UV and X-ray spectra of H I and O VI, O VII, and O VIII, one may be able to clarify the heating mechanism of this multiphase gas.

Enormous Ly alpha nebulae (ELANe), unique tracers of galaxy density peaks, are predicted to lie at the nodes and intersections of cosmic filamentary structures. Previous successful searches for ELANe have focused on wide-field narrowband surveys or have targeted known sources such as ultraluminous quasi-stellar objects (QSOs) or radio galaxies. Utilizing groups of coherently strong Ly alpha absorptions, we have developed a new method to identify high-redshift galaxy overdensities and have identified an extremely massive overdensity, BOSS1441, at z = 2-3. In its density peak, we discover an ELAN that is associated with a relatively faint continuum. To date, this object has the highest diffuse Ly alpha nebular luminosity of L-nebula = 5.1 +/- 0.1 x 10(44) erg s(-1). Above the 2 sigma surface brightness limit of SBLy alpha = 4.8 x 10(-18) erg s(-1) cm(-2) arcsec(-2), this nebula has an end-to-end spatial extent of 442 kpc. This radio-quiet source also has extended C IV lambda 1549 and He II lambda 1640 emission on greater than or similar to 30 kpc scales. Note that the Ly alpha, He II, and C IV emissions all have double-peaked line profiles. Each velocity component has an FWHM of approximate to 700-1000 km s(-1). We argue that this Lya nebula could be powered by shocks due to an active galactic nucleus-driven outflow or photoionization by a strongly obscured source.

We test the galactic outflow model by probing associated galaxies of four strong intergalactic C IV absorbers at z = 5-6 using the Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) ramp narrowband filters. The four strong C IV absorbers reside at z = 5.74, 5.52, 4.95, and 4.87, with column densities ranging from N-C IV = 10(13.8) to 10(14.8) cm(-2). At z = 5.74, we detect an i-dropout Ly alpha emitter (LAE) candidate with a projected impact parameter of 42 physical kpc from the C IV absorber. This LAE candidate has a Ly alpha-based star formation rate (SFRLy alpha) of 2 M-circle dot yr(-1) and a UV-based SFR of 4 M-circle dot yr(-1). Although we cannot completely rule out that this i-dropout emitter may be an [O II] interloper, its measured properties are consistent with the C IV powered galaxy at z = 5.74. For C IV absorbers at z = 4.95 and z = 4.87, although we detect two LAE candidates with impact parameters of 160 and 200 kpc, such distances are larger than that predicted from the simulations. Therefore, we treat them as nondetections. For the system at z = 5.52, we do not detect LAE candidates, placing a 3 sigma upper limit of SFRLy alpha approximate to 1.5 M-circle dot yr(-1). In summary, in these four cases, we only detect one plausible C IV source at z = 5.74. Combining the modest SFR of the one detection and the three nondetections, our HST observations strongly support that smaller galaxies (SFRLy alpha less than or similar to 2 M-circle dot yr(-1)) are main sources of intergalactic C IV absorbers, and such small galaxies play a major role in the metal enrichment of the intergalactic medium at z greater than or similar to 5.

This dissertation presents spectroscopic studies of gas in galaxy halos and large-scale structures through high-resolution quasar absorption lines. The broad goal of this effort is to learn how galaxies acquire their gas and how they return it to the intergalactic medium, or more generally, how galaxies interact with their environment. The study of the absorption lines due to the extraplanar 21cm "Outer Arm'' (OA) of the Milky Way toward two quasars, H1821+643 and HS0624+6907, provides valuable insight into the gas accretion processes. It yields the following results. (1) The OA is a multiphase cloud and high ions show small but significant offsets in velocity and are unlikely to be cospatial with the low ions. (2) The overall metallicity of the OA is Z=0.3-0.5 of the solar abundance, but nitrogen is underabundant. (3) The abundance of N, O, and S derived are roughly consistent with outer-galaxy emission-line abundances and the metallicity gradient derived from H II regions. The similarity of the OA kinematics to several nearby high velocity clouds (HVCs, e.g. Complexes C, G, and H) suggests that these clouds could be detritus from a merging satellite galaxy. To test this hypothesis, we build up a simple model including tidal tripping, ram-pressure stripping, and dynamical friction to consider whether the OA could be debris affiliated with the Monoceros Ring. Our model can roughly reproduce the spatial and velocity characteristics of the OA. Moreover, the metallicity of the OA is similar to the higher metallcities measured in the younger stellar components of the Monoceros Ring and the progenitor candidate, the CMa overdensity. However, both our model and the Galactic warp scenario can not explain other HVCs that are likely to be related to the OA. Instead of acquiring gas, some galaxies have their gas removed through various physical processes. Ram-pressure stripping and tidal interaction are important mechanisms for galaxies to loose their gas. The high-resolution spectrum of Mrk205 combined with H I 21 cm, CO emission, and infrared observations is utilized to study a unique transforming galaxy NGC4319. We find: (1) the object has lost most of its diffuse interstellar H I. (2) molecular hydrogen remains in the disk of the galaxy. The molecular hydrogen column density is low, but the molecular gas fraction is extraordinarily high. CO emission is also clearly detected, but only from the barred central region. (3) There is very little evidence of recent star formation in the galaxy. The results appears to match many of the predictions of Quilis et al. (2000), suggesting NGC4319 is undergoing a transformation from a spiral into an S0 due to ram-pressure stripping, possibly in tandem with tidal stripping. To understand the characteristics of gas (especially warm-hot intergalactic medium) in large scale structures, similar high resolution spectra of 31 quasars were selected based on the galaxy density showing in the 2MASS map. They provide a unbiased sample for the study of the correlation between O VI/H I absorbers and galaxies and 2MASS galaxy groups at low redshift (z<0.04). We totally discover 52 \lya\ absorbers and 7 O VI absorbers, and O VI is clearly detected using the stacking and "pixel optical depth'' techniques for nearby galaxies along the sightlines. It seems that the locations of the O VI absorbers do not correlated with the spacial distribution of large-scale structures manifested by galaxy groups, but more closely associated with individual galaxies. It indicates that the galactic winds and "feedback'' plays important role in polluting the IGM with O VI. Finally, we perform an extra investigation on the variable O VI and N V emission from the black hole binary LMC X-3 in our original absorption line study of the hot Galactic halo and the ISM of the LMC using LMC X-3 as a background source. We observe significant velocity and intensity variation in both O VI and N V emission. Their trends suggest that illumination of the B-star atmosphere by the intense X-ray emission from the accreting black hole creates a hot spot on one side of the B star, and this hot spot is the origin of the O VI and N V emission.

We present the first results from an ongoing survey to characterize the circumgalactic medium (CGM) of massive high-redshift galaxies detected as submillimeter galaxies (SMGs). We constructed a parent sample of 163 SMGQSO pairs with separations less than similar to 36" by cross-matching far-infrared-selected galaxies from Herschel with spectroscopically confirmed QSOs. The Herschel sources were selected to match the properties of the SMGs. We determined the sub-arcsecond positions of six Herschel sources with the Very Large Array and obtained secure redshift identification for three of those with near-infrared spectroscopy. The QSO sightlines probe transverse proper distances of 112, 157, and 198. kpc at foreground redshifts of 2.043, 2.515, and 2.184, respectively, which are comparable to the virial radius of the similar to 10(13) M circle dot halos expected to host SMGs. High-quality absorption-line spectroscopy of the QSOs reveals systematically strong H I Ly alpha absorption around all three SMGs, with rest-frame equivalent widths of similar to 2-3 A. However, none of the three absorbers exhibit compelling evidence for optically thick H I gas or metal absorption, in contrast to the dominance of strong neutral absorbers in the CGM of luminous z similar to 2 QSOs. The low covering factor of optically thick H I gas around SMGs tentatively indicates that SMGs may not have as prominent cool gas reservoirs in their halos as the coeval QSOs and that they may inhabit less massive halos than previously thought.

Simple models for bright, helium producing phases in the lives of massive galaxies are used to investigate the distance out to which they could be seen as individual objects. Roughly speaking, objects radiating at effective temperatures of ..;40,000 o could be detected out to redshifts as large as 8 -+12. Such redshifts correspond to densities at which we might reasonably have expected galaxy condensation to occur, except possibly for the lowest part of the probable range of go-values. Such Objects ought to be bluer than ordinary "nearby" galaxies, and for open cosmological models would be expected to be much more numerous than ordinary galaxies; for closed models the numbers of bright and ordinary galaxies should be comparable. The feasibility of detecting such objects by ground -based measures of their integrated skybrightness in the L and M windows is discussed, and it appears that such a technique would be feasible and superior to direct photographic detection only for relatively low effective temperatures in the 20,000 to 1+0,000 range. The possibility of explaining the lack of general Ljy -c4 absorption in distant WO as due to a high degree of ionization brought about by W radiation from these bright galaxies is investigated. The conclusion is that this mechanism will not usually be adequate -- and when it is adequate, the objects causing the ionization should be detectable -- unless the current mean density of uncondensed gas is very low, of the order of 10 -7 particles /cm3 or less.

The 3C 273 and RX J1230.8+0115 sight lines probe the outskirts of the Virgo Cluster at physical separations between the sight lines of 200 and 500 h70-1 kpc. We present an analysis of available Hubble Space Telescope STIS echelle and Far-Ultraviolet Spectroscopic Explorer (FUSE) UV spectroscopy of RX J1230.8+ 0115, in which we detect five Lyα absorbers at Virgo distances. One of these absorbers is a blend of two strong metal-line absorbers at a recession velocity coincident with the highest neutral hydrogen column density absorber in the 3C 273 sight line, ∼350 h70-1 kpc away. The consistency of the metal-line column density ratios in the RX J1230.8+0115 sight line allows us to determine the ionization mechanism (photoionization) for these absorbers. While the low signal-to-noise ratio of the FUSE spectrum limits our ability to model the neutral hydrogen column density of these absorbers precisely, we are able to constrain them to be in the range 1016-1017 cm -2. The properties of these absorbers are similar to those obtained for the nearby 3C 273 absorber studied by Tripp and collaborators. However, the inferred line-of-sight size for the 3C 273 absorber is only 70 pc, much smaller than those inferred in RX J1230.8+0115, which are 10-30 h70-1 kpc. The small sizes of all three absorbers are at odds with the ≥ 350 h70-1 kpc minimum transverse size implied by an application of the standard QSO line-pair analysis. On the basis of absorber associations between these two sight lines we conclude that a large-scale structure filament produces a correlated, not contiguous, gaseous structure in this region of the Virgo Supercluster. These data may indicate that we are detecting overdensities in the large-scale structure filaments in this region. Alternatively, the presence of a galaxy 71 h70-1 kpc from a 3C 273 absorber may indicate that we have probed outflowing, starburst-driven shells of gas associated with nearby galaxies.

We present Hubble Space Telescope (HST) Space Telescope Imaging Spectrograph (STIS) and Far Ultraviolet Spectroscopic Explorer (FUSE) spectra of the QSO PG 1211+143 (zem = 0.081) and a galaxy survey of the surrounding field. This sight line shows two strong intergalactic absorption systems at cz ≃ 15,300 and 19,300 km s-1. This sight line addresses the nature and origin of the O VI absorbers and their connection to galaxies. We explore the relationship of these absorbers to the nearby galaxies and compare them to other O VI-bearing absorbers in diverse environments. At 15,300 km s-1, we find four distinct H I components and associated C II, C III, C IV, Si II, Si III, Si IV, N V, and O VI, lying near a spiral-dominated galaxy group with a bright member galaxy 137 h 70-1 kpc from the sight line. The observed ions of C, Si, and N are likely to be photoionized, but the O VI is more consistent with collisional ionization. The ion ratios in this absorber resemble the highly ionized Galactic high-velocity clouds (HVCs); it may also trace the hot intragroup medium gas or the unbound wind of an undiscovered dwarf galaxy. At 19,300 km s-1, we find five H I components and associated C III, Si III, and collisionally ionized O VI lying 146 h70-1 kpc from an isolated galaxy. The properties of the O VI-bearing gas are consistent with an origin in strong shocks between low-metallicity gas (≥2%-6% solar) and one or more of the warm photoionized components. It is likely that these absorbers are related to the nearby galaxies, perhaps by outflows or gas stripped from unseen satellite galaxies by interactions. However, we cannot reject completely the hypothesis that they reside in the same large-scale structure in which the galaxies are embedded but are otherwise not directly related.