Bright Ly alpha blobs (LABs)-extended nebulae with sizes of similar to 100 kpc and Ly alpha luminosities of similar to 10(44) erg s(-1)-often reside in overdensities of compact Ly alpha emitters (LAEs) that may be galaxy protoclusters. The number density, variance, and internal kinematics of LABs suggest that they themselves trace group-like halos. Here, we test this hierarchical picture, presenting deep, wide-field Ly alpha narrowband imaging of a 1 degrees x. 0 degrees.5 region around a LAB pair at z = 2.3 discovered previously by a blind survey. We find 183 Lya emitters, including the original LAB pair and three new LABs with Ly alpha luminosities of (0.9-1.3) x 10(43) erg s(-1) and isophotal areas of 16-24 arcsec2. Using the LAEs as tracers and a new kernel density estimation method, we discover a large-scale overdensity (Bootes J1430+3522) with a surface density contrast of delta(Sigma) = 2.7, a volume density contrast of delta similar to 10.4, and a projected diameter of approximate to 20 comoving Mpc. Comparing with cosmological simulations, we conclude that this LAE overdensity will evolve into a present-day Coma-like cluster with log(M/M-circle dot) similar to 15.1 +/- 0.2. In this and three other wide-field LAE surveys re-analyzed here, the extents and peak amplitudes of the largest LAE overdensities are similar, not increasing with survey size, and implying that they were indeed the largest structures then and today evolve into rich clusters. Intriguingly, LABs favor the outskirts of the densest LAE concentrations, i.e., intermediate LAE overdensities of delta(Sigma) = 1-2. We speculate that these LABs mark infalling protogroups being accreted by the more massive protocluster.

Clues about the timing of reionization and the nature of the ionizing sources responsible are imprinted in the ionization and thermal state of the IGM. In this thesis, I use high-resolution quasar spectra in conjunction with state-of-the-art hydrodynamical simulations to probe the IGM at high redshift, focusing on the ionization and thermal state of the gas. After reionization, the ionization state of the IGM is set by the intensity of the ultraviolet background(UVB), quantified by the hydrogen photoionization rate, Γ_bkg. At high redshifts this has been estimated by measuring the mean flux in the Lyα forest, and scaling Γ_bkg in simulations such that the simulated mean flux matches the observed value. In Chapter 3 I investigate whether the precision of these estimates can be improved by using the entire flux probability distribution function (PDF) instead of only the mean flux. Although I find it cannot improve the precision directly, the flux PDF can potentially be used to constrain other sources of error in observational estimates of Γ_bkg, and so may increase the precision indirectly. The ionizing output of a quasar will locally dominate over the UVB, and this leads to enhanced transmission bluewards of the quasar Lyα line, known as the proximity effect. In Chapter 4 I present the first measurements of Γ_bkg at z > 5 from the proximity effect. The UVB intensity declines smoothly with redshift over 4.6 < z < 6.4, implying a smooth evolution in the mean free path of ionizing photons. This suggests that reionization ends at z > 6.4. There is a drop in Γ_bkg by roughly a factor of five, which corresponds to a drop in the ionizing emissivity by about a factor of two. Such a redshift evolution in the emissivity cannot continue to much higher redshift without reionization failing to complete, which suggests that reionization cannot have ended much higher than z = 6.4. Estimates of Γ_bkg from the proximity effect and the mean flux are generally discrepant at z ~ 2-4, with those from the proximity effect systematically higher. This is generally attributed to effects of the quasar environment. I investigate the significance of several environmental biases on proximity effect measurements at z ~ 5-6 in Chapter 5. The biases are found to be small, and so the proximity effect is expected to give relatively unbiased estimates of Γ_bkg at z > 5, in contrast to lower redshifts. Photoionization heats the gas in the IGM, and so the thermal history of the IGM provides important constraints on reionization. The thermal state of the IGM is reflected in the level of small-scale structure in the Lyα forest. In Chapter 6 I quantify the small-scale structure using two independent statistics, the curvature and the peakiness, and convert these into a temperature by comparing with simulations. These are the first measurements of the temperature in the general IGM at z > 5. Both statistics show an increase in the temperature by a factor of roughly two from z = 4.4 to 5.6. This rise is sensitive, however, to any smoothing of the gas density distribution due to the thermal history spanning reionization. I find that this should only be a small effect, as otherwise the corrected temperatures at z ~ 4-5 are implausibly low. The temperature evolution therefore suggests a late reionization. The temperatures at z ≥ 4.8 are well fit by an adiabatic cooling curve, for which reasonable peak temperatures at the end of reionization are reached at 6 ≲ z ≲ 7. The temperatures at z ~ 4-5 are consistent with reionization being carried out by Pop II stars. In conclusion, the ionization and thermal state of the IGM at z ~ 5-6 suggest a late hydrogen reionization, driven by star-forming galaxies and ending around 6.5 ≲ z ≲ 7. This is consistent with other recent lines of observational evidence, and supports theoretical models that infer a late reionization from the observed star formation rate history.

Since the discovery of the large (2 × 109 M ) intergalactic cloud known as the Leo Ring in the 1980s, the origin of this object has been the center of a lively debate. Determining the origin of this object is still important as we develop a deeper understanding of the accretion and feedback processes that shape galaxy evolution. We present Hubble Space Telescope/Cosmic Origins Spectrograph observations of three sightlines near the ring, two of which penetrate the high column density neutral hydrogen gas visible in 21 cm observations of the object. These observations provide the first direct measurement of the metallicity of the gas in the ring, an important clue to its origin. Our best estimate of the metallicity of the ring is 10% Z , higher than expected for primordial gas but lower than expected from an interaction. We discuss possible modifications to the interaction and primordial gas scenarios that would be consistent with this metallicity measurement.

We have used the Hubble STIS and FUSE archives of ultraviolet spectra of bright AGNs to identify intergalactic Lya absorbers in nearby (z ≤ 0.1) voids. From a parent sample of 651 Lyα absorbers, we identified 61 "void absorbers" located >1.4 h70-1 Mpc from the nearest L* or brighter galaxy. Searching for metal absorption in high-quality (S/N > 10) spectra at the location of three diagnostic metal lines (O VI λ1032, C IV λ1548, Si III λ1206), we detected no metal lines in any individual absorber, or in any group of absorbers using pixel co-addition techniques. The best limits on metal-line absorption in voids were set using four strong Lya absorbers with NHI > 1014 cm-2, with 3 σ equivalent-width limits ranging from 8 mÅ (O VI) to 7-15 mÅ (C IV) and 4-10 mÅ (Si III). Photoionization modeling yields metallicity limits Z < 10 -1.8±0.4 Z⊙ from nondetections of C IV and VI, some ∼6 times lower than those seen in Lyα/O VI absorbers at z < 0.1. Although the void Lyα absorbers could be pristine material, considerably deeper spectra are required to rule out a universal metallicity floor produced by bursts of early star formation, with no subsequent star formation in the voids. The most consistent conclusion derived from these low-z results and similar searches at z = 3-5 is that galaxy filaments have increased their mean IGM metallicity by factors of 30-100 since z ∼ 3.

We report the discovery of a dwarf (MB = -13.9) poststarburst galaxy coincident in recession velocity (within uncertainties) with the highest column density absorber (NHI = 1015.85 cm-2 at cz = 1586 km s-1) in the 3C 273 sight line. This galaxy is by far the closest galaxy to this absorber, projected just 71 h70-1 kpc on the sky from the sight line. The mean properties of the stellar populations in this galaxy are consistent with a massive starburst ≈3.5 Gyr ago, whose attendant supernovae, we argue, could have driven sufficient gas from this galaxy to explain the nearby absorber. Beyond its proximity on the sky and in recession velocity, the further evidence in favor of this conclusion includes both a match in the metallicities of absorber and galaxy and the fact that the absorber has an overabundance of Si/C, suggesting recent Type II supernova enrichment. Thus, this galaxy and its ejecta are in the expected intermediate stage in the fading dwarf evolutionary sequence envisioned by Babul & Rees to explain the abundance of faint blue galaxies at intermediate redshifts. While this one instance of a QSO metal-line absorber and a nearby dwarf galaxy is not proof of a trend, a similar dwarf galaxy would be too faint to be observed by galaxy surveys around more distant metal-line absorbers. Thus, we cannot exclude the possibility that dwarf galaxies are primarily responsible for weak (NHI = 1014-1017 cm-2) metal-line absorption systems in general. If a large fraction of the dwarf galaxies expected to exist at high redshift had a similar history (i.e., they had a massive starburst that removed all or most of their gas), these galaxies could account for at least several hundred high-z metal-line absorbers along the line of sight to a high-z QSO. The volume-filling factor for this gas, however, would be less than 1%.

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.

Galactic bulges of early-type spirals and elliptical galaxies comprise primarily old stars, which account for more than half of the total stellar mass in the local Universe. These stars collectively generate a long-lasting feedback via stellar mass loss and Type Ia supernovae. According to the empirical stellar mass loss and supernova rates, the stellar ejecta can be heated to more than 107 K, forming a very hot, diffuse, and ironrich interstellar medium. Conventionally a strong galactic wind is expected, especially in low- and intermediate-mass early-type galaxies which have a relatively shallow potential well. X-ray observations, however, have revealed that both the temperature and iron abundance of the interstellar medium in such galaxies are unexpectedly low, leading to the so-called “missing feedback” and “missing metal” problems. As an effort to address the above outstanding issues, we have carried out a series of hydrodynamic simulations of galactic bulge feedback on various scales. On galactic halo scales, we demonstrate that the feedback from galactic bulges can play an essential role in the halo gas dynamics and the evolution of their host galaxies. We approximately divide the bulge stellar feedback into two phases: 1) a starbusrtinduced blastwave from the formation of the bulge built up through frequent major mergers at high redshifts and 2) a gradual feedback from long-lived low mass stars. The combination of the two can heat the surrounding gas beyond the virial radius and stop further gas accretion, which naturally produces a baryon deficit around Milky Way-like galaxies and explains the lack of large-scale X-ray halos. On galactic bulge scales, we study the collective 3-dimensional effects of supernovae with their blastwaves resolved. We find that the sporadic explosions of supernovae can produce a wealth of substructures in the diffuse hot gas and significantly affect the spectroscopic properties of the X-ray-emitting gas. The differential emission measure in the temperature space has a broad lognormal-like distribution. Such distribution enhances the X-ray emission at both low and high energy bands. We further show that the SN Ia ejecta is not well-mixed with the ambient medium and the X-ray emission is primarily from the shocked stellar wind materials which in general have low metallicities. These 3-dimensional effects provide a promising explanation to the above “missing feedback” and “missing metal” problems. In addition, we demonstrate that the supernova iron ejecta forms a very hot bubbles, which have relatively larger radial velocities driven by buoyancy, resulting in a smaller iron mass fraction in the bulk outflow. These distinct properties give a natural explanation to the observed positive iron abundance gradient which has been a puzzle for decades.

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We introduce a new suite of radiation- hydrodynamical simulations of galaxy formation and reionization called Aurora. The Aurora simulations make use of a spatially adaptive radiative transfer technique that lets us accurately capture the small- scale structure in the gas at the resolution of the hydrodynamics, in cosmological volumes. In addition to ionizing radiation, Aurora includes galactic winds driven by star formation and the enrichment of the universe with metals synthesized in the stars. Our reference simulation uses 2 x 512(3) dark matter and gas particles in a box of size 25 h(-1) comoving Mpc with a force softening scale of at most 0.28 h(-1) kpc. It is accompanied by simulations in larger and smaller boxes and at higher and lower resolution, employing up to 2 x 1024(3) particles, to investigate numerical convergence. All simulations are calibrated to yield simulated star formation rate functions in close agreement with observational constraints at redshift z = 7 and to achieve reionization at z approximate to 8.3, which is consistent with the observed optical depth to reionization. We focus on the design and calibration of the simulations and present some first results. The median stellar metallicities of low- mass galaxies at z = 6 are consistent with the metallicities of dwarf galaxies in the Local Group, which are believed to have formed most of their stars at high redshifts. After reionization, the mean photoionization rate decreases systematically with increasing resolution. This coincides with a systematic increase in the abundance of neutral hydrogen absorbers in the intergalactic medium.