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.

The Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) will map the power spectrum of 0.8 million blindly discovered Lyman-alpha Emitting Galaxies (LAE) using a revolutionary new array of massively replicated, fiber-fed spectrographs dubbed the Visible Integral-Field Replicable Unit Spectrograph (VIRUS). In the era of the Hobby-Eberly Telescope wide-field upgrade, the current Low Resolution Spectrograph (LRS) must be replaced with a fiber instrument. In this thesis, I discuss the development of the second generation LRS (LRS2), which is an R>1200 multi-channel instrument based on the VIRUS design and fed by a 287 fiber, 7” x 12” microlens coupled integral field unit. I focus on the blue optimized version of the instrument (3720<[lamda] (Angstroms)<7000), specifically on the opto-mechanical design of the VPH grisms. With the purpose of making the instrument ideal for the follow-up of LAE in the HETDEX survey, I discuss the science drivers for selecting the spectral resolution of the instrument. To test the utility of such an instrument, I present R~2400 spectra of two LAE that were originally discovered in the HETDEX Pilot Survey (Adams et al. 2011). These data were taken with the VIRUS prototype spectrograph in a high-resolution mode at the McDonald Observatory Harlan J. Smith 2.7 m telescope. The Lyman-alpha line profiles are constrained by near-infrared observations of rest-frame optical emission lines from Finkelstein et al. (2011), which set the systemic redshift of the galaxies. I discuss the velocity offsets of the Lyman-alpha line from the systemic line center and the implications for the HETDEX survey. I compare the line profiles to theory, specifically to those describing dust attenuation, outflows or inflows of neutral gas on the galactic scale, and attenuation in the intergalactic medium. This study provides an example of how LRS2 can be used to probe Lyman-alpha emission in 2<z<3 star-forming galaxies. / text

Theory of cosmic structure formation outlines how stars, galaxies, clusters of galaxies, and large-scale structures formed out of primordial density fluctuations. It presents us a picture of cosmic mass assembly, and places strong constraints on cosmological model. Both observations and theories suggest that structures formation follows a "bottom up" process, in which small, low-mass component form first, and gradually develop into larger, more massive systems. This dissertation focuses on three crucial stages of cosmic structure formation: first generation stars, quasar host galaxies and the large-scale galaxy overdensities. In Chapter 1, I present an overview of structure formation, acquainting readers with a general picture from first object in the Universe to large-scale structures at later epochs. In Chapter 2 and Chapter 3, I derive strong constraints to the star formation rates (SFRs) of very massive Population III (Pop III) stars in two high redshift galaxies at z = 7. By probing the He II emission lines for both galaxies, I conclude that the contributions of very massive Pop III stars to total the SFRs are less than 3%. In Chapter 4, I move to more massive systems, quasar host galaxies at z ~ 3. Using damped Lyman alpha absorption systems as natural coronagraphs, I report that rest-frame far-UV emission of quasar host galaxy correlates strongly with quasar luminosity. This result suggests a co-evolution of supermassive black holes and their host galaxies. In Chapter 5, I develop a novel method for searching the most massive protoclusters at z = 2-3, by utilizing intergalactic Lyman alpha absorption. My investigations suggest that large intergalactic Lyman alpha absorption systems effectively trace the most overdense regions at large scale of ~ 15 h⁻¹ Mpc. In Chapter 6, I present our imaging observations of an extreme galaxy overdensity (protocluster) BOSS1441+4000, which is discovered using the techniques developed in Chapter 5. Furthermore, I report an intergalactic-scale Lyman alpha nebula detected at the density peak of BOSS1441+4000. This discovery, together with previously discovered Slug nebula, provide us a first look of intergalactic medium in emission in the early Universe. In the Chapter 7, I give a summary of this dissertation and discuss several future prospects.

Cosmological simulations suggest a strong correlation between high optical-depth Lya absorbers, which arise from the intergalactic medium, and 3D mass overdensities on scales of 10-30 h(-1) comoving Mpc. By examining the absorption spectra of similar to 80,000 QSO sight lines over a volume of 0.1 Gpc(3) in the Sloan Digital Sky Survey III (SDSS-III), we have identified an extreme overdensity, BOSS1441, which contains a rare group of strong Lya absorbers at z = 2.32 +/- 0.02. This absorber group is associated with six QSOs at the same redshift on a 30 comoving Mpc scale. Using Mayall/MOSAIC narrowband and broadband imaging, we detect Lya emitters (LAEs) down to 0.7 x L-Ly alpha ' * a and reveal a large-scale structure of LAEs in this field. Our follow-up LBT observations have spectroscopically confirmed 20 galaxies in the density peak. We show that BOSS1441 has an LAE overdensity of 10.8 +/- 2.6 on a 15 comoving Mpc scale, which could collapse to a massive cluster with M greater than or similar to 10(15) M-circle dot at z similar to 0. This overdensity is among the most massive large-scale structures at z similar to 2 discovered to date.

We present a comparison between several observational tests of the post-reionization intergalactic medium and the numerical simulations of reionization completed under the Cosmic Reionization On Computers (CROC) project. The CROC simulations match the gap distribution reasonably well, and also provide a good match for the distribution of peak heights, but there is a notable lack of wide peaks in the simulated spectra and the flux-probability distribution functions are poorly matched in the narrow redshift interval 5.5 < z < 5.7, with the match at other redshifts being significantly better, albeit not exact. Both discrepancies are related: simulations show more opacity than the data.

<p> A study of metal enrichment of the intergalactic medium (IGM) using a series of smooth particle hydrodynamics (SPH) simulations is presented, employing models for metal cooling and the turbulent diffusion of metals and thermal energy. An adiabatic feedback mechanism was adopted where gas cooling was prevented on the timescale of supernova bubble expansion to generate galactic winds without explicit wind particles. The simulations produced a cosmic star formation history (SFH) that is broadly consistent with observations until z ~ 0.5, and a steady universal neutral hydrogen fraction (OHI) that compares reasonably well with observations. The evolution of the mass and metallicities in stars and various gas phases was investigated. At z=O, about 40% of the baryons are in the warm-hot intergalactic medium (WHIM), but most metals (80%-90%) are locked in stars. At higher redshifts the proportion of metals in the IGM is higher due to more efficient loss from galaxies. The results also indicate that IGM metals primarily reside in the WHIM throughout cosmic history, which differs from simulations with hydrodynamically decoupled explicit winds. The metallicity of the WHIM lies between 0.01 and 0.1 solar with a slight decrease at lower redshifts. The metallicity evolution of the gas inside galaxies is broadly consistent with observations, but the diffuse IGM is under-enriched at z ~ 2.5. Metals enhance cooling which allows WHIM gas to cool onto galaxies and increases star formation. Metal diffusion allows winds to mix prior to escape, decreasing the IGM metal content in favour of gas within galactic halos and star forming gas. Diffusion significantly increases the amount of gas with low metallicities and improves the density-metallicity relation. </p> <p> The galactic wind generation mechanism and the wind properties from our simulations were investigated. It was found that: 1. Galactic winds are most efficient for halos in the intermediate mass range 10^10Mo - 10^11 Mo . These winds dominate the metal ejection at all redshifts, although towards lower redshift the contributions from larger halos become relatively more important. At the low mass end gas is prevented from accreting onto halos and has very low metallicities. At the high mass end, the fraction of halo baryons escaped as winds declines along with the decline of stellar mass fraction in these halos. The decrease in wind ejection is likely because of the decreases in star formation activity, wind mass loading and wind escape efficiency as the halo mass increases. 2. The adiabatic feedback can generate winds with mass loading factors comparable to the ones used in explicit superwind models. The mass loading factor decreases towards lower redshift, implying that smaller halos have larger mass loading. 3. Metals located at lower density were generated at earlier epochs from small halos, suggesting that the wind traveling speed can affect the metal distribution in the IGM. </p> / Thesis / Doctor of Philosophy (PhD)

Using Hubble Space Telescope Cosmic Origins Spectrograph observations of 89 QSO sightlines through the Sloan Digital Sky Survey footprint, we study the relationships between C IV absorption systems and the properties of nearby galaxies, as well as the large-scale environment. To maintain sensitivity to very faint galaxies, we restrict our sample to 0.0015 < z < 0.015, which defines a complete galaxy survey to L (SIC) 0.01 L-* or stellar mass M-* (SIC) 10(8) M-circle dot. We report two principal findings. First, for galaxies with impact parameter rho < 1 r(vir), C IV detection strongly depends on the luminosity/stellar mass of the nearby galaxy. C IV is preferentially associated with galaxies with M-* > 10(9.5) M-circle dot; lower-mass galaxies rarely exhibit significant C IV absorption (covering fraction f(C) = 9(-6)(+12)% for 11 galaxies with M-* < 10(9.5) M-circle dot.). Second, C IV detection within the M-* > 10(9.5) M-circle dot. population depends on environment. Using a fixed-aperture environmental density metric for galaxies with rho < 160 kpc at z < 0.055, we find that 57(-13)(+12)% (8/14) of galaxies in low-density regions (regions with fewer than seven L > 0.15 L* galaxies within 1.5 Mpc) have affiliated C IV absorption; however, none (0/7) of the galaxies in denser regions show C IV. Similarly, the C IV detection rate is lower for galaxies residing in groups with dark matter halo masses of M-halo > 10(12.5) M-circle dot. In contrast to C IV, H. I is pervasive in the circumgalactic medium without regard to mass or environment. These results indicate that C IV absorbers with log N(C IV). (SIC) 13.5 cm(-2) trace the halos of M-* > 10(9.5) M-circle dot galaxies but also reflect larger-scale environmental conditions.

Ly alpha nebulae, or "Ly alpha blobs," are extended (up to similar to 100 kpc), bright (L-Ly alpha greater than or similar to 10(43) erg s(-1)) clouds of Lya emitting gas that tend to lie in overdense regions at z similar to 2-5. The origin of the Lya emission remains unknown, but recent theoretical work suggests that measuring the polarization might discriminate among powering mechanisms. Here we present the first narrowband imaging polarimetry of a radio-loud Lya nebula, B3 J2330+3927, at z - 3.09, with an embedded active galactic nucleus (AGN). The AGN lies near the blob's Lya emission peak, and its radio lobes align roughly with the blob's major axis. With the SPOL polarimeter on the 6.5 m MMT telescope, we map the total (Ly alpha + continuum) polarization in a grid of circular apertures of a radius of 0.'' 6 (4.4 kpc), detecting a significant (>2 sigma) polarization fraction P-% in nine apertures and achieving strong upper limits (as low as 2%) elsewhere. P-% increases from <2% at similar to 5 kpc from the blob center to 17% at similar to 15-25 kpc. The detections are distributed asymmetrically, roughly along the nebula's major axis. The polarization angles theta are mostly perpendicular to this axis. Comparing the Ly alpha flux to that of the continuum and conservatively assuming that the continuum is highly polarized (20%-100%) and aligned with the total polarization, we place lower limits on the polarization of the Lya emission P-%,P-Ly alpha ranging from no significant polarization at similar to 5 kpc from the blob center to 3%-17% at 10-25 kpc. Like the total polarization, the Ly alpha polarization detections occur more often along the blob's major axis.

We investigate black hole-host galaxy scaling relations in cosmological simulations with a self-consistent black hole growth and feedback model. Our sub-grid accretion model captures the key scalings governing angular momentum transport by gravitational torques from galactic scales down to parsec scales, while our kinetic feedback implementation enables the injection of outflows with properties chosen to match observed nuclear outflows (star formation-driven winds are not included to isolate the effects of black hole feedback). We show that 'quasar mode' feedback can have a large impact on the thermal properties of the intergalactic medium and the growth of galaxies and massive black holes for kinetic feedback efficiencies as low as 0.1 per cent relative to the bolometric luminosity. None the less, our simulations indicate that the black hole-host scaling relations are only weakly dependent on the effects of black hole feedback on galactic scales, since black hole feedback suppresses the growth of galaxies and massive black holes by a similar amount. In contrast, the rate at which gravitational torques feed the central black hole relative to the host galaxy star formation rate governs the slope and normalization of the black hole-host correlations. Our results suggest that a common gas supply regulated by gravitational torques is the primary driver of the observed co-evolution of black holes and galaxies.

Using a sample of nearly half a million galaxies, intersected by over 7 million lines of sight from the Sloan Digital Sky Survey Data Release 12, we trace H alpha + [N II] emission from a galactocentric projected radius, r(p), of 5 kpc to more than 100 kpc. The emission flux surface brightness is alpha r(p) 1.9 +/- 0.4. We obtain consistent results using only the Ha or [N II] flux. We measure a stronger signal for the bluer half of the target sample than for the redder half on small scales, r(p) < 20 kpc. We obtain a 3 sigma detection of H alpha + [N II] emission in the 50-100 kpc r(p) bin. The mean emission flux within this bin is (1.10 +/- 0.35) x 10(-20) erg cm(-2) s(-1) angstrom(-1), which corresponds to 1.87 x 10(-20) erg cm(-2) s(-1) arcsec(-2) or 0.0033 Rayleigh. This detection is 34 times fainter than a previous strict limit obtained using deep narrow-band imaging. The faintness of the signal demonstrates why it has been so difficult to trace recombination radiation out to large radii around galaxies. This signal, combined with published estimates of n(H), leads us to estimate the temperature of the gas to be 12,000 K, consistent with independent empirical estimates based on metal ion absorption lines and expectations from numerical simulations.