The diffuse universe, consisting of baryons that have not yet collapsed into structures such as stars, galaxies, etc., has not been well studied. While the intergalactic and circumgalactic mediums (IGM & CGM) may contain 30-40% of the baryons in the universe, this low density gas is difficult to observe. Yet it is likely a key driver of the evolution of galaxies and star formation through cosmic time. The IGM provides a reservoir of gas that can be used for star formation, if it is able to accrete onto a galaxy. The CGM bridges the IGM and the galaxy itself, as a region of both inflows from the IGM and outflows from galactic star formation and feedback. The diffuse interstellar medium (ISM) gas and dust in the galaxy itself may also be affected by the CGM of the galaxy. Careful observations of the ISM of our own Galaxy may provide evidence of interaction with the CGM. These three regions of low density, the IGM, CGM, and ISM, are arbitrary divisions of a continuous flow of low density material into and out of galaxies. My thesis focuses on observations of this low density material using existing telescopes as well as on the development of technology and instruments that will increase the sensitivity of future missions. I used data from the Galaxy Evolution Explorer (GALEX) to create an all sky map of the diffuse Galactic far ultraviolet (FUV) background, probing the ISM of our own galaxy and comparing to other Galactic all sky maps. The FUV background is primarily due to dust scattered starlight from bright stars in the Galactic plane, and the changing intensity across the sky can be used to characterize dust scattering asymmetry and albedo. We measure a consistent low level non-scattered isotropic component to the diffuse FUV, which may be due in small part to an extragalactic component. There are also several regions of unusually high FUV intensity given other Galactic quantities. Such regions may be the location of interactions between Galactic super-bubbles and the CGM. Other ways of probing the CGM including direct detection via emission lines. I built a proto-type of the Circumgalactic Hα Spectrograph (CHαS), a wide-field, low-cost, narrow-band integral field unit (IFU) that is designed to observe Hα emission from the CGM of nearby, low-z galaxies. This proto-type has had two recent science runs, with preliminary data on several nearby galaxies. Additional probes of the CGM are emission lines in the rest ultra-violet. These include OVI, Lyα, CIV, SiIII, CIII, CII, FeII, and MgII. Such lines are accessible for low redshift galaxies in the space UV, historically a difficult wavelength range in which to work due in part to low efficiency of the available detectors. I have worked with NASA's Jet Propulsion Laboratory to develop advanced anti-reflection (AR) coatings for use on thinned, delta-doped charge coupled device (CCD) detectors. These detectors have achieved world record quantum efficiency (QE) at UV wavelengths (> 50% between 130 nm and 300nm), with the potential for even greater QE with a more complex coating. One of these AR coated detectors will be used on the Faint Intergalactic Redshifted Emission Balloon (FIREBall-2), a balloon-born UV spectrograph designed to observe the CGM at 205 nm via redshifted Lyα (at z=0.7), CIV (at z=0.3), and OVI (at z=1.0). FIREBall-2 will launch in the fall of 2015.

Cold gas is fundamental in understanding galaxy formation and evolution since it provides the fuel for star formation. In addition, the atomic gas can be used to probe the internal properties of galaxies, their halos, and their environment. Several of the remaining questions in galaxy evolution can be addressed by studying the gas properties in galaxies, in particular, the following three: (1) How do galaxies get their gas? (2) How do galaxies change over time? (3) How are galaxies affected by the environment? The work presented in this thesis addresses these questions. The thesis is divided into three parts that cover a range of topics related to gas in galaxies, including the fate of gas in a merger remnant, the evolution and distribution of halo gas, and how the gas properties of galaxies change as a function of redshift and environment. Part I consists of two chapters that present the atomic and molecular gas properties of a wet merger remnant (NGC 34). Chapter 2 is an analysis of the HI distribution and kinematics in NGC 34. We find that the progenitors of NGC 34 were gas-rich. The kinematics of the tidal tails suggest that some of the gas is returning to the central regions and forming an outer disk. In addition, we find puzzling absorption near the systemic velocity against the radio continuum. Chapter 3 is a follow-up study consisting of CO observations done with CARMA and new VLA data with a large velocity coverage to search for outflows. We detect CO concentrated in the inner regions that matches the velocity range of the HI in absorption, indicating that there is a circumnuclear disk in the central regions of molecular and atomic gas. We do not detect the outflow seen in the optical spectrum in CO or HI, but are able to place upper limits on both. Part II is an analysis of halo gas in a Milky Way mass galaxy. We use a cosmological high resolution hydrodynamic simulation to study the distribution, origin, and evolution of halo gas. At z=0, we find that the amount (~ 10⁸ M_sun), covering fraction and distribution are consistent with existing observations. The origin of halo gas is a combination of filamentary and satellite material. In addition, we find that the amount of halo gas is roughly constant between z=0.3 to z=0, but increases at earlier times. Part III presents results from the COSMOS HI Large Extragalactic Survey (CHILES), an HI deep field done with the VLA. These observations show how galaxies grow in different environments across cosmic time. We are using the expanded capabilities of the VLA to probe HI in part of the COSMOS field with a 5" resolution. Chapter 5 presents results from the pilot that was observed during commissioning. We observed for 60 hr and covered the redshift range 0<z<0.19 in one setting. We report 33 direct detections in different environments across the redshift range, and a stacked HI mass of (1.8 ± 0.3) x 10⁹ M_sun for galaxies in a wall at z=0.12. The pilot demonstrated that the VLA was ready to carry a full HI deep field. The full survey will be 1002 hr spread over several B array configurations. Chapter 6 presents preliminary results for the first 178 hr of the survey (Phase I). We describe the data reduction from Phase I, lessons for upcoming configurations, and present preliminary results. We detect very extended HI disks in nearby dwarf galaxies, and present the highest redshift detection to date (z=0.376).

This dissertation consists of several projects designed to further our understanding of galaxies and galactic structures associated with intervening quasar absorption lines -- i.e., those selected via gas cross section. Surveys for MgII absorption were conducted utilizing QSO spectra from the Sloan Digital Sky Survey and data collected at the 6.5m Multiple Mirror Telescope Observatory on Mount Hopkins, AZ. The first survey expands the number of studied MgII systems by an order of magnitude, while the second extends the statistics to weaker systems and lower redshifts. The results provide high-precision measurements of the statistics and evolution of MgII absorbers. It is shown that the distribution of rest equivalent width steepens with decreasing redshift, especially at redshifts z<1, such that the total absorption co-moving cross section decreases at a rate proportional to rest equivalent width. This is interpreted as an evolution in the kinematic properties of the absorbing galaxy population. Evidence for multiple physical populations comprising MgII absorbers is presented and discussed. Early survey results were used to investigate the cosmic neutral-gas-phase metallicity and dust content. QSO spectra selected due to the presence of strong intervening MgII absorption were stacked in the absorption rest frame to create high signal-to-noise ratio composites with which to measure Zn and Cr abundances. It was found that metallicity of high-N(HI) gas is highly correlated with the kinematic properties of galaxies and both metallicity and dust content for these systems increase with decreasing redshift. Two projects were completed that involved the imaging of six low-redshift damped Lyman-alpha galaxies. Detailed properties of the identified absorber galaxies are described. They are shown to be drawn from a variety of morphological types with a range of luminosities, environments, and impact parameters.

We present new spectroscopy and Hubble Space Telescope imaging of protostellar jets discovered in an Hαsurvey of the Carina Nebula. Near-IR [Fe II] emission from these jets traces dense gas that is self-shielded from Lyman continuum photons from nearby O-type stars, but is excited by non-ionizing FUV photons that penetrate the ionization front within the jet. New near-IR [Fe II] images reveal a substantial mass of dense, neutral gas that is not seen in Hαemission from these jets. In some cases, [Fe II] emission traces the jet inside its natal dust pillar, connecting the larger Hαoutflow to the embedded IR source that drives it. New proper motion measurements reveal tangential velocities similar to those typically measured in lower-luminosity sources (100−200 km/s⁻¹). Combining high jet densities and fast outflow speeds leads to mass-loss rate estimates an order of magnitude higher than those derived from the Hαemission measure alone. Higher jet mass-loss rates require higher accretion rates, implying that these jets are driven by intermediate-mass (~ 2−8 M⊙) protostars. For some sources, the mid-IR luminosities of the driving sources are clearly consistent with intermediate-mass protostars; others remain deeply embedded and require long-wavelength, high-resolution images to confirm their luminosity. These outflows are all highly collimated, with opening angles of only a few degrees. With this new view of collimated jets from intermediate-mass protostars, we argue that these jets reflect essentially the same outflow phenomenon seen in low-mass protostars, but that the collimated atomic jet core and the material it sweeps up are irradiated and rendered observable. Thus, the jets in Carina offer strong additional evidence that stars up to ~ 8 M⊙ form by the same accretion mechanisms as low-mass stars.

One of the most compelling scientific quests ever undertaken is the quest to find life in our Universe somewhere other than Earth. An important piece to this puzzle is finding and characterizing extrasolar planets. This effort, particularly the characterization step, requires the ability to directly image such planets. This is a challenging task - such planets are much fainter than their host stars. One of the major solutions to this problem is Adaptive Optics (AO), which allows us to correct the turbulence in the Earth's atmosphere, and thereby further the hunt for exoplanets with ground based telescopes. The Magellan Adaptive Optics system has recently obtained its first on-sky results at Las Campanas Observatory, marking a significant step forward in the development of high-resolution high-contrast ground-based direct imaging. MagAO includes a visible wavelength science camera, VisAO, which - for the first time - provides diffraction limited imaging, in long exposures, on a large filled-aperture (6.5 m) telescope. In this dissertation we report on the design, development, laboratory testing, and initial on-sky results of MagAO and VisAO, which include the first ground-based image of an exoplanet (beta Pictoris b) with a CCD. We also discuss some of the exciting science planned for this system now that it is operational. We close with an analysis of a new problem in direct imaging: planets orbiting their stars move fast enough in the habitable zone to limit our ability to detect them.

What physical processes and sources of material contribute to exoplanet compositions? Specifically, what roles do the protoplanetary disk composition and structure, and host star abundances play in the different stages of planet formation? In this thesis, beginning with a brief literature review in Chapter 2, I trace oxygen and carbon species through these stages to inform how, when, and where planets form. In Chapter 3 I describe a study of the molecular emission from the warm inner disks of T Tauri stars, where terrestrial planets likely form. I report moderate correlations between HCN emission strength and both stellar accretion rate (measured from UV or optical excess emission associated with accretion) and X-ray luminosity. These correlations point towards accretion related processes being an important source of disk atmosphere heating, and suggests that efficient H₂O formation and/or UV dissociation of N₂ (both also associated with higher stellar accretion rates) may aid in the production of HCN. Studies following mine have further connected the abundance of HCN versus H₂O to the growth and migration of planetesimals in the disk, which helps control the formation of both giant and terrestrial planets. I shift to an already-formed exoplanet in Chapter 4, where I present optical photometry of the best-observed transiting super-Earth GJ 1214b with the goal of constraining the short-wavelength slope of its transmission spectrum. Most previous observations suggested a flat spectrum from the near-IR to the optical, corresponding to a low-scale-height, high-molecular-weight atmosphere. My observations are in general agreement with these findings, keeping the "door open" for a H₂O-rich atmosphere for GJ 1214b, which other published g-band observations appeared to contradict. Chapters 5-7 of my thesis focus on measuring stellar abundances, particularly C/O ratios, in transiting (mostly) hot Jupiter exoplanet host stars from high resolution optical spectroscopy. Host star abundances may indicate the precursor materials present in the disk and available for incorporation into planets. In hot Jupiters, the C/O ratio affects the partitioning of C in the major observable molecules, making C and O diagnostic of temperature structure and composition. I also demonstrate that extra caution is necessary in deriving carbon and oxygen abundances, especially for cool and metal-rich stars. Though exoplanetary C/O ratios are still uncertain, the more precise abundance analysis possible right now for their host stars can help constrain their formation environments and current compositions. I summarize my graduate school research in Chapter 8, and discuss the next steps I will take in my postdoctoral career.

Dust grains are a minor component by mass of the interstellar medium of a galaxy. Yet they can be the dominant source of luminosity. At z ∼ 1, the luminosity density of the Universe in the IR is ∼ 10 times higher than it is at z ∼ 0; common high-redshift galaxies have IR luminosities and dust masses that surpass those of even rare low-redshift galaxies. Dusty galaxies must transition to dust-poor galaxies. In this thesis, we attempt to understand the When? and Where? of this transition. We examine the redshift distribution of the cosmic millimeter background and the spatial distributions of dust in high-redshift galaxies. The cosmic millimeter background is the flux surface density, across the entire sky, from dust emission from all galaxies in the Universe. We stack the 1.16mm flux densities of a sample of dusty galaxies to determine the evolution of their contribution to the background. We resolve ∼ 35% of the background at 1.16mm and ∼ 50% of the background at 850 μm. We make two unique predictions for the redshift origins of the total 1.16mm background. Dust is responsible for more than the IR emission from a galaxy. The existence of dust is a necessary but not sufficient condition for the attenuation of a galaxy's intrinsic UV emission; the IR- and emergent UV-emitting regions must be spatially coincident. We establish a relation between the ratio of infrared to UV luminosity and β for dusty galaxies at z ∼ 2, which implies that their regions are coincident. We also argue that the dust is spread on galactic scales. In dust-poor galaxies at low redshift, the amount of dust attenuating the emission from ionizing stars is greater than the amount attenuating the emission from massive but nonionizing stars. For dusty galaxies at z ∼ 1.3, the amounts may be unequal--though this result is subject to the assumption that high-redshift dusty galaxies have the same spatial and grain size distributions as low-redshift dust-poor galaxies. The dust properties of high-redshift galaxies may be more diverse than they are in low-redshift galaxies.

High-redshift (z~6) quasars have been served as cosmological probes for studying the early universe. They provide crucial information on the growth of massive black holes (BHs) and formation of galaxies in the first billion years. I focus my dissertation work on exploring various properties of quasars at z~6.Based on our Gemini NIR observations, the metallicity in luminous z~6 quasars is supersolar with a typical value of ~4 Z_sun, and a comparison with low-redshift observations shows no strong evolution in metallicity up to z~6. Central BH masses are found to be 10^9 ~ 10^10 M_sun and Eddington luminosity ratios are of order unity. Our Spitzer observations show that most of z~6 quasars have prominent emission from hot dust. Their SEDs are similar to those of low-redshift quasars at rest-frame 0.15-3.5 um, suggesting that their accretion disks and hot-dust structures have reached maturity. However, two quasars were not detected in our deep 24 um images, and thus show no hot-dust emission, indicating different dust properties. Our ongoing survey of z~6 quasars has resulted in six quasars with z_AB<21 in the SDSS deep area. The bright-end power-law slope of the quasar luminosity function>(QLF) derived from available SDSS quasars is significantly steeper than the slope of the QLF at z~4. Based on this QLF, the quasar population cannot provide enough photons to ionize the IGM at z~6 unless the IGM is very homogeneous and the luminosity at which the QLF power law breaks is very low.My work also includes interesting topics of quasars at lower redshifts. Our deep spectroscopic survey of quasars at z<4 shows that the quasar density at>M_g<-22.5 peaks at z~2, which is later in cosmic time than the peak of z~2.5 found from surveys of more luminous quasars (M_g<-26). This confirms `cosmic downsizing' in quasar evolution. Using a sample of more than 30,000 quasars from SDSS, we find that the radio-loud fraction (RLF) in optically-selected quasars decreases rapidly with increasing redshift and decreasing optical luminosity. This result presents an important constraint on the radio emission mechanism and its cosmic evolution. We obtain 293 quasars with strong NIV] lambda 1486 or NIII] lambda 1750 emission lines from SDSS. These nitrogen-rich (N-rich) objects comprise ~1.1% of the SDSS quasars, and have high overall nitrogen abundances. They share many common properties with other quasars. However, the RLF in the N-rich quasars is much higher than that in other quasars with similar redshift and luminosity. This implies that the high nitrogen abundance in N-rich quasars could be an indicator of a special quasar evolution stage, in which the radio activity is also strong.

I use X-ray and optical data to investigate the structure of quasars, and its dependence on luminosity, redshift, black hole mass, and Eddington ratio. In order to facilitate my work, I develop new statistical methods of accounting for measurement error, non-detections, and survey selection functions. The main results of this thesis follow. (1) The statistical uncertainty in the broad line mass estimates can lead to significant artificial broadening of the observed distribution of black hole mass. (2) The z = 0.2 broad line quasar black hole mass function falls off approximately as a power law with slope ~ 2 for M_{BH} > 10^8 M_{Sun}. (3) Radio-quiet quasars become more X-ray quiet as their optical/UV luminosity, black hole mass, or Eddington ratio increase, and more X-ray loud at higher redshift. These correlations imply that quasars emit a larger fraction of their bolometric luminosity through the accretion disk component, as compared to the corona component, as black hole mass and Eddington ratio increase. (4) The X-ray spectral slopes of radio-quiet quasars display a non-monotonic trend with Eddington ratio, where the X-ray continuum softens with increasing Eddington ratio until L / L_{Edd} ~ 0.3, and then begins to harden. This observed non-monotonic trend may be caused by a change in the structure of the disk/corona system at L / L_{Edd} ~ 0.3, possibly due to increased radiation pressure. (5) The characteristic time scales of quasar optical flux variations increase with increasing M_{BH}, and are consistent with disk orbital or thermal time scales. In addition the amplitude of short time scale variability decreases with increasing M_{BH}. I interpret quasar optical light curves as being driven by thermal fluctuations, which in turn are driven by some other underlying stochastic process with characteristic time scale long compared to the disk thermal time scale. The stochastic model I use is able to explain both short and long time scale optical fluctuations.

In this dissertation, I present nulling interferometric observations of intermediate mass stars and their circumstellar environments. The observations constrain physical processes with regard to the evolution of circumstellar dust in primordial disks, as well as debris disks in main sequence objects. Observations were made in the N-band (near 10 microns) which traces primarily thermal emission from warm dust, and take advantage of the high spatial resolution afforded by nulling interferometry. The first part of the dissertation includes observations of 13 Herbig Ae stars using the BLINC-MIRAC instrument on the MMT and Magellan I (Baade) Telescopes. Three of the 13 objects were spatially resolved (AB Aurigae, HD 100546, and HD 179218). It appears that inferred disk sizes and limits are correlated to the submillimeter SED slope and fractional infrared luminosity of the objects. This implies that disk flaring may have an effect on the resolvability. Further examination of the results reveals evidence for a large inner gap in the HD 100546 disk, possibly resulting in the large inferred disk size. The second part of the dissertation includes observations of six nearby main sequence targets, all of which show no evidence for a positive detection of warm debris. Using a scaled up model of solar zodiacal emission, upper limits on dust density range from 500 to 10^4 Zody (1 Zody = the density of our own solar zodiacal cloud) depending on the particular star, which corresponds to limits of 10^-6 to 5 x 10^-5 earth masses of micron-sized dust. The well studied nature of the debris disks around Vega, epsilon Eridani, and zeta Leporis allows us to place these observations in the context of previous studies at other wavelengths to determine the physical processes responsible for shaping the debris disk in these systems.