Despite significant advances in the numerical modeling of galaxy formation and evolution, it is clear that a satisfactory theoretical picture of how galaxies acquire their baryons across cosmic time remains elusive. In this thesis we present a computational study which seeks to address the question of how galaxies get their gas. We make use of new, more robust simulation techniques and describe the first investigations of cosmological gas accretion using a moving-mesh approach for solving the equations of continuum hydrodynamics.

Supermassive black holes (SMBHs) are ubiquitous in the centers of galaxies. Their formation and subsequent evolution is inextricably linked to that of their host galaxies, and the study of galaxy formation is incomplete without the inclusion of SMBHs. The present work seeks to understand the growth and evolution of SMBHs through their interaction with the host galaxy and its environment. In the first part of the thesis (Chap. 2 and 3), we combine a simple semi-analytic model of outflows from active galactic nuclei (AGN) with a simulated dark matter density distribution to study the impact of SMBH feedback on cosmological scales. We find that constraints can be placed on the kinetic efficiency of such feedback using observations of the filling fraction of the Ly[alpha] forest. We also find that AGN feedback is energetic enough to redistribute baryons over cosmological distances, having potentially significant effects on the interpretation of cosmological data which are sensitive to the total matter density distribution (e.g. weak lensing). However, truly assessing the impact of AGN feedback in the universe necessitates large-dynamic range simulations with extensive treatment of baryonic physics to first model the fueling of SMBHs. In the second part of the thesis (Chap. 4-6) we use a hydrodynamic adaptive mesh refinement simulation to follow the growth and evolution of a typical disk galaxy hosting a SMBH, in a cosmological context. The simulation covers a dynamical range of 10 million allowing us to study the transport of matter and angular momentum from super-galactic scales all the way down to the outer edge of the accretion disk around the SMBH. Focusing our attention on the central few hundred parsecs of the galaxy, we find the presence of a cold, self-gravitating, molecular gas disk which is globally unstable. The global instabilities drive super-sonic turbulence, which maintains local stability and allows gas to fuel a SMBH without first fragmenting completely into stars. The fueling appears to be a stochastic process, with no preferred timescale for accretion over the duration of the simulation.

While mounting observational evidence suggests the coevolution of galaxies and their embedded massive black holes (MBHs), a comprehensive astrophysical understanding which incorporates both galaxies and MBHs has been missing. To tackle the nonlinear processes of galaxy formation, we develop a state-of-the-art numerical framework which self-consistently models the interplay between galactic components: dark matter, gas, stars, and MBHs. Utilizing this physically motivated tool, we present an investigation of a massive star-forming galaxy hosting a slowly growing MBH in a cosmological LCDM simulation. The MBH feedback heats the surrounding gas and locally suppresses star formation in the galactic inner core. In simulations of merging galaxies, the high-resolution adaptive mesh allows us to observe widespread starbursts via shock-induced star formation, and the interplay between the galaxies and their embedding medium. Fast growing MBHs in merging galaxies drive more frequent and powerful jets creating sizable bubbles at the galactic centers. We conclude that the interaction between the interstellar gas, stars and MBHs is critical in understanding the star formation history, black hole accretion history, and cosmological evolution of galaxies. Expanding upon our extensive experience in galactic simulations, we are well poised to apply this tool to other challenging, yet highly rewarding tasks in contemporary astrophysics, such as high-redshift quasar formation.

The evolution of a galaxy is pivotally governed by its pattern of star formation over a given period of time. The star formation rate at any given time is strongly dependent on the amount of cold gas available in the galaxy. Accretion of pristine gas from the Intergalactic medium (IGM) is thought to be one of the primary sources for star-forming gas. This gas first passes through the virial regions of the galaxy before reaching the Interstellar medium (ISM), the hub of star formation. On the other hand, owing to the evolutionary course of young and massive stars, energetic winds are ejected from the ISM to the virial regions of the galaxy. A bunch of interlinked, complex astrophysical processes, arising from the concurrent presence of both infalling as well as outbound gas, play out over a range of timescales in the halo region or the Circumgalactic medium (CGM) of a galaxy. It would not be incorrect to say that the CGM has a stronghold over the gas reserves of a galaxy and thus, plays a backhand, yet, rather pivotal role in shaping ...

This thesis focuses primarily on how two important processes --- galaxymergers and gas accretion from the surrounding intergalactic medium ---affect the evolution of galaxies. Using post-starburst, or E+A, galaxies as a marker sample that undergoesa rapid transition from gas-rich star-forming galaxies to quiescent, passively-evolving E/S0s, we study what triggers E+A evolution andwhat E+A galaxies will become after the fading of their young stellarpopulation. With high resolution HST WFPC2/ACS imaging, we investigatetheir small and large scale properties, including their detailedmorphologies, bulge fractions, color gradients, scaling relationships, and newly formed star-clusters. 70% of E+A galaxies show disturbancesand tidal features indicating a merger origin and all their propertiesare either consistent with those of E/S0s or, if left to evolve passively, will become like those of early-types. Using cosmological simulations, we study hydrogen and helium gravitationalcooling radiation from gas accretion by young galaxies, finding thatobserving optically thin cooling lines such as HeII 1640 and hydrogenHalpha is critical in understanding the nature of galaxies forming viagas-accretion. To obtain an unbiased sample of Lyman alpha blobs thatwill allow us to follow-up their optically thin Halpha lines in the NIR, we conduct a blind, wide-field, narrow-band imaging survey for Lymanalpha blobs. After searching over 4.82 deg2̂, we discover four blobsthat we spectroscopically confirm to lie at z=2.3. The properties ofthese blobs are diverse: two blobs are X-ray-detected and have broadoptical emission lines (e.g., CIV) characteristic of AGN. The other50\% of blobs are not X-ray or optically-detected as AGN down tosimilar limits. The number density of the four blobs is extremely low,3̃ x 10-̂6 Mpc-̂3, comparable to that of galaxy clusters at similarredshifts. The two X-ray undetected blobs are separated by only70"(550 kpc) and have almost identical redshifts (corresponding to

While mounting observational evidence suggests the coevolution of galaxies and their embedded massive black holes (MBHs), a comprehensive astrophysical understanding which incorporates both galaxies and MBHs has been missing. To tackle the nonlinear processes of galaxy formation, we develop a state-of-the-art numerical framework which self-consistently models the interplay between galactic components: dark matter, gas, stars, and MBHs. Utilizing this physically motivated tool, we present an investigation of a massive star-forming galaxy hosting a slowly growing MBH in a cosmological LCDM simulation. The MBH feedback heats the surrounding gas and locally suppresses star formation in the galactic inner core. In simulations of merging galaxies, the high-resolution adaptive mesh allows us to observe widespread starbursts via shock-induced star formation, and the interplay between the galaxies and their embedding medium. Fast growing MBHs in merging galaxies drive more frequent and powerful jets creating sizable bubbles at the galactic centers. We conclude that the interaction between the interstellar gas, stars and MBHs is critical in understanding the star formation history, black hole accretion history, and cosmological evolution of galaxies. Expanding upon our extensive experience in galactic simulations, we are well poised to apply this tool to other challenging, yet highly rewarding tasks in contemporary astrophysics, such as high-redshift quasar formation.

This thesis addresses two of the central processes which underpin the formation of galaxies: the formation of stars and the injection of energy into the interstellar medium from supernovae, called feedback. In her work Claudia Lagos has completely overhauled the treatment of these processes in simulations of galaxy formation. Her thesis makes two major breakthroughs, and represents the first major steps forward in these areas in more than a decade. Her work has enabled, for the first time, predictions to be made which can be compared against new observations which probe the neutral gas content of galaxies, opening up a completely novel way to constrain the models. The treatment of feedback from supernovae, and how this removes material from the interstellar medium, is also likely to have a lasting impact on the field. Claudia Lagos Ph.D. thesis was nominated by the Institute for Computational Cosmology at Durham University as an outstanding Ph.D. thesis 2012.