A majority of disk galaxies host stellar bars that regulate and amplify the flow of angular momentum, J, between disks and their parent dark matter (DM) halos. These bars constitute the prime factor driving internal galaxy evolution. Yet, a non-negligible fraction of disks lack this morphological feature, which led to adoption of the Hubble Fork Diagram. The complex evolution of barred galaxies has been studied by means of numerical simulations, complemented by observations. Despite prolonged efforts, many fundamental questions remain, in part because cosmological simulations still lack the necessary resolution to account for resonant interactions and simulations of isolated galaxies have ignored the cosmological spin of halos. The goal of my thesis is to analyze the J-redistribution in barred galaxies embedded in spinning DM halos, and quantify the DM response. Using high-resolution N-body stellar and DM numerical simulations, I model and analyze the dynamical and secular evolution of stellar bars in disk galaxies and their DM counterparts —induced DM bars in spinning halos with a range of cosmological spin parameter λ ~ 0-0.09. Using a novel method to create initial conditions for the self-consistent equilibrium disk-halo systems, and evolving them for 10 Gyr, I follow the basic parameters of stellar and DM bars, including their observational corollaries. My conclusions are based on nonlinear orbit analysis which quantifies the orbit trapping by the resonances. My main results emphasize a new effect: the DM halo spin has a profound effect on the evolution of stellar and DM bars. Specifically, with increasing λ in the prograde direction: (1) stellar bars develop faster dynamically, but (2) experience a reduced growth during the secular phase of evolution, and basically dissolve for λ > 0.06. These disks can represent the unbarred branch of galaxies on the Hubble Fork Diagram; (3) the stellar bar pattern speeds level off and lose less J; and (4) the stellar bars exhibit ratios of corotation-to-bar radii, RCR/Rbar > 2, representing the so-called slow bars without offset dust lanes. Furthermore, I find that (5) the induced DM bars reach maximal amplitudes which strongly depend on λ, while those of the stellar bars do not; (6) efficiency of resonance trapping of DM orbits by the DM bars, their masses and volumes — all increase with λ; (7) contribution of resonant transfer of J to the DM halo increases with λ as well. (8) prograde and retrograde DM orbits play different roles in J-transfer. (9) Finally, I find that dependence of DM response on λ has important implications for a direct detection of DM and of the associated stellar tracers, such as 'streamers.' Additional results relate the above analysis of corotating disks and halos with those of the counter-rotating ones.

The hierarchical assembly of mass, wherein smaller clumps of dark matter, stars, gas, and dust buildup over time to form the galaxies we see today in the local Universe through accretion events with other clumps, is a central tenet of galaxy formation theory. Supported by theoretically motivated simulations, and observations of the distribution of galaxies over a large range of redshift, the theory of hierarchical growth is now well established. However, on the scales of individual galaxies, hierarchical growth struggles to explain a number of observations involving the amount and distribution of dark matter in galaxies, and the timescale of both the formation of stars, and the assembly of those stars into galaxies. In this dissertation I attempt to address some of the central issues of galaxy formation. My work focuses on massive elliptical galaxies and employs the orbit-based, axisymmetric dynamical modeling technique of Schwarzschild to constrain the total mass of a galaxy to large radii. From this starting point a determination of the extent and shape of the dark matter halo profile is possible and can then be compared to the results of simulations of the formation of galaxies. These dynamical models include information on the stellar orbital structure of the galaxy, and can be used as a further point of comparison with N-body simulations and observations from other groups. Dynamical modeling results for both M49 and M87, the first and second rank galaxies in the Virgo Cluster, are presented and compared in Chapters 4 and 2 respectively. Although both galaxies are similar in mass, a closer analysis shows they exhibit very different dark matter halo profiles and stellar orbital structure, and likely followed very different formation pathways. My primary dataset comes from observations carried out on the Mitchell Spectrograph (formally VIRUS-P) at McDonald Observatory.\footnote{The instrument's name was changed over the last year. As some of this work was originally written when the instrument was named VIRUS-P, I have elected to use that name in those sections of this dissertation (Chapters 2 and 5). In Chapters 3, 4, and 6, I use the current name.} The Mitchell Spectrograph is a fiber-fed integral field spectrograph, and allows one to collect spectra at many positions on a galaxy simultaneously. With spectroscopy one is able to not only constrain the kinematics of the stars, but also their integrated chemical abundances. In the introduction I describe recent work I have carried out with my collaborators using the Mitchell Spectrograph to add further constraints to our picture of galaxy formation. In that work we find that the cores of massive elliptical galaxies have been in place for many billions of years, and had their star formation truncated at early times. The stars comprising their outer halos, however, come from less massive systems. Yet unlike the stars of present day, low-mass galaxies, whose star formation is typically extended, these accreted systems had their star formation shut off at high redshift. Although our current sample is relatively small, these observations place a rigid constraint on the timescale of galaxy assembly and indicate the important role of minor mergers in the buildup of the diffuse outer halos of these systems. All of these advances in our understanding of the Universe are driven, in large part, by advances in the instrumentation used to collect the data. The Mitchell Spectrograph is a wonderful example of such an advance, as the instrument has allowed for observations of the outer halo of M87 to unprecedented radial distances (Chapter 3). A significant component of my dissertation research has been focused on characterizing the fiber optics of both the Mitchell Spectrograph and the fiber optics for the VIRUS spectrograph. I cover the results of the work on the Mitchell Spectrograph optical fibers in Chapter 5. The affects of stress and motion on a fiber bundle, critical to the VIRUS spectrograph, are explored in Chapter 6. / text

How galaxies form and evolve is one of the primary outstanding problems in extragalactic astronomy. I conduct a quantitative census of the relative importance of the major structural components (flattened and dynamically cold disk-dominated components versus puffy and dynamically hot spheroidal or triaxial bulges/ellipticals) in massive galaxies over cosmic time and across different environments in order to explore how galaxies evolve under the action of the various assembly mechanisms (major mergers, minor mergers, gas accretion, and internal secular processes) in these different regimes. I perform three inter-related analyses focusing on massive galaxies from z ~ 0 - 3 in both field and rich cluster environments. Important strengths of this thesis include the use of high-resolution, panchromatic imaging from some of the largest and deepest galaxy surveys with the Hubble Space Telescope (HST), Spitzer, and Chandra space telescopes, and also the inclusion of detailed comparisons between the empirical data and hierarchical ΛCDM-based models of galaxy evolution. / text

In this thesis I study the links between Active Galactic Nuclei (AGN) and their surrounding large scale environments mainly at high redshift. I firstly use Spitzer space telescope data for one of the largest and most uniformly selected samples of radio-loud and radio-quiet AGN at high redshift. It consists of 173 AGN of both type-1 Sloan Digital Sky Survey (SDSS) Quasi- Stellar-Objects (QSOs) and type-2 radio-galaxies at the single cosmic epoch of z ∼ 1. I find significant (8 σ) over-densities of galaxies in the AGNs’ environments when compared to an offset field. Further to this I address the question of whether radio-loud AGN are found, on average, in denser environments than their radio-quiet counterparts. I show that there is a link between the environment and radio luminosity of the most powerful radioloud QSOs and RGs in the sample, and also reconcile the conflicting results in the literature by suggesting that there is only a link to the environment at the highest radio powers. I extend this work to higher redshift with data from the Spitzer extragalactic Representative Volume Survey (SERVS) and type-1 SDSS QSOs in the regions covered by SERVS. This deep data allowed me to study the environments of QSOs in the redshift range 1 < z < 4. Again I find significant (4 σ) over-densities of galaxies around the QSOs in this sample, this time making use of the 3.6-4.5 μm colour to select galaxies more likely to reside at the redshifts of interest. I show that the environments of these QSOs are comparable to those predicted for similarly large black holes in the Durham semi-analytic galaxy formation model (Galform). Finally I use data from the Herschel-Astrophysical Terahertz Large Area Survey with the recently launched Herschel space observatory to study the environments of type-1 QSOs in the far-infrared (FIR). I find a small excess of galaxies around the QSOs for which I find that the star-formation rate increases with increasing redshift. The star-formation rates are estimated by modelling the FIR spectral energy distribution of the galaxies with a modified black-body spectrum. This follows the general increase in starformation rate with redshift observed in the Universe as a whole. I also compare these findings with those made by the Submillimeter Common-User Bolometer Array (SCUBA) of higher redshift QSOs.

In extragalactic astronomy, a central challenge is that we cannot directly watch what happens to galaxies before and after they are observed. This dissertation focuses on linking predictions of galaxy time-evolution directly with observations, evaluating how interactions, mergers, and other processes affect the appearance of elliptical galaxies. The primary approach is to combine hydrodynamical simulations of galaxy formation, including all major components, with dust radiative transfer to predict their observational signatures. The current paradigm implies that a quiescent elliptical emerges following a formative starburst event. These trigger accretion onto the central supermassive black hole (SMBH), which then radiates as an active galactic nucleus (AGN). However, it is not clear the extent to which SMBH growth is fueled by these events nor how important is their energy input at setting the appearance of the remnant. This thesis presents results drawing from three phases in the formation of a typical elliptical: 1) I evaluate how to disentangle AGN from star formation signatures in mid-infrared spectra during a dust-enshrouded starburst, making testable predictions for robustly tracing SMBH growth with the James Webb Space Telescope ; 2) I develop a model for the rate of merger-induced post-starburst galaxies selected from optical spectra, resolving tension between their observed rarity and merger rates from other estimates; and 3) I present results from Hubble Space Telescope imaging of elliptical galaxies in galaxy clusters at 1 < z < 2, the precursors of present-day massive clusters with \(M \sim10^{15}M_{\odot}\), demonstrating that their stars formed over an extended period and ruling out the simplest model for their formation history. These results lend support to a stochastic formation history for ellipticals driven by mergers or interactions. However, significant uncertainties remain in how to evaluate the implications of galaxy appearance, in particular their morphologies across cosmic time. In the final chapter, I outline an approach to build a "mock observatory" from cosmological hydrodynamical simulations, with which observations of all types, including at high spatial and spectral resolutions, can be brought to bear in directly constraining the physics of galaxy formation and evolution. / Astronomy

I investigate the emission properties of the molecular interstellar medium in protoplanetary disks and galaxy mergers, though focus largely on the latter topic. I utilize both numerical models as well as observations to relate the emission characteristics to physical models for the formation and evolution of gas giant planets and galaxies. The main results of this thesis follow. (1) Gas giant protoplanets may be detectable via self-absorption signatures in molecular emission lines with sufficiently high critical density. Given the spatial resolution of e.g. ALMA, gas giant planets in formation may be directly imageable. (2) Starburst and AGN feedback-driven winds in galaxies can leave imprints on the molecular line emission properties via morphological outflows and high velocity peaks in the emission line spectra. Methods for distinguishing between high velocity peaks driven by dynamics versus those driven by winds are discussed. (3) CO line widths on average trace the virial velocity of z ∼ 6 quasar host halos. Thus, if the earliest quasars formed in ∼1013 M ⊙ halos, they are predicted to have broad molecular line widths. Selection effects may exist which tend quasars selected for optical luminosity toward molecular line widths narrower than the slightline-dependent mean. (4) Using the SMT, I observe a roughly linear relation between infrared luminosity and CO (J=3-2) luminosity in local galaxies confirming the results of recently observed L(IR)-HCN (J=1-0) relations. Subsequent modeling shows that observed SFR-molecular line luminosity relations owe to the average fraction of subthermally excited gas in galaxies, and are simply reflective of the assumed Schmidt law governing the SFR.

I investigate the chemical evolution of the Universe in a series of cosmological hydrodynamic simulations with the purpose of finding a self-consistent evolutionary scenario of galaxy formation able to reproduce key observables focusing on the enrichment of the intergalactic medium (IGM). The most successful models I run and analyze use the scalings of momentum-driven feedback whereby UV photons generated during the Main Sequence stage accelerate dust-driven winds while providing a significantly larger energy budget than from supernovae alone. The success of this outflow model relies on its ability to drive highly mass-loaded winds from small galactic haloes. These feedback relations, supported by observations of local starburst, are inserted into simulations at all epochs, reproducing observables including the C IV column density and linewidth distributions at z=6->1.5 and the O VI forest at z=0-0.5. Outflows at z>=5 propagate early nucleosynthetic products traced by C IV and lower ionization species into an otherwise metal-free IGM. Continual outflows at the peak ages of star formation (z=5->1.5) produce a non-evolving cosmic mass density of C IV despite continual enrichment increasing IGM metallicity by a factor of ten. The z=0-0.5 O VI forest is composed of weaker absorbers tracing photo-ionized diffuse IGM metals, sometimes injected by primordial galaxies, and stronger absorbers tracing recently injected metals, often unable to escape their parent haloes and sometimes collisionally ionized. Tracking the individual histories of metals in outflows shows the average outflow travels ~100 physical kpc and returns to galaxies on an average timescale of 1-2 Gyr; this result implies metals in superwinds do not remain in the IGM for a Hubble time and are more likely to rejoin galaxies. Metal absorbers aligned with Lyman-alpha are examined in detail, finding that the two often trace different phases of gas with the former tracing an inhomogeneous distribution of metals exhibiting turbulence imparted during the outflow phase dissipating on a Hubble timescale. I find this is the first model to self-consistently reproduce the wide range of IGM observables spanning the history of heavy metal production while being consistent with key galaxy observables. The link between star formation and galactic superwinds requires that a successful model of galaxy formation reproduces both the evolution of galaxies and the IGM.

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Remarkable progress has been made over the last few decades in furthering our understanding of the growth of cosmic structure. Nonetheless, there remains a great deal of uncertainty regarding the precise details of the complex baryonic physics that regulate galaxy formation. Any theory of star formation in galaxies must encompass the radiative cooling of gas into dark matter haloes, the formation of a turbulent, multiphase interstellar medium (ISM), the efficiency with which molecular gas is able to collapse into cores and ultimately stars, and the subsequent interaction of those stars with the gas through ionizing radiation, winds and supernova (SN) explosions. Given the highly non-linear nature of the problem, numerical simulations provide an invaluable tool with which to study galaxy formation. Yet, even with contemporary computational resources, the inherently large dynamical range of spatial scales that must be tackled makes the development of such models extremely challenging, inevitably leading to the adoption of `subgrid' approximations at some scale. In this thesis, I explore new methods of incorporating the physics of star formation and stellar feedback into high resolution hydrodynamic simulations of galaxies. I first describe a new implementation of star formation and SN feedback that I have developed for the state-of-the-art moving mesh code Arepo. I carry out a detailed study into various classes of subgrid SN feedback schemes commonly adopted in the literature, including injections of thermal and/or kinetic energy, two parametrizations of delayed cooling feedback and a 'mechanical' feedback scheme that injects the appropriate amount of momentum depending on the relevant scale of the SN remnant (SNR) resolved. All schemes make use of individually time-resolved SN events. Adopting isolated disk galaxy setups at different resolutions, with the highest resolution runs reasonably resolving the Sedov-Taylor phase of the SNR, I demonstrate that the mechanical scheme is the only physically well-posed method of those examined, is efficient at suppressing star formation, agrees well with the Kennicutt-Schmidt relation and leads to converged star formation rates and galaxy morphologies with increasing resolution without fine tuning any parameters. However, I find that it is difficult to produce outflows with high enough mass loading factors at all but the highest resolution. I discuss the various possible solutions to this effect, including improved modelling of star formation. Moving on to a more self-consistent setup, I carry out a suite of cosmological zoom-in simulations of low mass haloes at very high resolution, performed to z = 4, to investigate the ability of SN feedback models to produce realistic galaxies. The haloes are selected in a variety of environments, ranging from voids to crowded locations. In the majority of cases, SN feedback alone has little impact at early times even in low mass haloes ($\sim10^{10}\,\mathrm{M_\odot}$ at z = 0). This appears to be due largely to the build up of very dense gas prior to SN events, suggesting that other mechanisms (such as other stellar feedback processes) are required to regulate ISM properties before SNe occur. The effectiveness of the feedback also appears to be strongly dependent on the merger history of the halo. Finally, I describe a new scheme to drive turbulence in isolated galaxy setups. The turbulent structure of the ISM very likely regulates star formation efficiencies on small scales, as well as affecting the clustering of SNe. The large range of potential drivers of ISM turbulence are not fully understood and are, in any case, unlikely to arise ab initio in a whole galaxy simulation. I therefore neglect these details and adopt a highly idealised approach, artificially driving turbulence to produce an ISM structure of my choice. This enables me to study the effects of a given level of ISM turbulence on global galaxy properties, such as the fragmentation scale of the disk and the impact on SN feedback efficiencies. I demonstrate this technique in the context of simulations of isolated dwarfs, finding that moderate levels of turbulent driving in combination with SN feedback can produce a steady-state of star formation rates and global galaxy properties, rather than the extremely violent SN feedback that is produced by a rapidly fragmenting disk.