The intergalactic medium: Absorption, emission, disruption

Two fundamental predictions of modern cosmological models are that (i) galaxies form from small perturbations in the cosmic density field and (ii) there is a tenuous medium between the galaxies that traces the underlying dark matter distribution in a relatively simple way. This thesis concerns the structure of the intergalactic medium (IGM) and its relation to galaxies. Specifically, I analyze the nature of the IGM, observable via the Lyalpha transition of hydrogen, as predicted from cosmological hydrodynamic simulations of a cold dark matter + dark energy universe.;I first quantify the relation between galaxies and absorption in the Lyalpha forest on large (∼10 Megaparsec) and small (∼0.5 Megaparsec) scales and show that, in the absence of feedback from the galaxies themselves, observations of this relation can serve as robust tests of the inflationary cold dark matter model. I show that the strong bias of high redshift galaxies toward high density regions imprints a clear signature on the distribution of flux in the Lyalpha forest, and these predictions are examined as functions of galaxy baryon mass, star formation rate, and dark matter halo mass and occupation.;I then investigate the potential impact of galaxies on the IGM and find that supernova-driven winds (as predicted in cosmological simulations) can substantially impact their local surroundings, particularly via heating, but that only very powerful winds can create easily detectable "holes" in the IGM. The impact of winds on the Lyalpha optical depth near galaxies is less dramatic than their impact on gas temperature because winds heat only a small fraction of the gas present in the turnaround regions surrounding galaxies, all of which contribute to the Lyalpha forest near galaxies.;Finally, I combine a Monte Carlo radiative transfer code with cosmological hydrodynamic simulations to investigate the signature of fluorescent Lyalpha emission from large scale structure due to impinging radiation from the metagalactic ionizing background as well as local bright sources such as quasars. I compare these predictions with current observations and discuss future observing campaigns and realistic strategies for detecting fluorescence from the ambient metagalactic ionization as well as in the vicinity of bright quasars.