Investigating the Physics and Environment of Lyman Limit Systems in
  Cosmological Simulations
  In this work, I investigate the properties of Lyman limit systems (LLSs)
using state-of-the-art zoom-in cosmological galaxy formation simulations with
on the fly radiative transfer, which includes both the cosmic UV background
(UVB) and local stellar sources. I compare the simulation results to
observations of the incidence frequency of LLSs and the HI column density
distribution function over the redshift range $z=2-5$ and find good agreement.
I explore the connection between LLSs and their host halos and find that LLSs
reside in halos with a wide range of halo masses with a nearly constant
covering fraction within a virial radius. Over the range $z=2-5$, I find that
more than half of the LLSs reside in halos with $M < 10^{10}h^{-1}M_\odot$,
indicating that absorption line studies of LLSs can probe these low-mass
galaxies which H$_2$-based star formation models predict to have very little
star formation. I study the physical state of individual LLSs and test a simple
model (Schaye 2001) which encapsulates many of their properties. I confirm that
LLSs have a characteristic absorption length given by the Jeans length and that
they are in photoionization equilibrium at low column densities. Finally, I
investigate the self-shielding of LLSs to the UVB and explore how the
non-sphericity of LLSs affects the photoionization rate at a given $N_{\rm
HI}$. I find that at $z\approx 3$, LLSs have an optical depth of unity at a
column density of $\sim 10^{18} {\rm cm}^{-2}$ and that this is the column
density which characterizes the onset of self-shielding.
