  We present a detailed comparison between numerical cosmological hydrodynamic
zoom simulations and semi-analytic models (SAMs) run within merger trees
extracted from the simulations. The high-resolution simulations represent 48
individual halos with virial masses in the range 2.4*10^11M_sun < M_Halo <
3.3*10^13M_sun. They include radiative H & He cooling, photo-ionization, star
formation and thermal SN feedback. We compare with different SAM versions
including only this complement of physical processes, and also ones including
supernova driven winds, metal cooling, and feedback from AGN. Our analysis is
focused on the cosmic evolution of the baryon content in galaxies and its
division into various components (stars, cold gas, and hot gas). Both the SAMs
and simulations are compared with observational relations between halo mass and
stellar mass, and between stellar mass and star formation rate, at low and high
redshift. The simulations turn out to have much higher star formation
efficiencies (by about a factor of ten) than the SAMs. Therefore the cold gas
is consumed much more rapidly in the simulations and stars form much earlier.
Also, simulations show a transition between stellar mass growth that is
dominated by in situ formation of stars to growth that is predominantly through
accretion of stars formed in external galaxies. In SAMs, stellar growth is
always dominated by in situ star formation. In addition, SAMs overpredict the
overall gas accretion rates relative to the simulations, and overestimate the
fraction of "hot" relative to "cold" accretion. We discuss the reasons for
these discrepancies, and identify several physical processes that are missing
in our SAM. We also highlight physical processes that are neglected in the
simulations studied here, but which appear to be crucial in order to understand
the properties of real galaxies.
