In standard cosmology, both the dark matter and baryons are important constituents of the universe.Although in the perspective of observation, dark matter and baryons are distinct,
they are tightly correlated physically. This gives us a motivation to interpret the
observations by considering them together and
investigating their interactions. In this dissertation, I investigate the transverse proximity
effect in lya transmitted flux,
the baryon
fraction and stellar mass-to-light ratio in early-type galaxies,
and the relation between dark matter halos and
optical observables of galaxy clusters.
The proximity effect is the observed reduction in absorption by HI in the lya
forest in the proximity of QSOs.
This effect was explained as the excess ionization from QSO and used
to investigate the background QSO emission intensity. However, in some of the observations,
there is only very weak or no proximity effect observed at all. This might arise
from the QSOs residing in higher density regions. In this chapter, I investigate the
effect of enhanced density close to QSOs with synthetic spectra from
smoothed particle hydrodynamics (SPH) simulations at redshifts
z=2, z=3, and z=4.