  We present cosmological, radiation-hydrodynamics simulations of galaxy
formation during the epoch of reionization in an effort towards modelling the
interstellar medium (ISM) and interpreting ALMA observations. Simulations with
and without stellar radiation are compared at large (Mpc), intermediate (tens
of kpc), and small (sub kpc) scales. At large scales, the dense regions around
galaxies reionize first before UV photons penetrate the voids; however,
considerable amounts of neutral gas remain present within the haloes. The
spatial distribution of neutral gas is highly dynamic and is anti-correlated
with the presence of stars older than a few Myrs. For our specific feedback
implementation, most of the metals remain inside the virial radii of haloes and
they are proportionally distributed over the ionized and neutral medium by
mass. For our most massive galaxy with ${\rm M_h}\sim10^{11}$M$_{\odot}$, the
majority of the CII and OI mass are associated with cold neutral clumps. NII is
more diffuse and arises in warmer gas while OIII arises in hotter gas with a
higher ionization parameter, produced by photo-heating and supernovae. If
smaller pockets of high metallicity gas exist in the ISM, the emission from
these ions may be observable by ALMA while the low metallicity of the galaxy
may cause these systems to fall below the local [CII]-SFR relation. The
presence of dust can cause spatial offsets between UV/Ly$\alpha$ and [CII]
emission as suggested by the recent observations of Maiolino et al. [OIII] may
be spatially offset from both of these components since it arises from a
different part of density-temperature phase-space.
