  We present self-consistent models of gas in optically-thick dusty disks and
calculate its thermal, density and chemical structure. The models focus on an
accurate treatment of the upper layers where line emission originates, and at
radii $\gtrsim 0.7$ AU. We present results of disks around $\sim 1{\rm
M}_{\odot}$ stars where we have varied dust properties, X-ray luminosities and
UV luminosities. We separately treat gas and dust thermal balance, and
calculate line luminosities at infrared and sub-millimeter wavelengths from all
transitions originating in the predominantly neutral gas that lies below the
ionized surface of the disk. We find that the [ArII] 7$\mu$m, [NeII]
12.8$\mu$m, [FeI] 24$\mu$m, [SI] 25$\mu$m, [FeII] 26$\mu$m, [SiII] 35 $\mu$m,
[OI] 63$\mu$m and pure rotational lines of H$_2$, H$_2$O and CO can be quite
strong and are good indicators of the presence and distribution of gas in
disks. We apply our models to the disk around the nearby young star, TW Hya,
and find good agreement between our model calculations and observations. We
also predict strong emission lines from the TW Hya disk that are likely to be
detected by future facilities. A comparison of CO observations with our models
suggests that the gas disk around TW Hya may be truncated to $\sim 120 $ AU,
compared to its dust disk of 174 AU. We speculate that photoevaporation due to
the strong stellar FUV field from TW Hya is responsible for the gas disk
truncation.
