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.
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