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 . Although our models are applicable to stars of any mass , we present here only results around \sim 1 { 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 very tenuous and completely 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 } and CO can be quite strong and are good indicators of the presence and distribution of gas in disks . Water is an important coolant in the disk and many water emission lines can be moderately strong . Current and future observational facilities such as the Spitzer Space Telescope , Herschel Observatory and SOFIA are capable of detecting gas emission from young 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 .