The study of warm molecular gas in the inner regions of protoplanetary disks is of key importance for the study of planet formation and especially for the transport of H2O and organic molecules to the surfaces of rocky planets/satellites. Recent Spitzer observations have shown that the mid-infrared spectra of protoplanetary disks are covered in emission lines due to water and other molecules. Here, we present a non-LTE 2D radiative transfer model of water lines in the 10-36 mum range that can be used to constrain the abundance structure of water vapor, given an observed spectrum, and show that an assumption of local thermodynamic equilibrium (LTE) does not accurately estimate the physical conditions of the water vapor emission zones. By applying the model to published Spitzer spectra we find that: 1) most water lines are subthermally excited, 2) the gas-to-dust ratio must be one to two orders of magnitude higher than the canonical interstellar medium ratio of 100-200, and 3) the gas temperature must be higher than the dust temperature, and 4) the water vapor abundance in the disk surface must be truncated beyond ~ 1 AU. A low efficiency of water formation below ~ 300 K may naturally result in a lower water abundance beyond a certain radius. However, we find that chemistry, may not be sufficient to produce an abundance drop of many orders of magnitude and speculate that the depletion may also be caused by vertical turbulent diffusion of water vapor from the superheated surface to regions below the snow line, where the water can freeze out and be transported to the midplane as part of the general dust settling. Such a vertical cold finger effect is likely to be efficient due to the lack of a replenishment mechanism of large, water-ice coated dust grains to the disk surface.
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