We present a self-consistent model of a protoplanetary disk: ANDES (AccretioN disk with Dust Evolution and Sedimentation). ANDES is based on a flexible and extendable modular structure that includes 1) a 1+1D frequency-dependent continuum radiative transfer module, 2) a module to calculate the chemical evolution using an extended gas-grain network with UV/X-ray-driven processes surface reactions, 3) a module to calculate the gas thermal energy balance, and 4) a 1+1D module that simulates dust grain evolution. For the first time, grain evolution and time-dependent molecular chemistry are included in a protoplanetary disk model. We find that grain growth and sedimentation of large grains to the disk midplane lead to a dust-depleted atmosphere. Consequently, dust and gas temperatures become higher in the inner disk (R < 50 AU) and lower in the outer disk (R > 50 AU), in comparison with the disk model with pristine dust. The response of disk chemical structure to the dust growth and sedimentation is twofold. First, due to higher transparency a partly UV-shielded molecular layer is shifted closer to the dense midplane. Second, the presence of big grains in the disk midplane delays the freeze-out of volatile gas-phase species such as CO there, while in adjacent upper layers the depletion is still effective. Molecular concentrations and thus column densities of many species are enhanced in the disk model with dust evolution, e.g., CO2, NH2CN, HNO, H2O, HCOOH, HCN, CO. We also show that time-dependent chemistry is important for a proper description of gas thermal balance.
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