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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 t ransfer 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.
We investigate general aspects of molecular line formation under conditions which are typical of prestellar cores. Focusing on simple linear molecules, we study formation of their rotational lines by radiative transfer simulations. We present a therm alization diagram to show the effects of collisions and radiation on the level excitation. We construct a detailed scheme (contribution chart) to illustrate the formation of emission line profiles. This chart can be used as an efficient tool to identify which parts of the cloud contribute to a specific line profile. We show how molecular line characteristics for uniform model clouds depend on hydrogen density, molecular column density, and kinetic temperature. The results are presented in a 2D plane to illustrate cooperative effects of the physical factors. We also use a core model with a non-uniform density distribution and chemical stratification to study the effects of cloud contraction and rotation on spectral line maps. We discuss the main issues that should be taken into account when dealing with interpretation and simulation of observed molecular lines.
Molecular line observations of starless (prestellar) cores combined with a chemical evolution modeling and radiative transfer calculations are a powerful tool to study the earliest stages of star formation. However, conclusions drawn from such a mode ling may noticeably depend on the assumed thermal structure of the cores. The assumption of isothermality, which may work well in chemo-dynamical studies, becomes a critical factor in molecular line formation simulations. We argue that even small temperature variations, which are likely to exist in starless cores, can have a non-negligible effect on the interpretation of molecular line data and derived core properties. In particular, ``chemically pristine isothermal cores (low depletion) can have centrally peaked C$^{18}$O and C$^{34}$S radial intensity profiles, while having ring-like intensity distributions in models with a colder center and/or warmer envelope assuming the same underlying chemical structure. Therefore, derived molecular abundances based on oversimplified thermal models may lead to a mis-interpretation of the line data.
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