Transit observations in the MgI line of HD209458b revealed signatures of neutral magnesium escaping the upper atmosphere of the planet, while no atmospheric absorption was found in the MgII doublet. Here we present a 3D particle model of the dynamics of neutral and ionized magnesium populations, coupled with an analytical modeling of the atmosphere below the exobase. Theoretical MgI absorption line profiles are directly compared with the absorption observed in the blue wing of the line during the planet transit. Observations are well-fitted with an escape rate of neutral magnesium in the range 2x10^7-3.4x10^7 g/s, an exobase close to the Roche lobe (Rexo in the range 2.1-4.3 Rp, where Rp is the planet radius) and a planetary wind velocity at the exobase vpl=25km/s. The observed velocities of the planet-escaping magnesium up to -60km/s are well explained by radiation pressure acceleration, provided that UV-photoionization is compensated for by electron recombination up to about 13Rp. If the exobase properties are constrained to values given by theoretical models of the deeper atmosphere (Rexo=2Rp and vpl=10km/s), the best fit to the observations is found at a similar electron density and escape rate within 2 sigma. In all cases, the mean temperature of the atmosphere below the exobase must be higher than about 6100 K. Simulations predict a redward expansion of the absorption profile from the beginning to the end of the transit. The spatial and spectral structure of the extended atmosphere is the result of complex interactions between radiation pressure, planetary gravity, and self-shielding, and can be probed through the analysis of transit absorption profiles in the MgI line.
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