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Transits in the H I 1216 A (Lyman alpha), O I 1334 A, C II 1335 A, and Si III1206.5 A lines constrain the properties of the upper atmosphere of HD209458b.In addition to probing the temperature and density profiles in thethermosphere, they have implications for the properties of the loweratmosphere. Fits to the observations with a simple empirical model and a directcomparison with a more complex hydrodynamic model constrain the meantemperature and ionization state of the atmosphere, and imply that the opticaldepth of the extended thermosphere of the planet in the atomic resonance linesis significant. In particular, it is sufficient to explain the observed transitdepths in the H I 1216 A line. The detection of O at high altitudes impliesthat the minimum mass loss rate from the planet is approximately 6e6 kg/s. Themass loss rate based on our hydrodynamic model is higher than this and impliesthat diffusive separation is prevented for neutral species with a mass lowerthan about 130 amu by the escape of H. Heavy ions are transported to the upperatmosphere by Coulomb collisions with H+ and their presence does not provide asstrong constraints on the mass loss rate as the detection of heavy neutralatoms. Models of the upper atmosphere with solar composition and heating basedon the average solar X-ray and EUV flux agree broadly with the observations buttend to underestimate the transit depths in the O I, C II, and Si III lines.This suggests that the temperature and/or elemental abundances in thethermosphere may be higher than expected from such models...The detection ofSi2+ in the thermosphere indicates that clouds of forsterite and enstatite donot form in the lower atmosphere...

The escape of heavy atoms from the ionosphere of HD209458b. II. Interpretation of the observations