  Along the I24, I27 and I31 flybys of Io (1999-2001), the Energetic Particle
Detector (EPD) onboard the Galileo spacecraft observed localised regions of
energetic protons losses (155 keV-1250 keV). Using back-tracking particle
simulations combined with a prescribed atmospheric distribution and a
magnetohydrodynamics (MHD) model of the plasma/atmosphere interaction, we
investigate the possible causes of these depletions. We focus on a limited
region within two Io radii, which is dominated by Io's SO$_2$ atmosphere. Our
results show that charge exchange of protons with the SO$_2$ atmosphere,
absorption by the surface and the configuration of the electromagnetic field
contribute to the observed proton depletion along the Galileo flybys. In the
155-240 keV energy range, charge exchange is either a major or the dominant
loss process, depending on the flyby altitude. In the 540-1250 keV range, as
the charge exchange cross sections are small, the observed decrease of the
proton flux is attributed to absorption by the surface and the perturbed
electromagnetic fields, which divert the protons away from the detector. From a
comparison between the modelled losses and the data we find indications of an
extended atmosphere on the day/downstream side of Io, a lack of atmospheric
collapse on the night/upstream side as well as a more global extended
atmospheric component ($> 1$ Io radius). Our results demonstrate that
observations and modeling of proton depletion around the moon constitute an
important tool to constrain the electromagnetic field configuration around Io
and the radial and longitudinal atmospheric distribution, which is still poorly
understood.
