The work of modeling and simulation that is summarized in this manuscript deals with three multidisciplinary aspects of the interaction of high-energy ions with matter: physics, radiobiology and computers. The first part focuses on aspects of fundamental physics. It aims at describing and quantifying the mechanisms at work during the interaction of an ion with a material and the structural changes that are induced. The other two parts are directed towards the improvement of cancer treatment by light-ion beam (Hadrontherapy). The aim is to better simulate the physical dose and the biological dose deposited into the organs by the ion beams. While the physical dose reflects the transfer of energy between the ion and the tissues, the biological dose refers to biological effects. The latter cannot simply be deduced from the physical dose and should be modeled. The radiobiology part of the manuscript gathers my contribution to the development of descriptive and predictive models. An experimental evaluation of the predictive models is also presented. Whatever the level of refinement to the modeling of physical and biological dose, if tissue motion is not integrated, dose calculations will be inappropriate. Contention systems can reduce some external movements (head, neck, members ...), but hardly internal motions. The last part of this manuscript is thus dedicated to computer science and focus on the modeling of internal-organ motions, including respiratory motions. These models were constructed in such way that they can integrate the specificities of ion transport in matter.