The goal of radiation therapy is to eradicate tumour cells while minimising radiation dose to healthy tissues. Ions including protons and carbon ions have gained increasing interest for cancer treatment. Advantages of ion beam therapy are conformal dose distribution, and for ions heavier than protons increased biological effectiveness in cell killing, compared to conventional radiation therapy using photons. Despite these advantages, fundamental problems in ion beam therapy include accuracy of dose determination at the cellular level, and characterisation of the radiation quality at the microscopic scale. Due to the high density of interactions along ion tracks, inhomogeneity of dose and track parameters at the cellular level is one of the major concerns for ion beam therapy.

The aim of the thesis is to develop computational tools for dosimetry of ion tracks at the molecular level. Event-by-event Monte Carlo track structure (MCTS) simulations were developed for full-slowing-down tracks of protons and carbon ions in water representing cellular environment. In Paper I, the extension of the MCTS code KURBUC_proton was carried out to energies up to 300 MeV, covering the entire proton energy range used in radiation therapy. Physical properties and microdosimetry of proton tracks were investigated and benchmarked with the experimental data. Papers II-V describe the development of the MCTS code for full-slowing-down tracks of carbon ions. In Papers II-IV, the classical trajectory Monte Carlo (CTMC) model was developed for the calculation of interaction cross sections for low and intermediate energy carbon projectiles of all charge states (C⁰ to C⁶⁺) in water. In Paper V, the calculated cross sections were implemented in a new MCTS code KURBUC_carbon simulating carbon ions of energies 1-10⁴ keV/u in water. This development allows the investigation of track parameters in the Bragg peak region of carbon ion beams.

Publication of the thesis and the published papers make contribution to the physics of ion interactions in matter, and provide a new and complete database of electronic interaction cross sections for low and intermediate energy carbon projectiles of all charge states in water. The MCTS codes for protons and carbon ions provide new tools for biophysical study, including microdosimetry, of ion tracks at cellular and subcellular levels, in particular in the Bragg peak region of these ions.