The use of highly-energetic iOIl: beams for treating cancerous tumours is of increasing importance. In this study the damage caused to plasmid DNA by HO and H+ beams was investigated. Damage to dry DNA samples as a function of dose was assessed using gel electrophoresis. Results show enhanced levels of damage relative to that of x-rays and demonstrate an increase in damage with beam energy. Additionally, a considerable dependence on sample structure was shown. X-ray irradiation work has shown that doping samples with gold nanoparticles greatly enhances DNA damage and could enhance the effectiveness of cancer treatment. Hence in this study, damage to DNA samples containing gold nanoparticles was investigated, however, no enhancement was observed. TOF-MS was used to investigate fragment damage profiles at a molecular level. High-mass fragments corresponding to basal cleavage were not observed. Significant buffer residues in the dried samples were seen and identified. A model of DNA damage as a function of dose was constructed, providing quantitative conclusions about the effects of both gold nanoparticles and the different buffers used. Most of the energy deposited in the body by ionising radiation is absorbed by water molecules, leading to radical formation and, potentially, subsequent DNA damage. Current damage models use information on energy loss rates with penetration depth instead of information on radical production. In this work, fundamental fragmentation processes of water molecules irradiated with H+, HO and carbon ions and atoms were investigated. It was shown that it is imperative to consider the damage caused by fast neutrals in any dose profile modelling. Additionally, results for the ion production rate, to which free-radical production relates directly, show it is actually relatively uniform at a region where the ions come to rest and is not as sharply localised as suggested by the Bragg peak energy loss profiles.