Gallium nitride (GaN) has emerged as one of the most important semiconductors in modern technology. GaN-based device technology was mainly pushed forward by invention of p-type doping and the successful fabrication of light emitting diodes (LEDs) and laser diodes (LDs). Intensive studies in the last 20 years on GaN have significantly advanced the understanding of the properties and have expanded the range of practical applications. Beside basic lighting, current applications of GaN include high-power and high temperature electronics, microwave, optoelectronic devices, and so on.The successful production of optical devices demands efficient tuning of charge carrier lifetime where defect engineering plays a vital role. During growth, varying the level of recombination centers is difficult, whereas ion irradiation can do this job efficiently on a final product. On the other hand, during doping, undesirable defects can also be produced and epitaxial GaN is known to have a highly defective structure. Thus, having both positive and negative aspects, it is very important to have a detailed understanding of irradiation-induced defects.To explain experimental findings, atomic level understanding is necessary, but it is not always possible to have an atomistic view of defect dynamics in experiments. Some damage build-up studies by single ions have been reported in the literature, but not many by molecular ions. In this thesis, the irradiation of GaN by single and molecular ions by the means of atomistic simulations was studied. The irradiation response of both bulk and nano-structured GaN system were studied. For bulk studies, all projectiles were irradiated having the same energy per mass. The damage by molecular ions showed strong dynamic annealing. No non-linearity had been observed in the total number of point defects between single and molecular ions. On the other hand, molecular ions produce larger clusters of point defects than single ions. These large defect clusters can be one of the mechanisms of the experimentally observed faster carrier decay time for molecular projectiles. Defects were mostly concentrated at the surface and near-surface regions, which is also evident from experiments.ii Comparison between a similar mass single ion and a molecular ion show that a single ion produced more defect clusters than molecular ions. This suggests that heavy ions are even more efficient than similar mass cluster ions to quench the carrier lifetime.