AbstractThe irradiation of silica with ions of specific energy larger than ~0.1 MeV/u produces very high electronic excitations that induce permanent changes in the physical, chemical and structural properties and give rise to defects (colour centres), responsible for the loss of sample transparency at specific bands. This type of irradiation leads to the generation of nanometer-sized tracks around the ion trajectory. In situ optical reflection measurements during systematic irradiation of silica samples allowed us to monitor the irradiation-induced compaction, whereas ex situ optical absorption measurements provide information on colour centre generation. In order to analyse the results, we have developed and validated an atomistic model able to quantitatively explain the experimental results. Thus, we are able to provide a consistent explanation for the size of the nanotracks, the velocity and thresholding effects for track formation, as well as, the colour centre yield per ion and the colour centre saturation density. In this work we will discuss the different processes involved in the permanent modification of silica: collective atomic motion, bond breaking, pressure-driven atom rearrangement and ultra-fast cooling. Despite the sudden lattice energy rise is the triggering and dominant step, all these processes are important for the final atomic configuration.