This article presents the results of the simulated irradiation with protons and alpha particles of two different geometrical models, representing a cell nucleus and its chromatin content. The characteristics of the energy deposition are studied at both micrometric and nanometric length scales. In particular, the stochastic distributions of the quantities associated with the total energy deposit in the micrometric volume are derived and compared with the physical characteristics of the clusters of energy deposits. An innovative multi-scale correlation method is introduced and tested against the simulations’ data. This new approach links the two relevant length scales exploiting the differences in the kinetic energy spectra of the secondary electrons produced by the primary particles. The characteristics of the energy deposition of the electrons in the chosen material are determined in the first instance. Few free parameters of the model, linking the electrons energy deposits with the total energy deposit of the primary particles, can be used for summarising the characteristic of the irradiation with the chosen radiation quality at the two different length scales.