This thesis delves into the critical study of particle transport in matter, particularly emphasising its implications for machine protection at CERN's accelerator complex and facilities. To conduct studies of this nature, FLUKA and Geant4 stand out within a small group of general-purpose, multi-particle Monte Carlo codes, validated in energies reaching the multi-TeV. However, their structural differences and user interface philosophies present significant challenges in obtaining results with both codes for the same problems. Overcoming these challenges is crucial, considering the inherent limitations of MC codes due to their physical models and reliance on specific databases for particle transport calculations. A significant contribution of this work is the development of "Moira", a new software that integrates the infrastructure of Geant4 with the capability to process FLUKA inputs. This novel Geant4 application allows for a unique comparison of results between the two codes, enabling simulations with equivalent characteristics, with the primary distinction being the physical models used. Using "Moira", this thesis presents a series of simulations using alternative models to FLUKA's, to analyse shielding and machine protection studies, focusing mainly in scenarios covering sections that span hundreds of meter in the Large Hadron Collider. Doing these simulations with multiple physics models permit to obtain a better quantification of the systematic errors, and also contribute significantly to the development of Monte Carlo codes.