Despite the fact that the first-order beam dynamics models allow an approximated evaluation of the beam properties, their contribution is essential during the conceptual design of an accelerator or beamline. However, during the commissioning some of their limitations appear in the comparison against measurements. The extension of the linear model to higher order effects is, therefore, demanded. In this paper, the effects of particle-matter interaction have been included in the model of the transport lines in the proton therapy facility at the Paul Scherrer Institut (PSI) in Switzerland. To improve the performance of the facility, a more precise model was required and has been developed with the multi-particle open source beam dynamics code called OPAL (Object oriented Particle Accelerator Library). In OPAL, the Monte Carlo simulations of Coulomb scattering and energy loss are performed seamless with the particle tracking. Beside the linear optics, the influence of the passive elements (e.g. degrader, collimators, scattering foils and air gaps) on the beam emittance and energy spread can be analysed in the new model. This allows for a significantly improved precision in the prediction of beam transmission and beam properties. The accuracy of the OPAL model has been confirmed by numerous measurements.
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