Monte Carlo studies were conducted related to the design of the Northeast Proton Therapy Center (NPTC). These studies were also helpful for commissioning the beam delivery performance of the facility. The calculations included preventing proton leakage from the beam delivery nozzle, anomalies in the dose distributions and studies, which could influence future beam delivery techniques. Using simulations it was possible to reduce the proton leakage by over an order of magnitude, while minimizing the weight of the assembly. Interestingly, the thickness of the brass shielding has no influence on the secondary neutron radiation since the number of generated neutrons is almost independent of the amount of brass if the primary beam is completely stopped. Monte Carlo simulations are able to study the effect of small beam misalignments with respect to apertures in the nozzle. Such tolerances are very difficult to define experimentally. Studying the effects of nuclear interactions we showed that, if the dose distributions would be optimized theoretically using the primary proton dose alone, there would be about a 5 % dose increase at the proximal end of a SOBP. In radiobiology studies we found that the RBE at beam entrance increases due to the build-up of the secondary particle fluence.