A system and method for simulating energy transport between particles and an object in radiotherapy is provided. A three-dimensional representation, having a plurality of voxels, is generated for a portion of a patient to be treated. A material index for each of the plurality of voxels is determined. The material index has an identifier for a first boundary material corresponding to a voxel and a percentage of the voxel associated with a second boundary material. The method further comprises simulating energy transport between a particle and the object by calculating an amount of energy deposited by a particle within the patient based on the material indices of the voxels and a list of boundary materials.