1. A method, comprising: condensing, by a processor, an original voxel-beamlet matrix stored in a memory device into a reduced dataset for proton beam simulation and therapy, the original voxel-beamlet matrix having a row for each of a plurality of voxels in a three-dimensional patient volume and a column for each of a plurality of radiation beamlets, wherein said condensing step comprises: determining protobeams to be extracted from the original voxel-beamlet matrix, the protobeams being columns (i) selected from the original voxel-beamlet matrix based on comparisons performed between the columns in the original voxel-beamlet matrix or (ii) created by combining at least some of the columns in the original voxel-beamlet matrix, in a matrix condensing process; extracting the protobeams from the original voxel-beamlet matrix; and storing the protobeams as the reduced dataset in the memory device.