To improve the MixAlco process and biomass pretreatment, five studies were conducted. Three studies related to fermentation, whereas the other two investigated the effectiveness of shock tube pretreatment. In the first study, the constant-selectivity assumption used in the continuum particle distribution model (CPDM) was determined to be invalid. Future revisions to CPDM should incorporate a non-constant selectivity term. In the second study, a revised procedure was developed to provide a more accurate determination of moisture content of mixed-acid fermentation samples. The third study determined essential parameters for pretreating sugarcane bagasse using shock tube pretreatment in a variety of pretreatment regimens. In the fourth study, fixed-bed batch fermentation of pretreated sugarcane bagasse was performed. The fifth study investigated the potential of pretreated corn stover as a ruminant animal feed. Pretreated samples were analyzed for composition and in vitro digestibility.