In order to improve the economic viability of biofuels production, it is necessary to increase the yields of xylose during acid pretreatment. We have used experimental measurements and molecular modeling to understand the mechanisms for xylan hydrolysis to form xylose and the reactions that result in the degradation of xylose. At high temperatures, dehydration reactions can result in a significant loss of sugar. Quantum mechanical molecular modeling showed that attack of the hydronium ion at the O2 hydroxyl group of xylose yields furfural, while attack at O3 yields formic acid. Reversion reactions that yield xylodimers can also result in loss of xylose. These self-reactions are strongly dependent upon xylose concentration, and at the high biomass (> 20 wt%) loadings dictated by economics, reversion reactions are possible. The rates of reversion reactions were measured using a microwave-heated reactor system and HPLC to analyze the products. Kinetic parameters have been extracted from this data and compared to results from quantum molecular dynamics modeling. Finally, the hydrolysis of xylan has been studied in order to understand and model the limits biomass structure place upon mass transfer. The kinetics of hydrolysis of xylo-oligomer, neat xylan and xylan in biomass samples were measured, and in some instances particle size affected kinetics. These results will be discussed in the context of plant cell structure and mass transfer. The kinetics determined from these studies will help optimize reactor performance for higher yields and reduced cost.