To improve the performance of a percolation reactor in dilute-acid pretreatment of biomass containing biphasic hemicellulose, a reactor simulation study was conducted focusing on the refinement of operating strategies and conditions. The optimum temperature difference in step-change operation was determined to be 30 degrees C for a wide range of reaction temperature. Application of temperature step change along with flow-rate step change brought about a 0.6% improvement in product yield over the case with temperature step change alone. The most significant improvement, however, was seen with the application of the two-stage reverse-flow reactor arrangement with temperature change (a design concept originally developed at NREL). Use of this reactor has given an additional 5% improvement in product yield over that of the best-case percolation reactor employing temperature step change. In addition, the effect of intraparticle diffusion on product yield was investigated. The critical chip size (above which the effect of diffusion becomes significant) was determined to be 0.40 cm for 140-170 degrees C operation and 0.29 cm for 150-180 degrees C operation.