With growing concerns over emissions, homogeneous charge compression ignition (HCCI) engines offer a promising solution through reducing NOx and particulate emissions and increasing efficiency. However, this technology is not without its challenges and numerical modeling of these engines can offer some insight into addressing these challenges. This study uses domain decomposition with FORTRAN MPI to subdivide computationally intensive sections of a 10 zone simulation model. Using an Intel i7 quadcore workstation the parallelized model reduced runtimes by half compared to serial computations. From here, two sets of biofuel experimental data were used to improve the validation base of the model. The fuels used were a simulated biomass derived gas (consisting of H2, CH4, CO, CO2, and N2) and a butanol/n-heptane blend. Once calibrated, the model showed good pressure, heat release, and products of incomplete combustion prediction for biogas. NOx emissions were high, however the overall trend was captured. Similarly, once calibrated to the butanol/n-heptane data to account for some of the effects of negative valve overlap (NVO), excellent pressure and heat release predictions were obtained. However, products of incomplete combustion and NOx were low and this was attributed to the inability of the model to properly account for inhomogeneity and all the effects of NVO. Once again though, the overall trend in NOx levels was captured by the model. It was also found that the model does not operate very well near the misfire limit of the engine as it cannot capture the cyclic variability that can occur here. Based on the two new validation cases, it is concluded that once calibrated, the model can be used as a predictive tool for pressure, heat release, and combustion phasing of biofuelled HCCI engines. Furthermore, to improve its predictive capabilities, it is recommended that the model be restructured to incorporate mass transfer between zones, a fixed crevice volume and variable thermal boundary layer, and a CFD solver to improve emissions predictions and reduce reliance on calibration. Finally, changing the zone distribution from ring like zones to lumped stirred reactors is recommended to allow for more realistic modeling of actual experimental HCCI conditions