Homogeneous charge compression ignition (HCCI) is a viable alternative to current internal combustion modes. HCCI engines exhibit high thermal efficiencies and produce near-zero NOx and soot emissions. In this study, a numerical multi-zone model has been developed in order to predict experimental data from an HCCI engine fuelled with PRF20. The experimental study used dilution to indirectly control combustion and map out the knocking and misfire engine operating limits. These operating limits were examined with the multi-zone model and the trends based on dilution with EGR and excess air ratio were reproduced. Results also indicated that small changes of initial temperature within the reported experimental variance were able to capture the cyclic variability observed in the data. Two PRF chemical kinetic mechanisms of varying detail were contrasted and did not show significant differences in predicted results. Introducing trapped residual gases also did not drastically change the modeled trends.