A heavy-duty diesel engine (ETH-LAV single cylinder MTU396 heavy duty research engine) was simulated by RANS and advanced reacting flow models to gain insight into its soot and NOx emissions. Due to symmetry, a section of the engine containing a single injector-hole was simulated. Dodecane was used as a surrogate to emulate the evaporation properties of diesel and a 22-step reaction mechanism for n-heptane was used to describe combustion. The Conditional Moment Closure (CMC) method was used as the combustion model in two ways. In a more conventional modelling approach, CMC was fully interfaced with the CFD and a two-equation model was employed for determining soot while the extended Zeldovich mechanism was used for NOx. In a second approach called the Imperfectly Stirred Reactor (ISR) method, the CMC equation was integrated over space and the previous RANS-CMC solution was further analysed in a post-processing step with the focus on soot. Here, a complex sectional soot model called the Napoli sectional (NAPS) model was used to calculate soot particle size distributions (PSD). Three different cases with variations in the start of injection (SOI) were analysed. The calculated pressure trace showed very good agreement with the experiment for all conditions studied. The resulting soot mass fraction from the simulations was found to increase as the SOI was progressed closer to the top dead centre (TDC). The opposite behaviour was observed for NOx in that its mass fraction decreased with progressing SOI. These trends show good agreement with the results from experiments and are consistent with previous studies. Finally, the ISR results for soot were analysed for both two-equation and NAPS models. Soot mass fraction and PSDs were overestimated by the ISR model but the sooting trends for varying conditions were correctly captured.