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Physics-based models in a closed-loop feedback control of a premixed charge compression ignition (PCCI) engine can improve the combustion efficiency and potentially reduce harmful NOx and soot emissions. A stand-alone multi-zone combustion model has been proposed in the literature using a physics-based mixing approach. The scalar dissipation rate emerged as the determining parameter in the model for mixing among different zones in the mixture fraction space. However, the calculation of the scalar dissipation rate depends on three approaches: three-dimensional computational fluid dynamics (3-D CFD) combustion simulations based on representative interactive flamelet (RIF) model, tabulation, or an empirical algebraic model of the scalar dissipation rate fitted for the given operating conditions of the engine. While the 3-D CFD approach provides accurate results, it is computationally too expensive to use the multi-zone model in closed-loop control.