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High heat release rates limit the operating range of homogeneous charge compression–ignition engines to low and medium loads. Thermal stratification has been shown to stagger autoignition, lower heat release rates, and extend the operating range of homogeneous charge compression–ignition engines. However, the dependence of naturally occurring thermal stratification on the engine size, speed, and internal residual dilution is not fully understood. A three-dimensional computational fluid dynamics model with large eddy simulations and detailed chemical kinetics was developed using CONVERGE. This model was used to simulate two different engines: (1) a light-duty 2.0 GM Ecotec Engine modified for homogeneous charge compression–ignition combustion in one of the cylinders and (2) a medium-duty Cummins B-series engine modified for homogeneous charge compression–ignition combustion in one of the cylinders. For the light-duty engine, five consecutive modeled cycles were compared with experimental data from 300 consecutive cycles using residual gas dilution at 2000r/min. For the medium-duty engine, five consecutive modeled cycles were compared with experimental data from 100 consecutive cycles using air dilution with intake heating at 1200r/min. In the light-duty engine, it was found that incomplete mixing between fresh charge and residual gas increased thermal stratification early in the compression stroke for residual dilution compared to air dilution. Residual stratification at the onset of ignition was small and not directly coupled with thermal stratification. Heat losses to the walls were the dominant source of thermal stratification at the onset of ignition. The reduced oxygen concentration due to residual dilution, increased the temperature requirement for autoignition, which increased heat transfer losses and increased the thermal stratification around top dead center. The thermal stratification before ignition reduced when the engine speed increased because of the lower heat transfer losses. The light-duty engine was found to have larger portion of the fuel energy lost to heat transfer than the medium-duty engine, which resulted in larger thermal stratification before ignition. [ABSTRACT FROM AUTHOR]