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In the present work, a multi-zone model is presented for the simulation of HCCI engines. This model is an improvement of a previous one developed by the authors. The present model describes the combustion, heat and mass transfer processes for the closed part of the engine cycle, i.e. compression, combustion and expansion. The zones occupy geometrical positions within the engine cylinder and exchange heat and mass throughout the compression and expansion strokes, based on their spatial configuration. Heat exchange is considered between zones and to the cylinder wall. A phenomenological model has been developed to describe mass exchange between zones and the flow of a portion of the in-cylinder mixture in and out of the crevice region. The crevice flow is a new feature and is included in the present model since the crevice regions are considered to contribute to unburned HC emissions. Another new feature is the incorporation of chemical kinetics, based on combustion chemistry reactions.