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The introduction of more stringent standards for engine emissions requires a steady development of exhaust gas aftertreatment in addition to an optimized cylinder combustion. The reduction of the cold start phase can help significantly to lower cycle emissions. With the goal of optimizing the overall emission performance this study presents a comprehensive simulation approach. A well established 1D gas dynamics and engine simulation model is extended by three key features. These are models for combustion and pollutant production in the cylinder, models for the pollutant conversion in a catalyst, and a general species transport model. This allows to consider an arbitrary number of chemical species and reactions in the entire system.