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Alternative combustion modes such as homogeneous charge compression ignition (HCCI) and low temperature combustion (LTC) have shown very promising engine-out emissions. However, these combustion modes are close to the combustion stability boundaries and very sensitive to in-cylinder condition variations. Thus, transient control of engines operating in alternative combustion modes are very challenging compared with control of engines with conventional combustion mode only. This paper presents some advanced air-path control and estimation techniques/practice for multiple and alternative combustion mode engine transient operation. Based on the mean-value engine dynamic models, robust controllers can be designed to track the desired air-path performance variables to ensure desirable combustion during transient operation.