Direct injection Diesel engines are a propulsion technology that is continuously developed to meet emission standards. Great optimization potential lies in the combustion process itself. The application of closed loop combustion control allows reacting online to environmental conditions and stabilizing the combustion regarding performance and emissions. Dedicated real-time plant models help to develop and calibrate control algorithms in office and hardware in the loop environments. The present work describes a real-time capable, crank-angle resolved engine, cylinder and combustion model. The cylinder applies an 0D, two-zone approach and a phenomenological combustion model describes ignition delay, premixed and diffusive combustion. The latter is enhanced by a quasi-dimensional description of the injection spray. The model is validated with dedicated measurements. The plant model is applied in two use-cases for closed loop combustion control. The tradeoff between fuel consumption and noise is optimized via the timing of multiple injections. The interaction between air path control and fuel path control is investigated during a transient load pickup.