Transported probability density function (PDF) methods have shown promise in modeling canonical flame configurations. More recently, they have been applied to simple engine configurations to demonstrate their feasibility in more practical applications, and to demonstrate the importance of accurate accounting for turbulence/chemistry interactions in IC engines. In this work we take PDF methods one step further: skeletal-level chemistry (30 species), a composition PDF method, and a liquid fuel spray model are integrated to compute autoignition and emissions for practical direct-injection diesel and PCCI engine configurations. The detailed information provided by this high-level modeling is used to develop a more fundamental understanding of the underlying physical processes that drive the combustion event and emissions formation. Salient aspects of the physical modeling and numerical methods are discussed, comparisons between results obtained with versus without the PDF model are presented, and comparisons between model results and experimental data are made.