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The three-dimensional CFD codes KIVA-II and KIVA-3 have been used together to study the effects of intake generated in-cylinder flow structure on fuel-air mixing and combustion in a direct injected (DI) Diesel engine. In order to more accurately account for the effect of intake flow on in-cylinder processes, the KIVA-II code has been modified to allow for the use of data from other CFD codes as initial conditions. Simulation of the intake and compression strokes in a heavy-duty four-stroke DI Diesel engine has been carried out using KIVA-3. Flow quantities and thermodynamic field information were then mapped into a computational grid in KIVA-II for use in the study of mixing and combustion. A laminar and turbulent timescale combustion model, as well as advanced spray models, including wave breakup atomization, dynamic drop drag, and spray-wall interaction has been used in KIVA-II.