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This study presents an extended Conditional Moment Closure (CMC) model [1] for turbulent spray combustion of a diesel engine. A spatially integrated CMC equation involves multiple flame structures, evaporation source terms for mixture fraction variance and scaled conditional scalar dissipation rates (CSDR) and probability density functions (PDF). An independent transport equation is solved for each flame group with equal mass of sequentially injected and evaporated fuel group. The implementation strategy in KIVA is to determine mean scalar variables instead of mean reaction rates in terms of conditional flame structures and local PDF's. Simulation is performed to test the suggested CMC model for a heavy duty diesel engine with early injection timings. NOx chemistry [2] is combined with skeletal chemistry of n-heptane [3] while soot is modeled by both one equation model [4] and two equation model [5].