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A numerical simulation and optimization study was conducted for a medium speed direct injection diesel engine. The engine's operating characteristics were first matched to available experimental data to test the validity of the numerical model. The KIVA-3V ERC CFD code was then modified to allow independent spray events from two rows of nozzle holes. The angular alignment, nozzle hole size, and injection pressure of each set of nozzle holes were optimized using a micro-genetic algorithm. The design fitness criteria were based on a multi-variable merit function with inputs of emissions of soot, NOx, unburned hydrocarbons, and fuel consumption targets. Penalties to the merit function value were used to limit the maximum in-cylinder pressure and the burned gas temperature at exhaust valve opening. The optimization produced a 28.4% decrease in NOx and a 40% decrease in soot from the baseline case, while giving a 3.1% improvement in fuel economy.