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A multi-objective genetic algorithm methodology was applied to a heavy-duty diesel engine at three different operating conditions of interest. Separate optimizations were performed over various fuel injection nozzle parameters, piston bowl geometries and swirl ratios (SR). Different beginning of injection (BOI) timings were considered in all optimizations. The objective of the optimizations was to find the best possible fuel economy, NOx, and soot emissions tradeoffs. The input parameter ranges were determined using design of experiment methodology. A non-dominated sorting genetic algorithm II (NSGA II) was used for the optimization. For the optimization of piston bowl geometry, an automated grid generator was used for efficient mesh generation with variable geometry parameters. The KIVA3V release 2 code with improved ERC sub-models was used. The characteristic time combustion (CTC) model was employed to improve computational efficiency.