In this paper, optimized operating parameters were found using multi-dimensional engine simulation software (KIVA-3V) and micro-genetic algorithm for heavy duty diesel engine. The engine operating condition considered was at 1,737 rev/min and 57 % load. Engine simulation model was validated using an engine equipped with a high pressure electronic unit injector (HEUI) system. Three important parameters were used for the optimization - boost pressure, EGR rate and start of injection timing. Numerical optimization identified HCCI-like combustion characteristics showing significant improvements for the soot and $NO_X$ emissions. The optimized soot and $NO_X$ emissions were reduced to 0.005 g/kW-hr and 1.33 g/kW-hr, respectively. Moreover, the optimum results met EPA 2007 mandates at the operating point considered.