This study investigates the effect of air-injection during the late combustion period produced by an air-cell on emissions from a direct injected diesel engine. The engine considered is a Caterpillar 3401 test engine which was modeled with an air-cell included as part of the piston geometry.A version of the KIVA-II code with updated submodels for diesel combustion and emissions was modified to allow for geometries with walls interior to the domain. This modified version of KIVA-II was then used to model an air-cell equipped diesel engine for four different air-cell configurations.Of the four air-cell configurations simulated, one proved successful in reducing the predicted engine emissions by more than a factor of two while simultaneously reducing NOx by a slight amount, thus moving the engine off its particulate-NOx tradeoff curve defined by varying the fuel injection timing. This air-cell configuration demonstrates that air-injection during the late combustion period can be effective at reducing engine emissions. The other three air-cell configurations simply moved the engine along its particulate-NOx tradeoff. However, this study highlights potential difficulties for designing an air-cell equipped engine. Namely, the large effect produced by the interaction of the turbulence and the in-cylinder flow in the proximity of the air-cell inlet on the overall operation of the air-cell.