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To elucidate the processes controlling the auto-ignition timing and overall combustion duration in homogeneous charge compression ignition (HCCI) engines, the distribution of the auto-ignition sites, in both space and time, was studied. The auto-ignition locations were investigated using optical diagnosis of HCCI combustion, based on laser induced fluorescence (LIF) measurements of formaldehyde in an optical engine with fully variable valve actuation. This engine was operated in two different modes of HCCI. In the first, auto-ignition temperatures were reached by heating the inlet air, while in the second, residual mass from the previous combustion cycle was trapped using a negative valve overlap. The fuel was introduced directly into the combustion chamber in both approaches. To complement these experiments, 3-D numerical modeling of the gas exchange and compression stroke events was done for both HCCI-generating approaches.