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Multi-zone CFD simulations with detailed kinetics were used to model iso-octane HCCI experiments performed on a single-cylinder research engine. The modeling goals were to validate the method (multi-zone combustion modeling) and the reaction mechanism (LLNL 857 species iso-octane) by comparing model results to detailed exhaust speciation data, which was obtained with gas chromatography. The model is compared to experiments run at 1200 RPM and 1.35 bar boost pressure over an equivalence ratio range from 0.08 to 0.28. Fuel was introduced far upstream to ensure fuel and air homogeneity prior to entering the 13.8:1 compression ratio, shallow-bowl combustion chamber of this 4-stroke engine. The CFD grid incorporated a very detailed representation of the crevices, including the top-land ring crevice and head-gasket crevice. The ring crevice is resolved all the way into the ring pocket volume. The detailed grid was required to capture regions where emission species are formed and retained.