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We have developed a methodology for predicting combustion and emissions in a Homogeneous Charge Compression Ignition (HCCI) Engine. The methodology judiciously uses a fluid mechanics code followed by a chemical kinetics code to achieve great reduction in the computational requirements; to a level that can be handled with current computers. In previous papers, our sequential, multi-zone methodology has been applied to HCCI combustion of short-chain hydrocarbons (natural gas and propane). Applying the same procedure to long-chain hydrocarbons (iso-octane) results in unacceptably long computational time. In this paper, we show how the computational time can be made acceptable by developing a segregated solver. This reduces the run time of a ten-zone problem by an order of magnitude and thus makes it much more practical to make combustion studies of long-chain hydrocarbons.