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We propose a procedure by which a two-zone thermodynamic model combined with a flame propagation sub-model can used for predicting the cycle-to-cycle variations of combustion in a spark ignition (SI) engine operating at very lean and high exhaust gas residual conditions. Under such conditions, the variations have been shown to consist of both deterministic and stochastic components. The deterministic component is inherent to the non-linear nature of the combustion efficiency variation with equivalence ratio (or dilution level) while the stochastic component results primarily from noise associated with the parameters (that are inevitable in a mechanical system) that affect combustion. Since the overall dynamics of the instabilities are driven by the low order deterministic component, if a model can be made to capture this component, the stochastic component is easily modeled by adding noise to the parameters.