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The Extended Coherent Flamelet Model (ECFM) is limited to lower order upwinding schemes to minimize the numerical discrepancy between species and tracers, which can lead to inaccurate estimates of the progress variable and consequently negative conditional mass fractions in the burned gases after ignition. The recently developed Species-Based ECFM (SB-ECFM) removes the species tracers from the definition of the progress variable, and allows the use of higher order schemes. In this study, SB-ECFM is coupled with the Imposed Stretch Spark Ignition Model (ISSIM) to simulate a spark-ignition engine, the transparent combustion chamber (TCC) engine. To examine the spatial discretization effect and demonstrate the improvement due to using higher order schemes, Reynolds-Averaged-Navier-Stokes (RANS) simulations performed with a first-order upwinding scheme and a second-order central differencing scheme are compared.