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An integrated experimental and Large-Eddy Simulation (LES) study is presented for homogeneous premixed combustion in a spark-ignition engine. The engine is a single-cylinder two-valve optical research engine with transparent liner and piston: the Transparent Combustion Chamber (TCC) engine. This is a relatively simple, open engine configuration that can be used for LES model development and validation by other research groups. Pressure-based combustion analysis, optical diagnostics and LES have been combined to generate new physical insight into the early stages of combustion. The emphasis has been on developing strategies for making quantitative comparisons between high-speed/high-resolution optical diagnostics and LES using common metrics for both the experiments and the simulations, and focusing on the important early flame development period. Results from two different LES turbulent combustion models are presented, using the same numerical methods and computational mesh. Both models yield Cycle-to-Cycle Variations (CCV) in combustion that are higher than what is observed in the experiments. The results reveal strengths and limitations of the experimental diagnostics and the LES models, and suggest directions for future diagnostic and simulation efforts. In particular, it has been observed that flame development between the times corresponding to the laminar-to-turbulent transition and 1% mass-burned fraction are especially important in establishing the subsequent combustion event for each cycle. This suggests a range of temporal and spatial scales over which future experimental and simulation efforts should focus.