Modern internal combustion engines (ICE) operate at the ragged edge of stable operation characterized by high cycle-to-cycle variations (CCV). A key scientific challenge for ICE is the understanding, modeling, and control of CCV in engine performance, which can contribute to partial burns, misfire, and knock. The objective of the current study is to use high-fidelity numerical simulations to improve the understanding of the causes of CCV. Nek5000, a leading high-order spectral element, open source code, is used to simulate the turbulent flow in the engine combustion chamber. Multi-cycle, wall-resolved large-eddy simulations (LES) are performed for the General Motors (GM), Transparent Combustion Chamber (TCC-III) optical engine under motored operating conditions. The mean and root-mean-square (r.m.s.) of the in-cylinder flow fields at various piston positions are validated using PIV measurements during the intake and compression strokes. The large-scale flow structures, including the swirl and tumble flow patterns, are analyzed in detail and the causes for cyclic variabilities in these flow features are explained. The energy distribution across the different scales of the flow are quantified using one-dimensional energy spectra, and the effect of the tumble breakdown process on the energy distribution is examined. The insights from the current study can help us develop improved engine designs with reduced cyclic variabilities in the in-cylinder flow leading to enhanced engine performance.