A wall-resolved large eddy simulation is performed to study secondary tones generated by a NACA0012 airfoil at $alpha = 3^{circ}$ with freestream Mach number $M_{infty} = 0.3$ and Reynolds number $Re = 5 times 10^4$. Laminar separation bubbles are observed over the suction side and near the trailing edge on the pressure side. Flow visualization and spectral analysis are employed to investigate vortex shedding aft of the suction side separation bubble. Vortex interaction results in merging or bursting such that coherent structures or turbulent packets are advected towards the trailing edge leading to different levels of noise emission. Despite the intermittent occurrence of laminar-turbulent transition, the noise spectrum depicts a main tone with multiple equidistant secondary tones. To understand the role of flow instabilities on the tones, the linearized Navier-Stokes equations are examined in its operator form through bi-global stability and resolvent analyses, and by time evolution of disturbances using a matrix-free method. These linear global analyses reveal amplification of disturbances over the suction side separation bubble. Non-normality of the linear operator leads to further transient amplification due to modal interaction among eigenvectors. Two-point correlations of pressure along the spanwise direction elucidate aspects of the acoustic feedback loop mechanism in both the linear and non-linear solutions. This feedback process is self-sustained by acoustic waves radiated from the trailing edge, which reach the most sensitive flow location between 10 and 18% of the airfoil chord as identified by the resolvent analysis.
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