Aerosol jet printing (AJP) is a direct-write additive manufacturing method, which has been utilized particularly for the fabrication of flexible and hybrid electronics (FHE). In spite of the advantages of AJP — e.g., high-resolution material deposition on nonplanar surfaces and accommodation of a wide renege of ink viscosity — AJP inherently is a complex process, prone to nonlinear process changes. Consequently, real-time process monitoring and control (with an understanding of the physics behind aerosol generation and transport) are inevitable. The overarching goal of this work is to establish a physics-based framework for process monitoring and closed-loop control (for correction) in AJP. In pursuit of this goal, the objective is to forward a CFD model to explain the underlying physical phenomena behind aerosol nebulization in AJP. To realize this objective, a 3D compressible, turbulent multi-phase flow CFD model is forwarded. The geometry of the pneumatic atomizer is modeled based on X-ray computed tomography (CT) imaging. The boundary conditions of the problem are defined based on experimental observations. The outcome of this study paves the way for understanding the complex mechanisms of aerosol generation in AJP and also design of efficient atomizers.