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Composite materials are made by combining different materials with distinct properties to create a more unique and superior material. Nowadays, composites such as polymer matrix composites (PMCs) are extensively used in aerospace applications due to their excellent thermal stability, high strength, and light weight. Perhaps, the greatest advantage of using composite materials over metals is the ability to tailor the properties of the material by properly choosing the resin, and reinforcement materials. Epoxy polymers are often used as the matrix of advanced PMCs. The failure in PMCs occur mainly in the matrix. Therefore, manipulating the properties of PMCs requires a deep understanding of properties of the matrix. However, despite the excellent service record of PMCs, especially in aerospace applications, in many cases there remains a considerable lack of basic understanding of the microstructure and mechanisms that control their properties. Thus, there is a strong need to develop a better understanding of the role of the microstructure and the dominant deformation mechanisms to improve upon the properties of PMCs for more advanced applications. In this thesis, a coarse-grained molecular dynamics model for modeling a highly cross-linked bisphenol a diglycidyl ether (DGEBA) system are developed to study the effects of microstructural variations on the behavior of PMCs. First, a coarse-grained molecular dynamics model is developed to simulate the thermomechanical properties of large scale epoxy systems. The interactions between particles in the coarse-grained structure are formulated by the inversion of the Boltzmann distribution of …