Cement is the key strengthening and the most energy-intensive ingredient in concrete. With increasing pressure for reducing energy consumption in cement manufacturing, there is an urgent need to understand the basic deformation mechanisms of cement. In this thesis, we develop a computational framework based on molecular dynamics to study two common types of defects, namely screw and edge dislocations, in complex, anisotropic crystalline polymorphs of cement clinkers and cement hydration products. We found the likelihood of these defects in regions with higher Young moduli. We also found the preferred cement polymorphs that require less energy for grinding via analysis of Peierls stresses. Together, the results provide a detailed understanding of the role and type of defects in cement phases, which impact the rate of hydration, crystal growth and grinding energy. To our knowledge, this is the first study with atomic-resolution on deformation-based mechanisms in cement crystalline phases.