Artificial construction of atomically defined metal oxide layers is important in making electronics devices including high temperature superconducting oxide films, magnetic and optical devices. Hence, the atomistic understanding of the epitaxial growth process of metal oxide surfaces is desired to fabricate atomically controlled structure that exhibits unexplored and interesting physical properties. Recently, computational chemistry has played an important role to clarify the nature and property of various materials. However its targets are limited to the materials of which structures are already known experimentally. In order to realize the theoretical design of novel materials with unexplored and interesting properties, the prediction of completely new structures by using the computational chemistry is essential. However, no theoretical simulations have been devoted to the prediction of new structures. Hence, we developed a new crystal growth simulator MOMODY based on molecular dynamics approach and applied it to the investigation on various epitaxial growth processes of metal oxide thin films in order to design completely new structures.