Molecular Dynamics

This chapter outlines approaches to the hyperordered structures using molecular dynamics simulations. Molecular dynamics is a simulation technique that can be applied to a wide range of materials, from proteins to inorganic materials, and can be a valuable tool for understanding the essential aspects of the hidden hyperordered structure in materials. A more attractive feature of molecular dynamics is the ability to directly evaluate dynamical properties via the simulations, such as rotation, translation, and vibration of molecules. Conventional molecular dynamics calculations cannot explicitly deal with the bond breaking and formation that accompany chemical reactions and phase transition. With the improvement of such limitations of traditional molecular dynamics, reaction force field and ab initio molecular dynamics are now available to understand chemical reactions around hyperordered structures. As a new trend, machine-learning molecular dynamics calculations, in which the interatomic potentials are described by a machine-learning model trained by ab initio calculations, are progressing. We describe the simulation of a metal complex in protein as a typical hyperordered structure. In the case of silicate materials, we discuss the simulations of radiation-induced defect structures related to the hyperordered structures and unique coordination structures in silicate materials. We also show the application of machine-learning molecular dynamics simulations to elucidate the structures in oxides and metal alloys.