Double-stranded DNA in which genetic information is encoded is folded into compact protein-DNA complex structures, called “chromatin”, in a nucleus of cell. When DNA is transcribed into RNA for gene expression, chromatin has to be in relaxed conformations. These conformational changes are regulated by chemical modifications of histones and so on. To study the complicated mechanism of life, three-dimensional structures of nucleosomes that compose the chromatin were constructed virtually and molecular dynamics (MD) simulations based on physical laws such as the equation of motion were conducted using the K computer. Such MD calculations enable us to simulate and observe dynamic behaviors of chromatin structures precisely.