Abstract: Nucleosomes are the fundamental units of the chromatin structure and the smallest units of gene storage in eukaryotes. They consist of a histone octamer and DNA wrapped around it. The dynamic nucleosome structure can regulate interactions between DNA and binding proteins by hiding or exposing the binding sites on DNA, eventually governing gene expression. Experimental methods can be used to study the interactions between nucleosomes and binding proteins at the molecular level but cannot provide mechanistic explanations at the atomic level. Molecular dynamics simulations provide a highresolution method at the atomic level for studying nucleosomes, enabling the visualization of nucleosome behavior and serving as a powerful complement to experimental methods. Herein, the study reviewed the progress in molecular dynamics simulations of the nucleosome structure, regulation of nucleosome function by histone tails, and interactions between nucleosomes. Additionally, the applications of the three acceleration algorithms of molecular dynamics simulations in nucleosome research were discussed.

Key words: nucleosome, molecular dynamics, histone, accelerated sampling method