Chromatin dynamics by polymer models and Brownian dynamics with collisions

The primary structure of chromosome is a complex of histone octamer wrapped by double stranded DNA, that is, nucleosome, and the linker DNA connecting them. The mechanism of the chromosome condensation and decondensation processes is to be fully understood, particularly in order to elucidate such dynamics in morphogenetic stages in human. So far, some tertiary structures of chromosome have been proposed, but recent experiments revealed that polymer-melt-like state was found without any specific tertiary structure. These suggest that the dynamics in a dense phase for a longer time span is to be theoretically investigated. However, in general, the Brownian dynamics method assumes constant external force, and is valid with a short time step (1ps ~ 1ns). It is insufficient to simulate chromatin dynamics ina morphogenetic stage in human. The purpose of this research is to investigate and develop an extension of the Brownian dynamics by implementing two types of collision algorithms. Our results confirmed the diffusive nature of nucleosomes in a HeLa cell.