Chromatin Dynamics in Human Cells by Improved Brownian Dynamics Method

The mechanisms of chromosome condensation and decondensation processes plays a key role in regulating transcriptions and gene expressions, but it is not sufficiently understood, especially in human cells. So far, three types of chromosome models have been proposed and widely known, while recent experiments have shown that there is polymer-melt-like state which is absent in those models(1). These indicates that the fluidic and density effects by crowded polymers should be taken into dynamical models explicitly in order to explain the above dynamical nature. One of the prototypes for such models is the Rouse model with the Brownian dynamics method. But the method comes with a short time step (1ps ~ 1ns) for its constant force assumption. In this study, we aim to realise in-silico chromatin dynamics in human cells by improving the Brownian dynamics for longer time intervals than picoseconds, and by implementing the density effect as collisions. To the generalized collision process, we simulated the motion of two nucleosomes including the LJ potential and extracted their existence probabilities as discrete data from conputer experiments. Furthermore, by increasing the number of samples, we examined what arbitrary probability density function we could converge to. As a result, the particle movements imply a certain distribution with two peakes whose gap is about the particle radius in the perpendicular direction to the initial to the initial axis of the pair.This suggests the collision process may be generalized.