Micro-phase assembly of active sites in a coarse-grained model of chromatin by Monte Carlo simulation

A coarse-grained model is used to study the self-assembly of active sites in a DNA (chromatin) chain. The chromosome is described by a bond-fluctuating chain of two types of nodes A (interacting) and B (non-interacting), distributed randomly with concentration $C$ and $1-C$ respectively. Active nodes interact with a Lennard-Jones (\textit{LJ}) potential and execute their stochastic motion with the Metropolis algorithm. The depth of the \textit{LJ} potential ($f)$, a measure of interaction strength and the concentration ($C)$ of the active sites are varied. A number of local and global physical quantities are studied such as mobility ($M_{n})$ profile of each node, their local structural profile, root mean square (RMS) displacement ($R)$, radius of gyration ($R_{g})$, and structure factor $S(q)$. We find that the chain segments assemble into microphase of blobs which requires higher concentration of active sites at weaker interaction. These findings are consistent with that of a dynamic loop model of chromatin on global (large) scale but differ at small scales.