Monte Carlo Simulations of a Semiflexible Chain Model Under Three-Dimensional Extreme Confinements

Investigating the thermodynamically possible structures of a single semiflexible bead-chain model under three-dimensional (3D) extreme confinements is of fundamental interest and may provide insight into genome organization in biological systems. However, it remains difficult to perform equilibrium simulations, and the sampling is usually insufficient and computationally demanding. Based on appropriate approximations and assumptions, we found it feasible to simulate a densely packed semiflexible chain under 3D confinements by performing Monte Carlo (MC) simulations on quasi-lattices. Using the Metropolis algorithm combined with suitable MC updates, we observed confined conformations that exhibit spool-like structures or local nematic order. The simulated chain sizes range from fewer than 100 beads to as many as 10,000 beads.