A toy model for nucleus-sized crowding confinement

We conduct Monte Carlo simulations to understand the spatial distribution of a polymer molecule confined within a rigid spherical capsule under crowding conditions, via a bead-spring chain model. To adjust the crowding level, the polymer is mixed with spherical crowders. As the interior of the capsule becomes more crowded, chain monomers tend to move to the capsule boundary under the penalty of conformational entropy. By incorporating some attraction between monomers and crowders, the polymer chain moves away from the capsule boundary. The interplay, between the conformational entropy, DNA-protein interaction, and molecular crowding induced depletion force between the chain and capsule boundary, may be essential to elucidate the heterogeneous chromatin structure in nuclei. Furthermore, the effects of chain length and size disparity between the monomers and the crowders are also investigated preliminarily.