  Depletion forces play a role in the compaction and de-compation of
chromosomal material in simple cells but it remains debatable whether they are
sufficient to account for chromosomal collapse. We present coarse-grained
molecular dynamics simulations, which reveal that depletion-induced attraction
is sufficient to cause the collapse of a flexible chain of large structural
monomers immersed in a bath of smaller depletants. These simulations use an
explicit coarse-grained computational model that treats both the supercoiled
DNA structural monomers and the smaller protein crowding agents as
combinatorial, truncated Lennard-Jones spheres. By presenting a simple
theoretical model, we quantitatively cast the action of depletants on
supercoiled bacterial DNA as an effective solvent quality. The rapid collapse
of the simulated flexible chromosome at the predicted volume fraction of
depletants is a continous phase transition. Additional physical effects to such
simple chromosome models, such as enthalpic interactions between structural
monomers or chain rigidity, are required if the collapse is to be a first-order
phase transition.
