  The volume occupied by the unconstrained genomic DNA of prokaryotes in saline
solutions is thousand times larger than the cell. Moreover, it is not separated
from the rest of the cell by a membrane. Nevertheless, it occupies only a small
fraction of the cell called the nucleoid. The mechanisms leading to such
compaction are the matter of ongoing debates. The present work aims at
exploring a newly proposed mechanism, according to which the formation of the
nucleoid would result from the demixing of the DNA and non-binding globular
macromolecules of the cytoplasm, like ribosomes. To this end, a coarse-grained
model of prokaryotic cells was developed and demixing was analyzed as a
function of the size and number of crowders. The model suggests that compaction
of the DNA is actually governed by the volume occupancy ratio of the crowders
and remains weak almost up to the jamming critical density. Strong compaction
is however observed just before jamming, suggesting that crowding and
electrostatic repulsion work synergetically in this limit. Finally, simulations
performed with crowders with different sizes indicate that the DNA and the
largest crowders demix preferentially. Together with the recent observation of
the gradual compaction of long DNA molecules upon increase of the concentration
of BSA proteins and silica nanoparticles, this work supports the demixing
mechanism as a key player for the formation of the nucleoid.
