We use coarse-grained Langevin dynamics simulations to study packing of semiflexible polymers into a spherical capsid, with and without a tail, inside a crowded cell. We use neutral and charged, but highly screened, polymers and compare packing rates of the two. Such packing conditions are relevant, for example, to λ DNA packing inside Escherichia coli bacterial cells, where the crowd particles are proteins, bacterial DNA, and salts. For a neutral polymer packing into a capsid with a tail, attractive interactions with the crowd particles make packing slightly harder at higher crowd densities, but repulsive interactions make it easier. Our results indicate that packing into a tailless capsid is less efficient at low crowd densities than into one with a long tail. However, this trend becomes opposite at higher densities. In addition, packing into a capsid with a long tail shows a highly variable waiting time before packing initiates, a feature absent for a tailless capsid. Electrical interactions at physiological conditions do not have much effect. Some bacterial cells, such as Pseudomonas chlororaphis, form a nucleuslike structure encapsulating the phage 201φ2-1 DNA. We also study here the packing dynamics with the nucleus present. We find packing is faster compared to the case of no-nucleus packing. We also observe knot formations but these knots untangle quickly while the polymer translocates. This knot formation is independent of polymer charge and presence of crowd particles.
ASJC Scopus subject areas
- Statistical and Nonlinear Physics
- Statistics and Probability
- Condensed Matter Physics