Persistence lengths and structure factors of wormlike polymers under confinement

The behavior of semiflexible chains modeling wormlike polymers such as DNA and actin in confined spaces was explored by coarse-grained Monte Carlo simulations. The persistence length,P, mean end-to-end distance < R-2 >, mean radius of gyration < R-2 >, and the size ratio < R-2 >/< R-2 > were computed for chains in slits, cylinders, and spheres. It was found that the intrinsic persistence length of a free chain undergoes on confinement substantial alteration into the apparent persistence length. The qualitative differences were found in trends of the apparent persistence lengths between slits and cylinders on one side and spheres on the other side. The quantities P, < R-2 >, < R-g(2)>, and < R-2 >/< R-g(2)> display similar dependences upon squeezing the chains in nanopores. The above quantities change nonmonotonically with confinement in slits and cylinders, whereas they drop smoothly with decreasing radius of a sphere. For elongation of a chain in a cylinder, two regimes corresponding to strong and moderate confinements were found and compared to experiments and predictions of the blob and Odijk theories. In a spherical cavity, the toroidal chain structure with a hole in the center was detected under strong confinements. The scattering form factor S(q) computed for semiflexible confined chains revealed three regimes of behavior in a slit and a cylinder that matched up well with the scaling theory. The complex form of the function S(q) computed for a sphere was interpreted as a sign of the toroidal structure. A reasonable agreement was found between the simulations and measurements of DNA and actin filaments, confined in nano- and microfluidic channels and spherical droplets, pertaining to the changes of the persistence lengths, chain elongation, and toroidal structure formation.