Static and dynamic properties of a semiflexible polymer in a crowded environment with randomly distributed immobile nanoparticles.

Molecular dynamic simulations are performed for semiflexible polymers in a crowded environment with randomly distributed immobile nanoparticles (NPs). Herein, the effects of chain stiffness (kθ), polymer-NP interaction (εPN), and concentration of NPs (CNP) on the static and dynamic properties of the polymers have been studied. The mean square radius of gyration RG2 can be increased, decreased, or unchanged depending on these three variables. For a fully flexible polymer (kθ = 0), RG2 changes non-monotonously with εPN and CNP. However, for a semiflexible polymer (kθ = 10 with its persistence length larger than the inter-particle distance of the NPs), RG2 decreases monotonously or remains unchanged with an increase in εPN or CNP; this indicates the softening of polymer by the NPs. Moreover, the translational diffusion and rotation of the polymer are retarded by the NPs. Subdiffusion is observed for both the fully flexible polymer and semiflexible polymer at a sufficiently large εPN. The effect of NPs on the translational diffusion is more obvious for the fully flexible polymer because more monomers are in contact with the NPs in the fully flexible polymer. In contrast, the effect of NPs on rotation is more obvious for the semiflexible polymer because it is in contact with more NPs. Furthermore, the rotational relaxation time τR of the semiflexible polymer increases faster with an increase in εPN or CNP than that of the fully flexible polymer.

Temperature dependence of the translocation time of polymer through repulsive nanopores.

The forced translocation of a polymer chain through repulsive nanopores was studied by using Langevin dynamics simulations. The polymer is in the compact globule state at low temperature and in the random coil state at high temperature. Simulation results show that the mean translocation time 〈τ〉 is highly dependent on the temperature T and the minimal 〈τ〉 is located near the coil-globule transition temperature. Moreover, the scaling behaviors 〈τ〉 ∼ Nα and 〈τ〉 ∼ F-δ are studied, with N the polymer length and F the driving force inside the nanopore. Universal values α = 1.4 and δ = 0.85 are observed for the polymer in the random coil state. While for the polymer in the compact globule state, α decreases from α = 2 at weak driving to 1.2 at strong driving for short N and δ increases with decreasing T in the low F region, but we find universal exponents α = 1.6 for long N and δ = 0.85 in the large F region. Results show that polymer's conformation plays a much more important role than the diffusion coefficient in controlling the translocation time of the polymer chain.