The condensation of DNA induced by spermine is studied by atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics (SMD) simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA-cation complexes.
The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. In this paper,we focus on the collapse of the polyethylene knotted ring chain,and also present the results of linear and ring chains for comparison. At high temperatures,a fully extensive knot structure is observed. The mean-square radius of gyration per bond S 2/(Nb2) and the shape factor δ depend on not only the chain length but also the knot type. With temperature decreasing,chain collapse is observed,and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity C v ,and the knotted ring chain undergoes gas-liquid-solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse,which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains.
The self-assembly of linear ABC triblock copolymers under cylindrical confinements is investigated in two-dimensional space using the real-space self-consistent field theory. The effects of confinement degrees and preferential strengths on the triblock copolymer phase behaviors with special polymer parameters are first considered. On one hand, different confinement degrees cause different phase behaviors in nanopores with the neutral surfaces. Moreover, the strongly preferential surface fields can surpass the confinement degrees and volume fractions in determing the confined phase behaviors. On the other hand, in contrast, confined morphologies are more sensitive to the variations in the A-preferential surface field strength. Subsequently, the incompatibility degrees between different blocks are systematically varied under cylindrical nanopore confinements. Under cylindrical nanopore confinements, the morphologies are very sensitive to the variations in the incompatibility degrees. Meanwhile, nanopore confinements can affect order-disorder and order-order transition points in the bulk. The corresponding free, internal, and entropic energies as well as the order parameters are also quantificationally examined to deeply investigate the confined phase mechanisms, and a number of morphological transitions are confirmed to be of first-order. These findings may guide the design of novel nanostructures based on triblock copolymers by introducing confinements.
The dynamic behaviours of the translocations of closed circular polymers and closed knotted polymers through a nanopore, under the driving of an applied field, are studied by three-dimensional Langevin dynamics simulations. The power-law scaling of the translocation time τ with the chain length N and the distribution of translocation time are investigated separately. For closed circular polymers, a crossover scaling of translocation time with chain length is found to be τ～ N α , with the exponent α varying from α = 0.71 for relatively short chains to α = 1.29 for longer chains under driving force F = 5. The scaling behaviour for longer chains is in good agreement with experimental results, in which the exponent α = 1.27 for the translocation of double-strand DNA. The distribution of translocation time D(τ) is close to a Gaussian function for duration time τ < τ p and follows a falling exponential function for duration time τ > τ p . For closed knotted polymers, the scaling exponent α is 1.27 for small field force (F = 5) and 1.38 for large field force (F = 10). The distribution of translocation time D(τ) remarkably features two peaks appearing in the case of large driving force. The interesting result of multiple peaks can conduce to the understanding of the influence of the number of strands of polymers in the pore at the same time on translocation dynamic process and scaling property.
