Conformations/Dynamics Of Semiflexible And Knotted Polymer Chain Under Confined/Flow Conditions

In recent years, the aggregation behavior, configuration and migration behaviors of polymer as well as the properties of knotted polymer have induced large interest for researchers. The result of computer simulation is very effective to exhibit the properties of the polymer as well as monitor the properties of the polymer. So, computer simulation is obviously very important method to study the properties of polymer. In this thesis, we adopt computer simulation method to study the self-assembly behavior of nanorods on soft elastic shells, the configurantion and migration behavior of polymer chain under poiseuille flow, in addition, the phase behavior and the dynamics process of a knotted polymer chain.In chapter2, using the molecular dynamics (MD) simulation method, we investigate the self-assembly behavior of nanorods (NRs) on soft elastic shells. The self-assembly structures of the adsorbed nanorods depend on the length of the nanorods as well as the bending energy of the soft elastic shells. For short nanorods, the aggregates consist of regular pentagons around the gibbosity at low bending energies, and the ordered structures are gradually broken when the bending energy increases. In the meantime, the adsorption ability of the nanorods on the elastic shells decreases w:hen the binding energy increases. For long nanorods, the binding energy can induce the nanorods to aggregate in clusters on shells with low or moderate bending energy, and each cluster is formed by several parallel long nanorods. However, the self-assembly structures of long nanorods disappear for shells with high bending energy because the adsorption becomes isotropic for nanorods on a rigid shell. Meanwhile, the adsorption of nanorods on the shell can affect the shape of the soft elastic shell.In chapter3, we use molecular dynamics method (MD) combined with multi-particle collision dynamics (MPCD) method to investigate the effect of poiseuille flow on the conformations and migration behaviors of semiflexible chains confined in two infinite flat planes. At low shear rates, the semiflexible chain keeps semirigid conformation in the plane parallel to the infinite flat wall. At high shear rates, the semiflexible chain extends in the flow direction, and it migrates away from the two plat planes with considering hydrodynamics interactions between polymers and solvent molecules. Comparisons with flexible chains are also made.In chapter4, the phase behavior of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. 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 <S2>/(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 Cv, 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.In chapter5, we take3, knot as an example, it passing through a pore is studied by molecular dynamics method. And found that, the size of the knot fluctuates until the knot is unknotted during the process of translocation. The effect of the knot on the translocation velocity of the knotted chain is discussed qualitatively. For the given external force, the average translocation time r satisfies the scaling relation τ～Nα, and the scaling exponent α increases with the external force f For short knotted polymer chains, the average translocation time r decreases when the external force f increases. However, for very long knotted polymer chains, the average translocation time τ increases when the external force f increases. In the meantime, the position of knot in a knotted polymer chain also affects the average translocation time τ strongly. The closer the knot approaches the first translocated monomer, the longer the average translocation time.