| The translocation of the polymer chain through nanopore can be observed in many life processes,such as transmembrane transport of proteins in cells,transfer of RNA through the nucleus of cells,injection of DNA from viruses into target cells.It also has broad potential application in biology,medicine,chemical and other aspects,for instance,convenient and cheap DNA sequencing technology based on nanopore translocation,bio-controlled drug transport,colloidal electrophoresis,and gene therapy.In this thesis,we use Langevin dynamics simulation and Fokker-Planck theory to study the influence of polymer properties on the translocation process of polymer chain through nanopores.The main results and conclusions are summarized as follows.?1?The translocation time of partially charged polymer chains through neutral nanopores was calculated by using the Fokker-Planck equation under adsorption-adsorption boundary conditions.For a polymer chain with one charged monomer,we found that the translocation time depends on the position of the charged monomer and the strength of the driving force acting on the charged monomer inside the pore.When the charge is located in the front half of the polymer chain,the translocation time is greater than that of the neutral polymer chain,and it increases with the driving force;when the charge is located at the back half of the polymer chain,the translcation time is smaller than that of the neutral polymer chain,and it decreases as the driving force increases.We also studied the translocation time of the polymer chain with two symmetric distributed charges,and that of the polymer chain with two randomly distributed charges.All of out results show that the translocation time is related to the charge position and the driving force.?2?The influence of the chain stiffness on the translocation of a semi-flexible polymer through nanopore is studied by using the Langevin dynamics simulation.The simulation results show that the translocation time increases with the chain stiffness,because the rigid polymer suffers stronger viscous force than the flexible polymer.The scale relationship between the translocation time and the chain stiffness,the polymer length,and the driving force depends on the chain stiffness and the polymer length.It can be seen from these scaling laws that when the chain stiffness is small and the chain length is long?the radius of the gyration is greater than the persistence length?,we can regard the semi-flexible polymer chain as a flexible one.Otherwise?the radius of the gyration is smaller than the persistence length?,it can be regarded as a rigid polymer.The simulation results also show that the out-of-equilibrium effect during the translocation process is weakened with the increasing chain stiffness.?3?The conformational properties of charged polymer chains are related to the system temperature.The polymer chain is in a random coil state at high temperatures and in a tightly globule state at low temperatures.The influence of temperature on the escape of charged polymer chains from nanopores with repulsive interactions was investigated using Langevin dynamics simulation.The scaling relationship between the escape time and the length of the polymer chain is<?esp>N?,with the exponent?=2.43?0.05 independent of temperature.The behavior of polymer escape is similar to that of unbiased polymer translocation.The escape time decreases exponentially with increasing temperature as<?esp>exp?A/T?.We find there are three temperature regimes with different temperature-dependent behaviors,i.e.,A=0.76?0.02 in the high temperature regime T>TH=0.75,0.80?0.02 in the low temperature regime T<TL=0.23,and 0.18?0.01 in the intermediate temperature regime TL<T<TH.We analyze the physical mechanism for small A in the intermediate temperature regime and also uncover the reason for the existing of these three temperature regimes from the viewpoint of free energy.For the escape of polymer,<?esp>can be expressed as the product of the total number of escape steps and the time required for each step.As the temperature decreases,we further find that the time required for each step increases steply at TH while the total number of escape steps increases sharply at TL. |
PDF Full Text Request