The Behavior Of Polymer Chains Translocation Through A Nanopore

The translocation of polymers across nanopore is an important process in biology, such as DNA and RNA translocation across nuclear pores, protein transport through membrane channels, and virus injection into cells. Theoretical and experimental studies of this process have attracted considerable attentions due to the importance of this process in biological technique. These results can improve the understanding of the complex transport processes, and bring various potential technological applications, such as rapid DNA sequencing, gene therapy, and controlled drug delivery.In Chapter 2, the dynamics of the translocation of linear polymers through a nanopore under the driving of an applied field is studied by three-dimensional Langevin dynamics simulations. There is a crossover scalingτ～N2v for relatively short chains andτ～N1+v for longer chains. The distribution of translocation time D(τ) is close to a Gaussian function for duration time shorter thanτp and follows a falling exponential function for duration time longer thanτp.In Chapter 3, the dynamics of the translocation of closed circular, closed knotted and folded polymers is also studied by the same method. For closed circular polymers, a crossover scaling of translocation time with chain lengthτ～Nαis found under different field forces. The scaling behavior of longer chains is in good agreement with experimental results. The scaling exponents are much smaller than that of linear polymers for both short chains and long chains. The distribution of translocation time D(τ) shows the same sharp as that of linear polymers. For closed knotted polymers, a remarkable feature of the distribution of translocation time D(τ) is that there are two peaks. With the increase of driving force F, the sub-peak, appearing duration time shorter than mainτp, first increases and reaches a maximum. and then decreases until disappearance. For folded polymers, the distribution of translocation time D(τ) of symmetrical-folded polymers is different from that of dissymmetrical-folded polymers. There is a clear evidence of one-peak for symmetrical-folded polymers and multiple-peak for dissymmetrical-folded polymers. The sharp of translocation time distribution of symmetrical-folded polymers is similar to that of closed circular polymers. A non-single peak distribution of translocation time can distinguish a dissymmetrical-folded polymer from a linear polymer or a symmetrical-folded polymer in the DNA-mixture translocation experiment.In Chapter 4, the dynamics of the translocation of single-stranded DNA and RNA polymers through a nanopore is studied by the same method. A new method is proposed to predict the sequence of single-stranded DNA and RNA by recording the residence time of monomer. The method is utilized to predict the sequence of twenty different chains, and the average accuracy is at about 94.7%. If the residence time of monomer can be well recorded in the DNA translocation experiment, the sequence of the whole DNA will be predicted once and for all. The method provides a low-cost high-throughput way to predict the sequence of DNA.