Conformations And Dynamics Of Confined Polymer Chain

In recent years, the study about confined polymer has attracted considerable attention. On the one hand, this study can help us comprehend many phenomena deep in biology;on the other hand, it has widespread and important prospect on technological applications. The dynamics of confined polymer is complicated. It results in much difficulty of direct experimental detection in detail. Computer simulation is very effective to monitor the dynamical process. With the putting forward of new simulation technology and model and the development of computer hardware, computer simulation will play a more and more important role. In the thesis, polymer confined in different enviroment is studied by computer simulation. We examine influence of different confining medium on comformation and dynamics of polymer.In biology, DNA confined in cell is very common. In chapter 2, the folding process of semiflexible polymer confined in a sphere is studied by the dynamical Monte Carlo(MC) method. An very interesting conformation is observed:local structure is helical and it wraps around the monomers which do not form helical structure. The combination of whole chain's dihedral anglesφand the correlation functions between the tangent vectors u(l)·u(s) can be very effective to characterize the local helical structure. The influence of sphere radius R and bending energy b on the local helical structure is our study focus.When both R and b are moderate, the local helical structure is most ordered and the number of helix turn Nh is largest. Under the other condition,Nh either decreases with the decrease of R and b, or decreases with the increase of R and b.In the chapter 3, Two separated polymers are confined between two soft membranes. The dynamical process of the two chains Under the compression of soft membranes is studied by dynamical MC mothed.We examined the initial distance d between two chains'center of mass and surface tensionσproduce influence on the polymer system. There exists a critical distance dc for d. When d=dc, the state of polymer system shifts from separation state to aggregation state withσincrease;for d<dc, the two chains always aggregate together for anyσ, while for d>dc, the two chains are always in separation state. Meantime it is found that dc～N0.46, N is chain length. When the whole system reaches equilibrium, each chain's conformation is globule for separated polymers, and conformation of aggregated polymers is globule.To own biological activities, protein, especially globule protein, must fold into compact structure. Compact polymer chain can embody such structure. In chapter 4, translocation of compact polymer chain through nanopore is studied by dynamical MC method based on larson model.We examine the influence of N, electric field strength E, middle nanochannel length L and contact energyεc on scaling behaviour and translocation time distribution. Average translocation timeτ～Nα. When L=1 and E is very small, there is no crossover behaviour; under the other condition, there exists crossover behaviour because long chain can produce blockage effect, and crossover behaviour becomes more and more obvious with E andε(?) increase.With E increase,translocation time distribution of compact polymer chain shifts from gaussian distribution to right-skew distribution, however, for long chains, there is an interim process that their translocation time distribution is two-peak distribution.α-helix is the secondary structure of protein and is most common, typical and abundant content in protein.Studying it can help scientists understand the translocation process of protein deep.In chapter 5, the translocation ofα-helix chains through a nanopore is studied by Langevin dynamics method.We found a very special translocation process:unfolding of helical structure→translocation→refold into helical structure.τ～Nα. When the external force f is large, a andτincrease with f increase;when f is small,αandτdecrease with f increase. Meantime, our theoretical results show thatτ～Nl+v/2f-1/2 for moderate f,where v is Flory exponent ofα-helix. The simulative result wholly agrees with it.