Dynamics Of Polymers In Cofinded And Crowded Environments

Biological macromolecules live in confinded cell spaces which are much smaller than their natural sizes. Meanwhile, intracellular space is occupied by a plenty of macromolecules such as proteins, ribosomes, lipids, cytoskeleton fibers, and chromosomes. The volume fraction of these macromolecules can be as large as 20-40%. Experiments have shown that in confined and crowded environments the dynamic properties of polymer such as diffusion rates, protein folding rates, reaction rates and equilibria in vivo are quite different compared with those in dilute solutions. Thus, the influences of confinement and macromolecular crowding on the dynamics of biopolymers have become one of the central issues in understanding the intracellular biochemical and biophysical reactions.First, using both theoretical analysis and Langevin dynamics simulations in two dimensions, we investigate the dynamics of polymer translocation through a nanopore induced by different sizes of the mobile crowding agents, where the crowding agents have equal area fraction (?) and their diameters are σ and σb≥σ at cis and trans sides, respectively. The chain prefers moving to the side with bigger crowding agents as expected, however, we find the size difference between crowding agents plays a complicated role in the probability of polymer translocation from cis to trans side, the translocation time τ and its distribution, and the translocation exponent. In particular, with increasing σb, the translocation probability shows a maximum value and r has a minimum value. These results can be interpreted by the interplay between the driving force f and the resisting force fr.Next, using Langevin dynamics simulations, we investigate the influences of crowders and the attractive interaction between the polymer and a small number of crowders on segregation of two overlapping polymers under a cylindrical confinement. We find that the segregation time increases with increasing the volume fraction of crowders due to the slower chain diffusion in crowded environments. For a fixed volume fraction of crowders, the segregation time decreases with increasing the size of crowders. Moreover, the attractive interaction between the polymer and a small number of crowders can significantly facilitate the chain segregation. Thus, we propose that the binding interaction between histone-like proteins and chromosomal DNA always provides an effective driving force, which can help the newly replicated chromosomal DNA to segregate into the offspring.In the last chapter, using Langevin dynamics simulations, we investigate the influences of chain rigidity on the ejection dynamics of polymers from a cylindrical nanochannel. We find that there exist two distinct regimes regardless of chain rigidity which depending on whether the chain is fully or partially confined in the channel. At the short chain regime, semiflexible chains eject faster than flexible chains of the same chain length due to the longer occupying length. In contrast, at the long chain regime, semiflexible chains eject slower than flexible ones as the effective entropic driving force decreases. It indicates that the proportion of the time spending in the driven process rises for semi-flexible chains, which producing a greater deviation in the power law τmax～h3. Moreover, due to the high bending energy penalty, segments of semiflexible polymers outside the nanochannel would not accumulate around the nanochannel opening. It leads to a change of the scaling law τlong～h2. However, we find that the rigidity of the chain has no effect on the power lawτlong～P1/3D23, which is consistent with our simulation resluts. Based on these results, we propose that the nanochannels could be used to separate flexible and semiflexible chains effectively.