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Register a new userEjection dynamics of a ring polymer out of a nanochannel
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We investigate the ejection dynamics of a ring polymer out of a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. The ejection dynamics for ring polymers shows two regimes like for linear polymers, depending on the relative length of the chain compared with the channel. For long chains with length $N$ larger than the critical chain length $N_{c}$, at which the chain just fully occupies the nanochannel, the ejection for ring polymers is faster compared with linear chains of identical length due to a larger entropic pulling force; while for short chains ($N<N_c$), it takes longer time for ring polymers to eject out of the channel due to a longer distance to be diffused to reach the exit of the channel before experiencing the entropic pulling force. These results can help understand many biological processes, such as bacterial chromosome segregation.
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Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation through a nanochannel embedded in two dimensions under an applied external field. We examine the translocation time for various ratio of the channel length $L$ to the polymer length $N$. For short channels $Lll N$, the translocation time $tau sim N^{1+ u}$ under weak driving force $F$, while $tausim F^{-1}L$ for long channels $Lgg N$, independent of the chain length $N$. Moreover, we observe a minimum of translocation time as a function of $L/N$ for different driving forces and channel widths. These results are interpreted by the waiting time of a single segment.
We investigate the chain conformation of ring polymers confined to a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. We predict that the longitudinal size of a ring polymer scales with the chain length and the diameter of the channel in the same manner as that for linear chains based on scaling analysis and Flory-type theory. Moreover, Flory-type theory also gives the ratio of the longitudinal sizes for a ring polymer and a linear chain with identical chain length. These theoretical predictions are confirmed by numerical simulations. Finally, our simulation results show that this ratio first decreases and then saturates with increasing the chain stiffness, which has interpreted the discrepancy in experiments. Our results have biological significance.
Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy $epsilon$ between the chaperone and the chain and the chaperone concentration $N_c$ can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time $tau$ has a transition from long-tailed distribution to Gaussian distribution with increasing $epsilon$. $tau$ rapidly decreases and then almost saturates with increasing binding energy for short chain, however, it has a minimum for longer chains at lower chaperone concentration. We also show that $tau$ has a minimum as a function of the chaperone concentration. For different $epsilon$, a nonuniversal dependence of $tau$ on the chain length $N$ is also observed. These results can be interpreted by characteristic entropic effects for flexible polymers induced by either crowding effect from high chaperone concentration or the intersegmental binding for the high binding energy.
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in the channel. Such a setup mimics typical experimental situations in nano/micro-fluidics. During the the translocation process if the monomers in the channel can sufficiently quickly assume steady state motion, we observe the scaling $tausim N/F$ of the translocation time $tau$ with the driving force $F$ per bead and the number $N$ of monomers per chain. With smaller channel width $R$, steady state motion cannot be achieved, effecting a non-universal dependence of $tau$ on $N$ and $F$. From the simulations we also deduce the waiting time distributions under various conditions for the single segment passage through the channel entrance. For different chain lengths but the same driving force, the curves of the waiting time as a function of the translocation coordinate $s$ feature a maximum located at identical $s_{mathrm{max}}$, while with increasing the driving force or the channel width the value of $s_{mathrm{max}}$ decreases.
We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we characterize the coupled dynamics of knot size variation and knot diffusion along the polymer, which ultimately leads to spontaneous unknotting. We find that the knot grows to macroscopic size before disappearing. Interestingly, an external force applied to the ends of the confined polymer speeds up spontaneous unknotting.
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