Physics – Condensed Matter – Soft Condensed Matter
Scientific paper
2010-06-08
Physics
Condensed Matter
Soft Condensed Matter
Scientific paper
We employ 3D Langevin Dynamics simulations to study the dynamics of polymer chains translocating through a nanopore in presence of asymmetric solvent conditions. Initially a large fraction ($>$ 50%) of the chain is placed at the \textit{cis} side in a good solvent while the $trans$ segments are placed in a bad solvent that causes the chain to collapse and promotes translocation from the $cis$ to the $trans$ side. In particular, we study the ratcheting effect of a globule formed at the \textit{trans} side created by the translocated segment, and how this ratchet drives the system towards faster translocation. Unlike in the case of unbiased or externally forced translocation where the mean first passage time $\langle \tau \rangle $ is often characterized by algebraic scaling as a function of the chain length $N$ with a single scaling exponent $\alpha$, and the histogram of the mean first passage time $P(\tau/\langle\tau \rangle)$ exhibits scaling, we find that scaling is not well obeyed. For relatively long chains we find $\langle \tau \rangle \sim N^\alpha$ where $\alpha \approx 1$ for $\varepsilon/k_{B}T > 1$. In this limit, we also find that translocation proceeds with a nearly constant velocity of the individual beads(monomers), which is attributed to the coiling of the globule. We provide an approximate theory assuming rotat ional motion restricted on a 2D disc to demonstrate that there is a crossover from diffusive behavior of the center of mass for short chains to a single file translocation for long chains, where the average translocation time scales linearly with the chain length $N$.
Ala-Nissila Tapio
Bhattacharya Aniket
Lorscher Christopher
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