Translocation Time

Wei and Srivastava [8] reported diffusion of polymers to be several orders of magnitude faster than through the zeolite chaimels (of comparable size) and also report the translocation time through the nanotube scales as N, where N is the number of monomers in a polymer. Gao et al. [9] calculated that a single-stranded DNA will spontaneously insert into the nanotubes from water solutions provided that the nanotube is big enough, attributing the mechanism to van der Waals attraction. Ye H and Hummer studied electrophoretic transport of nucleic acids through 1.5-nm carbon nanotubes. Their simulation showed that without electric field, RNA would remain trapped in the hydrophobic pores. Sorin and Pande [10] recently also demonstrated that confinement inside a nanotube denatures protein helices. 

Milchev et al. [74, 75] found that it makes a big difference whether one studies the case in which in equilibrium a chain is not yet absorbed on the tram side (and still in a mushroom state when the chain gets through the pore) or whether adsorption occurs. In the first case, the problem is similar to unbiased translocation (which occurs by thermal fluctuations only [81, 82]), i.e., for any finite fraction of monomers that have already passed to the tram side there is still a non-zero probability that the whole chain returns to the cis side (and diffuses away). In this case, the translocation time is found to scale as t oc N N -, i.e., the time is simply of the order of the Rouse time of a single chain in a good solvent (note that the Monte Carlo modeling of Milchev et al. [74,75] uses implicit solvent... 

For strong forces, the translocation time can be estimated as < r >= Ci toAT + / /a + C2 To IV /Za where the first term dominates under condition... 

Figure 3. First-passage time of the tracer particle within steady-state flux. Mean translocation time of an individual particle within a non-equiUbrium steady-state flux through the channel, normalized by the transport time in an empty channel, 7 as a function of the flux through the channel. The lines are analytical results dots are the simulations. Based on Ref. 80.

The main conclusion is that the crowding increases the average translocation time, while decreasing the average time of abortive transport events, in which the particle returns from site 1. Surprisingly, for the uniform and symmetric process. 

Note that the transport probability is again the same as in the non-interacting particle case but the translocation time scales as AE. The model also allows to... 

The details of the time-dependence of the ionic current bear information on the manner in which polymer molecules attempt to translocate through a pore and the underlying molecular mechanism of polymer threading. Experiments show that the average translocation time, for single-file translocation processes. 

The probability distribution of the first passage time and its moments can be obtained from the Fokker-Planck equation for general situations of F x) and i/f (x), by following the standard procedures given in Section 6.6. In the present context, the average translocation time is the mean first passage time, which can be calculated by choosing the appropriate boundary conditions for P(x,t). 

Furthermore, the standard deviation or of the translocation time distribution is reported (Chen et al. 2004a) to be proportional to the average translocation time. 

In a parallel study (Storm et al. 2005a,b), using different solid-state nanopores, but with comparable pore diameters, the translocation time for... 

Figure 10.5 (a) Schematic diagram for the transport of DNA through a periodic array of entropic traps, (b) The average translocation time decreases with DNA length. (Adapted from Han, J. and Craighead, H.G., Science, 288, 1026, 2000.)... 

Most of the simulations on polymer translocation involve uncharged flexible chains, focusing on the dependence of the average translocation time on the chain length. The exponent a in the relation. 

Figure 10.9 (a) Sketch of a generic free energy profile for translocation as a function of the number of monomers that are already translocated into the receiver compartment, (b) Sketch of two trajectories for the time evolution of the number of monomers translocated into the receiver compartment. The translocation time is the first passage time. 

---