Characteristic time for the end monomers of a spherically confined polymer to find a nano-pore

Abstract

Translocation of a polymer through a nano-pore is relevant in a variety of contexts such as passage of RNAs through a nuclear pore and transportation of proteins across a membrane. An essential step in polymer translocation is for the end monomers to search the pore. This process requires a characteristic time, referred to as the “attempt time” in this work. Here, we study the attempt time τ of a confined polymer inside a spherical surface by combining a scaling approach and Langevin dynamics simulations. For a moderately to strongly confined polymer, our results suggest that τ ∼ R3.67 for R > P and τ ∼ R2.67 for R < P, where R is the radius of the spherical surface and P is the persistence length of the polymer. All simulation data obtained for an intermediate range of the volume fraction of monomers ϕ(≲ 0.2) tend to collapse onto each other. This implies that τ does not explicitly depend on ϕ, in agreement with the theoretical predictions. These results will be useful for interpreting translocation as a two-step process: the initial attempt to find the pore and eventual pore crossing.

Investigation of Markovian and Non-Markovian Search Processes of Monomers of a Rouse Chain Confined in a Spherical Cavity

“…Hence, the effect of the excluded volume interactions on the search process also deserves a detailed study in future work. Notably, the quantity of central interest is the attempt time in ref . This characteristic time scale is important for understanding the translocation process of confined polymers but differs from the search time considered in the present work.…”

“…Moreover, the Rouse model neglects the excluded volume interactions between monomers, a factor that has been known to affect the monomer distributions of both free and confined polymers. 69 Hence, the effect of the excluded volume interactions on the search process also deserves a detailed study in future work. Notably, the quantity of central interest is the attempt time in ref 69.…”

“…However, this problem is expected to be more complicated for polymers than for particles. Moreover, the Rouse model neglects the excluded volume interactions between monomers, a factor that has been known to affect the monomer distributions of both free and confined polymers . Hence, the effect of the excluded volume interactions on the search process also deserves a detailed study in future work.…”

Translocation of an active polymer into a two dimensional circular nano-container

“…An important factor that affects the translocation or ejection dynamics is the geometry of the trans side, i.e. the available space for the polymer in the trans side, which can be semispace [3,, confined in one dimension [33][34][35], or confined in two and three dimensions [36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52]. The latter case corresponds to the packing/ejection of a DNA or RNA of a virus into/from a capsid.…”

Ejection dynamics of spherically confined active polymers through a small pore

“…For the passive polymers, Bae-Yeun et al have found that the attempt time is related to the spherical cavity's radius and the chain's initial volume fraction, and multiple attempts are required. 46 In order to save simulation time and to focus more on the ejection process, as reported in previous studies, 16,18,47 we choose to put the first bead in the pore initially and prevent it from falling into the cavity.…”