Abstract
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer can accommodate several bases at the same time, making difficult accurate sequencing applications. More recently, the use of graphene membranes has paved the way to new sequencing capabilities, with the possibility to measure transverse currents, among other advances. The reduced thickness of these new membranes poses new questions on the effect of deformability and vibrations of the membrane on the translocation process, two features which are not taken into account in the well established theoretical frameworks. Here, we make a first step forward in this direction. We report numerical simulation work on a model system simple enough to allow gathering significant insight on the effect of these features on the average translocation time, with appropriate statistical significance. We have found that the interplay between thermal fluctuations and the deformability properties of the nano-pore play a crucial role in determining the process. We conclude by discussing new directions for further work.
Highlights
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies
In the last decade, outstanding experiments have involved translocations through nanopores carved in mono-atomic graphene sheets[11,17,18]. These new membranes may provide a solution for the thickness issue, since their width is substantially smaller than a nucleotide
In this paper we have investigated by Molecular Dynamics simulation the driven translocation process of structured polymers through nano-pores carved in thin membranes
Summary
We have devised a minimalistic bead-spring polymer model for single-stranded DNA, only including sterical repulsion and binding of the monomers (see Fig. 1a)). Inspired by the sensibly more elaborated description of ref. 33, we have introduced three types of beads: nP phosphate-like (P) and nS sugar-like (S) units are alternated to form the polymer backbone, while nB lateral base-like (B) units are grafted to the S-beads (Fig. 1a)). No distinction is made at this level between the four bases. NS =nB =n, while one additional P-bead is present at the beginning of the chain (nP =n + 1).
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