Deconvoluting chain heterogeneity from driven translocation through a nanopore

Department of Physics, University of Central Florida - Orlando, FL 32826-2385, USA

Received: 19 November 2014
Accepted: 19 January 2015

Abstract

We study translocation dynamics of a driven compressible semi-flexible chain consisting of alternate blocks of stiff and flexible segments of size m and n, respectively, for different chain length N in two dimensions (2D). The free parameters in the model are the bending rigidity which controls the three-body interaction term, the elastic constant k_F in the FENE (bond) potential between successive monomers, as well as the segmental lengths m and n and the repeat unit and the solvent viscosity γ. We demonstrate that due to the change in entropic barrier and the inhomogeneous viscous drag on the chain backbone a variety of scenarios are possible, amply manifested in the waiting time distribution of the translocating chain. This information can be deconvoluted to extract the mechanical properties of the chain at various length scales and thus can be used to nanopore based methods to probe bio-molecules, such as DNA, RNA and proteins.