Related papers: Single Stranded DNA Translocation Through a Fluctu…
Understanding excitation and charge transfer in disordered media is a significant challenge in chemistry, biophysics and material science. We study two experimentally-relevant measures for carriers transfer in finite-size chains, the…
We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the…
We simulate a tug-of-war (TOW) scenario for a model double-stranded DNA threading through a double nanopore (DNP) system. The DNA, simultaneously captured at both pores is subject to two equal and opposite forces $-\vec{f}_L= \vec{f}_R$…
Translocation through a nanopore is a new experimental technique to probe physical properties of biomolecules. A bulk of theoretical and computational work exists on the dependence of the time to translocate a single unstructured molecule…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…
The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the…
We present a one-dimensional model for diffusion in a fluctuating lattice; that is a lattice which can be in two or more states. Transitions between the lattice states are induced by a combination of two processes: one periodic…
We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional (2D) fluctuating bond model with single-segment Monte Carlo moves. To overcome the…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavour to match any…
We consider the dynamics of pore-driven polymer translocation through a nanopore to semi-infinite space when the chain is initially confined and equilibrated in a narrow channel. To this end, we use Langevin dynamics (LD) simulations and…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
We investigate the translocation dynamics of a folded linear polymer which is pulled through a nanopore by an external force. To this end, we generalize the iso-flux tension propagation (IFTP) theory for end-pulled polymer translocation to…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one…
General upper bounds on fluctuations of trajectory observables were recently obtained. It turned out that the size of fluctuations of dynamical observable is limited from below and from above. For the moment generating function of general…
Plastic deformation mediated by collective dislocation dynamics is investigated in the two-dimensional phase-field crystal model of sheared single crystals. We find that intermittent fluctuations in the dislocation population number…
The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of…