Related papers: Exploring DNA translocation through a nanopore via…
Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Ionic currents accompanying DNA translocation strongly depend on molarity of the electrolyte solution and the shape and surface charge of the nanopore. By means of the Poisson-Nernst-Planck equations it is shown how conductance is modulated…
Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the…
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
We investigate nanoflows through dilute disordered media by means of joint lattice Boltzmann (LB) and molecular dynamics (MD) simulations -- when the size of the obstacles is comparable to the size of the flowing particles -- for randomly…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces.…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
We present a simplified model of the dynamics of translocation of RNA through a nanopore which only allows the passage of unbound nucleotides. In particular, we consider the disorder averaged translocation dynamics of random, two-component,…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
Polymer dynamics in a turbulent flow is a problem spanning several orders of magnitude of length and time scales. A microscopic simulation covering all those scales from the polymer segment to the inertial scale of turbulence seems…
We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension…