Related papers: Sequence dependence of DNA translocation through a…
We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe…
Quantum transport for DNA conduction has widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works with concerning the electronic…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…
Understanding the dynamics of molecules adsorbed to surfaces or confined to small volumes is a matter of increasing scientific and technological importance. Here, we demonstrate a pulse protocol using individual paramagnetic nitrogen…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Longitudinal resolution and lateral sensitivity are decisive characteristics that determine the suitability of a nanopore sensor for sequencing a strand of DNA as well as other important polymers. Previous modeling of DNA induced ionic…
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical…
We study the driven translocation of polymers under time-dependent driving forces using $N$-particle Langevin dynamics simulations. We consider the force to be either sinusoidally oscillating in time or dichotomic noise with exponential…
Nanofabrication techniques for achieving dimensional control at the nanometer scale are generally equipment-intensive and time-consuming. The use of energetic beams of electrons or ions has placed the fabrication of nanopores in thin…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
Extracting the sequence information of DNA from the blocked ionic current is the crucial step of the ionic current-based nanopore sequencing approaches. The thinnest graphene nanopore, which contained only one layer of carbon atoms,…
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…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
We employ 3D Langevin Dynamics simulations to study the dynamics of polymer chains translocating through a nanopore in presence of asymmetric solvent conditions. Initially a large fraction ($>$ 50%) of the chain is placed at the…
We report theoretical studies of charge transport in single-stranded DNA in the direction perpendicular to the backbone axis. We find that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries…
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…
Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…