Related papers: Single Stranded DNA Translocation Through A Nanopo…
We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across…
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the 2D fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength $E$,…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
We investigate a model of chaperone-assisted polymer translocation through a nanopore in a membrane. Translocation is driven by irreversible random sequential absorption of chaperone proteins that bind to the polymer on one side of the…
The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the…
We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics.…
The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples…
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.…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
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…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site…
Using Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a circular nanocontainer through a nanopore under a driving force $F$. We observe that the translocation probability initially increases and then…
Motivated by experiments in which a polynucleotide is driven through a proteinaceous pore by an electric field, we study the diffusive motion of a polymer threaded through a narrow channel with which it may have strong interactions. We show…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
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 systematic study of electron or hole transfer along DNA dimers, trimers and polymers is presented with a tight-binding approach at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters…