Related papers: Chain deformation helps translocation
Given the piecewise approach to modeling intermolecular interactions for force fields, they can be difficult to parameterize since they are fit to data like total energies that only indirectly connect to their separable functional forms.…
A transient analysis for vesicle deformation under DC electric fields is developed. The theory extends from a droplet model, with the additional consideration of a lipid membrane separating two fluids of arbitrary properties. For the…
Stress relaxation following deformation of an entangled polymeric liquid is thought to be affected by transient reforming of chain entanglements. In this work, we use single molecule techniques to study the relaxation of individual polymers…
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…
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 propose a method for the theoretical investigation of polymer translocation through composite pore structures possessing arbitrarily specified geometries. Translocation through each constituent part of the composite is treated as being…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
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…
In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in…
We propose an analytical method for understanding the problem of long range electron transfer reaction in solution, modeled by a particle undergoing diffusive motion under the influence of many potentials which are involved (donor - bridge…
We study the behavior of single linear polyelectrolytes condensed by trivalent salt under the action of electric fields through computer simulations. The chain is unfolded when the strength of the electric field is stronger than a critical…
We study the driven translocation of a flexible polymer through an interacting conical pore using Langevin dynamics simulations. We find that, for a fixed value of externally applied force and pore polymer interaction strength, the mean…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We study translocation dynamics of a driven compressible semi-flexible chain consisting of alternate blocks of stiff ($S$) and flexible ($F$) segments of size $m$ and $n$ respectively for different chain length $N$ in two dimension (2D).…
We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and…
Conformational properties of a single flexible polyelectrolyte chain in a poor solvent are studied using constant temperature molecular dynamics simulation. The effects of counterions are explicitly taken in to account. Structural…
Contrary to existing theoretical models, experimental evidence points out that electroporation (membrane defect formation under external electric fields) starts to occur within the range of transmembrane voltages that cells may routinely…
It has become increasingly clear that a full understanding of the physics of electrons in disordered systems requires an approach in which both disorder and interactions are taken into account. Work on small numbers of electrons has…