Related papers: Anomalous zipping dynamics and forced polymer tran…
We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…
Monte Carlo simulations have been performed to analyze the sub-diffusion dynamics of a tagged monomer in self-avoiding polymerized membranes in the flat phase. By decomposing the mean square displacement into the out-of-plane ($\parallel$)…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
The non-equilibrium structural and dynamical properties of a semiflexible polymer confined in a cylindrical microchannel and exposed to a Poiseuille flow is studied by mesoscale hydrodynamic simulations. For a polymer with a length half of…
We use lattice-Boltzmann molecular dynamics (LBMD) simulations to study the compression of a confined polymer immersed in a fluid and pushed by a large spherical colloid with a diameter comparable to the channel width. We examined the…
We consider the dynamics of a translocation process of a flexible linear polymer through a nanopore into an environment of active rods in the {\it trans} side. Using Langevin dynamics simulations we find that the rods facilitate…
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is…
We perform two-dimensional Langevin dynamics simulations of electric-field driven polymer translocation through an attractive nanopore. We investigate the effect of the location of the attractive region using different pore patterns. This…
We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
I did off-lattice 3D Monte Carlo simulations for polymer translocation through a narrow pore at low external field, trying to be as close to a direct approach as possible. The process was found non equilibrium globally, but dynamics of the…
We study hairpin folding dynamics by means of extensive computer simulations, with particular attention paid to the influence of helicity on the folding time $\tau$. We find that the dynamical exponent $\alpha$ of the anomalous scaling…
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
We investigate a reversible polymerization process in which individual polymers aggregate and fragment at a rate proportional to their molecular weight. We find a nonequilibrium phase transition despite the fact that the dynamics are…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer…
It has been recently shown that the phase space trajectories for the anomalous dynamics of a tagged monomer of a polymer --- for single polymeric systems such as phantom Rouse, self-avoiding Rouse, Zimm, reptation, and translocation through…