Related papers: Translocation time of periodically forced polymer …
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
Polymer thin films exhibit pronounced interfacial mobility gradients that modify chain relaxation, yet how these gradients govern chain-scale dynamics across depth remains incompletely understood. Using molecular dynamics simulations of…
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.…
Taking into account the nonequivalence of fixed-force and fixed-length ensembles in the weak-force regime, equations of state are derived that describe the equilibrium extension or compression of an ideal Gaussian polymer chain in response…
The Rouse-Zimm equation for the position vectors of beads mapping the polymer is generalized by taking into account the viscous aftereffect and the hydrodynamic noise. For the noise, the random fluctuations of the hydrodynamic tensor of…
The structural properties of a linear polymer and its evolution in time have a strong bearing on its anisotropic stress response. The mean-square bond length and mean bond angle are the critical parameters that influence the time-varying…
During polymer translocation driven by e.g. voltage drop across a nanopore, the segments in the cis-side is incessantly pulled into the pore, which are then pushed out of it into the trans-side. This pulling and pushing polymer segments are…
We investigated the static and dynamic properties of a Rouse ring polymer modified by introducing an effective, spherically symmetric, attractive potential of entropic nature and a memory function describing the effect of dynamic…
The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the…
This paper reports the force spectroscopy analysis of a polymer that translocates from one side of a membrane to the other side through an extended pore, pulled by a cantilever that moves with constant velocity against the damping and the…
We consider the thermally activated fragmentation of a homopolymer chain. In our simple model the dynamics of the intact chain is a Rouse one until a bond breaks and bond breakdown is considered as a first passage problem over a barrier to…
In a typical single molecule experiment, dynamics of an unfolded proteins is studied by determining the reconfiguration time using long-range Forster resonance energy transfer where the reconfiguration time is the characteristic decay time…
The non-equilibrium structural and dynamical properties of a flexible polymer tethered to a reflecting wall and subject to oscillatory linear flow are studied by numerical simulations. Polymer is confined in two dimensions and is modeled as…
In this chapter we review the rich behavior of polymer chains embedded in a quenched random environment. We first consider the problem of a Gaussian chain free to move in a random potential with short-ranged correlations. We derive the…
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…
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is…
Assuming Gaussian chain statistics along the chain contour, we generate by means of a proper fractal generator hyperbranched polymer trees which are marginally compact. Static and dynamical properties, such as the radial intrachain pair…
Directed transport is a characteristic feature of numerous biological systems in response to signals such as nutrient and chemical gradients. These signals often depend on time owing to the high complexity of interactions in these systems.…
We derive the stochastic equations of motion for a tracer that is tightly attached to a semiflexible polymer and confined or agitated by an externally controlled potential. The generalised Langevin equation, the power spectrum, and the…
The presence of a viscoelastic mechanism distinctly different from the segmental a-relaxation and the Rouse modes within the glass-rubber transition zone of polymers had been justified by theoretical considerations, and subsequently…