Related papers: Translocation time of periodically forced polymer …
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 extend the Rouse model of polymer dynamics to situations of non-stationary chain growth. For a dragged polymer chain of length $N(t) = t^\alpha$, we find two transitions in conformational dynamics. At $\alpha= 1/2$, the propagation of…
We investigate numerically the dynamics of a single polymer in a linear shear flow. The effects of thermal fluctuations and randomly fluctuating velocity gradients are both analyzed. Angular, elongation and tumbling time statistics are…
We study the Langevin dynamics of a two-dimensional discrete oscillator chain absorbed on a periodic substrate and subjected to an external localized point force. Going beyond the commonly used harmonic bead-spring model, we consider a…
There have been increasing reports that the diffusion coefficient of macromolecules depends on time and fluctuates randomly. Here, a novel method to elucidate the fluctuating diffusivity from trajectory data is developed. The time-averaged…
The dynamics of ring polymer melts are studied via molecular dynamics simulations of the Kremer-Grest bead-spring model. Rouse mode analysis is performed in comparison with linear polymers by changing the chain length. Rouse-like behavior…
We study the dynamics of a polymer, described as a variant of a Rouse chain, driven by an active terminal monomer (head). The local active force induces a transition from a globule-like to an elongated state, as revealed by the study of the…
We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high…
This paper examines the effect of cooling on disentanglement forces in polymers and the implications for both single chain pullout and polymer dynamics. I derive the explicit dependence of the distribution of these forces on temperature,…
We present a Brownian dynamics theory with full hydrodynamics (Stokesian dynamics) for a Gaussian polymer chain embedded in a liquid membrane which is surrounded by bulk solvent and walls. The mobility tensors are derived in Fourier space…
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…
The correlation between the fast cage dynamics and structural relaxation is investigated in a model polymer system. It is shown that the cage vibration amplitude, as expressed by the Debye-Waller factor, and the relaxation time…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and…
We show that in driven systems the Gaussian nature of the fluctuating force and time-reversibility are equivalent properties. This result together with the potential condition of the external force drastically restricts the form of the…
This study deals with polymer looping, an important process in many chemical and biological systems. We investigate basic questions on the looping dynamics of a polymer under tension using the freely-jointed chain (FJC) model. Previous…
The Langevin dynamics of a self - interacting chain embedded in a quenched random medium is investigated by making use of the generating functional method and one - loop (Hartree) approximation. We have shown how this intrinsic disorder…
Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium.…
We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory…
We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the…