Related papers: Influence of polymer-pore interactions on transloc…
We study the dynamics of a polymer that is pulled by a constant force through a viscoelastic medium. This is a model for a polymer being pulled through a cell by an external force, or for an active biopolymer moving due to a self generated…
We employ computer simulations to study the dynamics of a self-propelled spherical tracer particle in a viscoelastic medium, made of a long polymer chain. Here, the interplay between viscoelasticity, stickiness, and activity…
In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question is to quantitatively explain how self-propulsion particles with directional memory diffuse in such a medium. Based…
Translocation dynamics of an active semi-flexible polymer through a nano-pore into a rigid two dimensional circular cavity, and the polymer packing dynamics have been studied by using Langevin dynamics (LD) simulations. The results show…
We review recent progress on the theory of dynamics of polymer translocation through a nanopore based on the iso-flux tension propagation (IFTP) theory. We investigate both pore-driven translocation of flexible and a semi-flexible polymers,…
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…
We study analytically a model of a two dimensional, partially directed, flexible or semiflexible polymer, attached to an attractive wall which is perpendicular to the preferred direction. In addition, the polymer is stretched by an…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…
We deduce the qualitative phase diagram of a long flexible neutral polymer chain immersed in a poor solvent near an attracting surface using phenomenological arguments. The actual positions of the phase boundaries are estimated numerically…
We study the driven translocation of a semi-flexible polymer through a nanopore by means of a modified version of the iso-flux tension propagation theory (IFTP), and extensive molecular dynamics (MD) simulations. We show that in contrast to…
Dynamic Monte Carlo simulations are used to study coupled transport (co-transport) through sub-nanometer-diameter pores. In this classic Hodgkin-Keynes mechanism, an ion species uses the large flux of an abundant ion species to move against…
Transport of molecules across membrane channels is investigated theoretically using exactly solvable one-dimensional discrete-state stochastic models. An interaction between molecules and membrane pores is modeled via a set of binding sites…
We use the Bond Fluctuation Model (BFM) to study the pore-blockade times of a translocating polymer of length $N$ in two dimensions, in the absence of external forces on the polymer (i.e., unbiased translocation) and hydrodynamic…
The dynamics of a polymer ring enclosing a constant {\sl algebraic} area is studied. The constraint of a constant area is found to couple the dynamics of the two Cartesian components of the position vector of the polymer ring through the…
Langevin dynamics is used to study equilibrium properties of the suspension of magnetic filaments (chains of nanoparticles permanently crosslinked with polymers). It is shown that the filament suspension generally has a larger magnetic…
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…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores in physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl…
We investigate the translocation of rods with different charge distributions using hybrid Langevin Dynamics and Lattice Boltzmann (LD-LB) simulations. Electrostatic interactions are added to the system using the $P^3M$ algorithm to model…
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…