Related papers: Influence of polymer-pore interactions on transloc…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…
Memory effects, sometimes, can not be neglected. In the framework of continuous time random walk, memory effect is modeled by the correlated waiting times. In this paper, we derive the two-point probability distribution of the stochastic…
We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the mean-first-passage time as a function of the…
The self-avoid random walk algorithm has been extensively used in the study of polymers. In this work we study the basic properties of the trajectories generated with this algorithm when two interactions are added to it: contact and folding…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
The collapse and swelling behavior of a generic homopolymer is studied using implicit-solvent, explicit-cosolvent Langevin dynamics computer simulations for varying interaction strengths. The systematic investigation reveals that polymer…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
This work investigates the effects of tangent polar activity on the conformational and dynamic properties of entangled polymer melts through Langevin molecular dynamics simulations. We examine systems composed of all self-propelled,…
We analyze theoretically the effects of excluded-volume interactions between motors on the dynamics of a cargo driven by multiple motors. The model considered shares many commons with other recently proposed in the literature, with the…
Active filament-like systems propelling along their backbone exist across the scales ranging from motor-driven bio-filaments to worms and robotic chains. In macroscopic active filaments such as chain of robots, in contrast to their…
We revisit the Fokker-Planck based theory of driven polymer translocation through a narrow nanopore. A bead-spring model of a uniformly charged polyelectrolyte chain translocating through a semi-implicit model of a nanopore embedded in a…
While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different. Here we study the dynamics of polymers in a viscous medium containing…
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…
The relaxation dynamics of a polymer wound around a fixed obstacle constitutes a fundamental instance of polymer with twist and torque and it is of relevance also for DNA denaturation dynamics. We investigate it by simulations and Langevin…
Using molecular dynamic simulations we study a system of particles interacting through a continuous core-softened potentials consisting of a hard core, a shoulder at closest distances and an attractive well at further distance. We obtain…
We investigate the dynamics of pore-driven polymer translocation by theoretical analysis and molecular dynamics (MD) simulations. Using the tension propagation theory within the constant flux approximation we derive an explicit equation of…
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
We study the attractive interactions between rod-like charged polymers in solution that appear in the presence of multi-valence counterions. The counterions condensed to the rods exhibit both a strong transversal polarization and a…