Related papers: Driven translocation of a flexible polymer through…
Dynamical simulations of polaron transport in conjugated polymers in the presence of an external time-dependent electric field have been performed within a combined extended Hubbard model (EHM) and Su-Schrieffer-Heeger (SSH) model. Nearly…
While the dynamics of a fully flexible polymer ejecting a capsid through a nanopore has been extensively studied, the ejection dynamics of semiflexible polymers has not been properly characterized. Here we report results from simulations of…
The characterization of the interactions between two fully flexible self-avoiding polymers is one of the classic and most important problems in polymer physics. In this paper we measure these interactions in the presence of active…
Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
Starting from the reported experimental evidence that the residence time of contacts between the ends of biopolymers is length dependent, we investigate the kinetics of contact breaking in simple polymer models from a theoretical point of…
The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of…
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…
We analyze the translocation of a charged particle across an Alpha-Hemolysin (aHL) pore in the framework of a driven diffusion over an extended energy barrier generated by the electrical charges of the aHL. A one-dimensional electrostatic…
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 ($\parallel$)…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time…
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…
We consider the statics and dynamics of a flexible polymer confined between parallel plates both in the presence and absence of hydrodynamic interactions. The hydrodynamic interactions are described at the level of the fluctuating,…
We analyze the conformational dynamics and statistical properties of an active polymer model. The polymer is described as a freely-jointed bead-rod chain subject to stochastic active force dipoles that act on the suspending solvent where…
Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest neighbour attraction. The bias corresponds to opposite forces applied to the first…
Polymer transport is investigated for two paradigmatic laminar flows having open and closed streamlines, respectively. For both types of flows we find transport depletion owing to the action of the polymers elastic degree of freedom. For…
The way tension propagates along a chain is a key to govern many of anomalous dynamics in macromolecular systems. After introducing the weak and the strong force regimes of the tension propagation, we focus on the latter, in which the…
We present a hybrid quantum-classical simulation of charge-polaron transport in conjugated polymers. The charge, which couples to the angular rotations of the monomers, is modeled via the time-dependent Schr\"odinger equation, while the…
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…