Related papers: Phase diagram for unzipping DNA with long-range in…

We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…

The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…

The model of directed polymer in a random environment is a fundamental model of interaction between a simple random walk and ambient disorder. This interaction gives rise to complex phenomena and transitions from a central limit theory to…

For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…

Langevin Dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is…

Within self-consistent field theory we study the phase behavior of a symmetrical binary AB polymer blend confined into a thin film. The film surfaces interact with the monomers via short range potentials. One surface attracts the A…

Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…

We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…

We introduce an anisotropic mean-field approach for the dynamics of semiflexible polymers under intermediate tension, the force range where a chain is partially extended but not in the asymptotic regime of a nearly straight contour. 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…

Hydrodynamic forces may significantly affect the motion of polymers. In sheet-like cavities, such as the cell's cytoplasm and microfluidic channels, the hydrodynamic forces are long-range. It is therefore expected that that hydrodynamic…

We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force Fc and the number of unzipped monomers M…

We study the activated motion of adsorbed polymers which are driven over a structured substrate by a localized point force.Our theory applies to experiments with single polymers using, for example, tips of scanning force microscopes to drag…

The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…

We study the non-equilibrium steady states in a closed system consisting of interacting particles obeying exclusion principle with quenched hopping rate. Cluster mean field approach is utilized to theoretically analyze the system dynamics…

DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…

The role of solvent quality in determining the universal material properties of dilute polymer solutions undergoing steady simple shear flow is examined. A bead-spring chain representation of the polymer molecule is used, and the influence…

The dynamics of flexible polymers in dilute solution is usually described in terms of the pure Rouse or Zimm bead-spring models assuming continuous distribution of the internal relaxation modes. We show that this approach may lead to…

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 study numerically the phase diagram and the response under a driving force of the phase field crystal model for pinned lattice systems introduced recently for both one and two dimensional systems. The model describes the lattice system…