Related papers: The dynamics of loop formation in a semiflexible p…
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 systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
We consider a model of a Rouse polymer extended by the mechanism of active loop extrusion. The model is based on a kinetic equation that is valid provided that the extrusion rate is high enough and the resulting loop ensemble is…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
A formula is derived for stiffness of a polymer chain in terms of the distribution function of end-to-end vectors. This relationship is applied to calculate the stiffness of Gaussian chains (neutral and carrying electric charges at the…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA. The two parameters of the model, $T^*$ and $\nu$, are chosen to match its experimental force-extension…
Polyampholytes (PA) are charged polymers composed of positively and negatively charged monomers along their backbone. The sequence of the charged monomers and the bending of the chain significantly influence the conformation and dynamical…
Lattice model of directed self avoiding walk has been solved analytically to investigate adsorption desorption phase transition behaviour of a semiflexible sequential copolymer chain on a two dimensional impenetrable surface perpendicular…
In this paper, we present a new approach to the Kratky-Porod Model (KP) of semiflexible polymers. Our solution to the model is based on the definition of a generating function which we use to study the statistical mechanics of semiflexible…
We study the dynamics of a single chain polymer confined to a two dimensional cell. We introduce a kinetically constrained lattice gas model that preserves the connectivity of the chain, and we use this kinetically constrained model to…
Based on a recently established formalism (U. Ebert, J. Stat. Phys. 82, 183 (1996)) we analyze the diffusive motion of a long polymer in a quenched random medium. The medium is modeled by a frozen semidilute polymer system. In the framework…
Brownian dynamics simulations are used to study highly entangled solutions of semiflexible polymers. Bending fluctuations of semiflexible rods are signficantly affected by entanglement only above a concentration $c^{**}$, where $c^{**}\sim…
By large-scale Monte Carlo simulations of semiflexible polymers in $d=2$ dimensions the applicability of the Kratky-Porod model is tested. This model is widely used as "standard model" for describing conformations and force versus extension…
The persistence length of macromolecules is one of their basic characteristics, describing their intrinsic local stiffness. However, it is difficult to extract this length from physical properties of the polymers, different recipes may give…
In the present work the dynamics of a continuous inextensible chain is studied. The chain is regarded as a system of small particles subjected to constraints on their reciprocal distances. It is proposed a treatment of systems of this kind…
We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system…
We calculate the distribution function of the end--to--end distance of a semiflexible polymer with large bending rigidity. This quantity is directly observable in experiments on single semiflexible polymers (e.g., DNA, actin) and relevant…
The behavior of mobile linkers connecting two semi-flexible charged polymers, such as polyvalent counterions connecting DNA or F-actin chains, is studied theoretically. The chain bending rigidity induces an effective repulsion between…