Related papers: Condensation of circular DNA
Characteristics of relaxed density profile and conformation of polymer chains are studied by a Monte Carlo simulation on a discrete lattice in three dimensions using different segmental (kink-jump $K$, crank-shaft $C$, reptation $R$)…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
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…
The non-equilibrium structural and dynamical properties of semiflexible polymers confined to two dimensions are investigated by molecular dynamics simulations. Three different scenarios are considered: The force-extension relation of…
A phase diagram for a surface-interacting long flexible polymer chain in a two-dimensional poor solvent where the possibility of collapse exists is determined using exact enumeration method. A model of a self-attracting self avoiding walk…
We consider the one-dimensional Schroedinger equation on a ring, with the cubic term, of either self-attractive or repulsive sign, confined to a narrow segment. This setting can be realized in optics and Bose-Einstein condensates. For the…
Forced desorption of a semiflexible polymer chain on a solid substrate is theoretically investigated. The pulling force versus displacement is studied for different adsorption energy and persistence length P. It is found that the…
Taking into account the nonequivalence of fixed-force and fixed-length ensembles in the weak-force regime, equations of state are derived that describe the equilibrium extension or compression of an ideal Gaussian polymer chain in response…
The field theory approach to the statistical mechanics of a system of N polymer rings linked together is generalized to the case of links that have a fixed number $2s$ of maxima and minima. Such kind of links are called plats and appear for…
We investigate the properties of a system of semi-diluted polymers in the presence of charged groups and counter-ions, by means of self-consistent field theory. We study a system of polyelectrolyte chains grafted to a similarly, as well as…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non-equilibrium materials, which exhibit time-varying rheological properties, are topics of intense investigation. Here, we push composites of circular…
DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a…
A simple model is presented for the appearance of attraction between two like charged polyions inside a polyelectrolyte solution. The polyions are modeled as rigid cylinders in a continuum dielectric solvent. The strong electrostatic…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
The collective behavior of active semiflexible filaments is studied with a model of tangentially driven self-propelled worm-like chains. The combination of excluded-volume interactions and self-propulsion leads to several distinct dynamic…