Related papers: Bending stiff charged polymers: the electrostatic …
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
Using analytical approach and Monte-Carlo (MC) simulations, we study the elastic behaviour of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We…
We consider random walk model of a semi-flexible polymer chain on a square and a cubic lattice to enumerate conformations of the polymer chain in two and three dimensions, respectively. The bending energy of the chain is assumed as the key…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Building on theories of Persson, we derive a simpler theory for electroadhesion between rough surfaces using BAM (Bearing Area Model) of Ciavarella, or previous ideas by Persson and Tosatti. Rather surprisingly, in terms of stickiness, we…
We use coarse-grained Monte Carlo simulations to study the elastic properties of charged membranes in solutions of monovalent and pentavalent counterions. The simulation results of the two cases reveal trends opposite to each other. The…
We make use of the previously developed formalism for a monomer ensemble and include angular dependence of the segments of the polymer chains thus described. In particular we show how to deal with stiffness when the polymer chain is…
The study of configurational parameters of deformed DNA is a relevant problem in research of such important biological process as double helix compactization in cell. The deformations accompanied with local disruptions of the regular…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for…
We study the influence of some quenched disorder in the sequence of monomers on the entropic elasticity of long polymeric chains. Starting from the Kratky-Porod model, we show numerically that some randomness in the favoured angles between…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid.…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
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…
We study theoretically the osmotic pressure of a suspension of charged objects (e.g., colloids, polyelectrolytes, clay platelets, etc.) dialyzed against an electrolyte solution using the cell model and linear Poisson-Boltzmann (PB) theory.…
Force versus extension curves measure entropic elasticity of single polymer chain in force spectroscopy experiments. A Worm-like Chain model is used to describe force extension experiments with an intrinsic chain parameter called…
A large electric field is typically present in anodic or passive oxide films. Stresses induced by such a large electric field are critical in understanding the breakdown mechanism of thin oxide films and improving their corrosion…
We introduce a class of models of semiflexible polymers. The latter are characterized by a strong rigidity, the correlation length associated to the gradient-gradient correlations, called the persistence length, being of the same order as…