Related papers: Exact theory of kinkable elastic polymers
A conceptual difficulty in the Hooke's-law description of ideal Gaussian polymer-chain elasticity is sometimes apparent in analyses of experimental data or in physical models designed to simulate the behavior of biopolymers. The problem,…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a…
This study presents a Eulerian theory to elucidate the molecular kinematics in polymer networks and their connection to continuum deformation, grounded in fundamental statistical physics and thermodynamics. Three key innovations are…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
Reptation theory has been highly successful in explaining the unusual material properties of entangled polymer solutions. It reduces the complex many-body dynamics to a single-polymer description where each polymer is envisaged to be…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
We study three-dimensional deformations of thin inextensible elastic rods with non-vanishing spontaneous curvature and torsion. In addition to the usual description in terms of curvature and torsion which considers only the configuration of…
We discuss the appropriate techniques for modelling the geometry of open ended elastic polymer molecules. The molecule is assumed to have fixed endpoints on a boundary surface. In particular we discuss the concept of the winding number, a…
The statistical mechanics of a ribbon polymer made up of two semiflexible chains is studied using both analytical techniques and simulation. The system is found to have a crossover transition at some finite temperature, from a type of short…
We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link…
We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact…
Quantum transport for DNA conduction has widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works with concerning the electronic…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
Traditional models of wormlike chains in shear flows at finite temperature approximate the equation of motion via finite difference discretization (bead and rod models). We introduce here a new method based on a spectral representation in…
Dendronized polymers consist of an elastic backbone with a set of iterated branch structures (dendrimers)attached at every base point of the backbone. The conformations of such molecules depend on the elastic deformation of the backbone and…
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is…
By using the blob theory and computer simulations, we investigate the properties of a linear polymer performing a stationary rotational motion around a long impenetrable rod. In particular, in the simulations the rotation is induced by a…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
We theoretically study the nematic ordering transition of rods that are able to elastically adjust their mutually excluded volumes. The model rods, which consist of a hard core surrounded by a deformable shell, mimic the structure of…