Related papers: Supercoiling DNA with a free end
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Recently it has been argued that weighting the writhe of unknotted self-avoiding polygons can be related to possible experiments that turn double stranded DNA. We first solve exactly a directed model and demonstrate that in such a subset of…
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…
We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications,…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
For an understanding of DNA elasticity at high mechanical loads (F > 30 pN), its helical nature needs to be taken into account, in the form of coupling between the twist and stretch degrees of freedom. The prevailing model for DNA…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
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 dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration,…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
The buckling and twisting of slender, elastic fibers is a deep and well-studied field. A slender elastic rod that is twisted with respect to a fixed end will spontaneously form a loop, or hockle, to relieve the torsional stress that builds.…
Motivated by recent experiments on DNA torsion-force-extension characteristics we consider the writhing geometry of open stiff molecules. We exhibit a cyclic motion which allows arbitrarily large twisting of the end of a molecule via an…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
The relaxation of twist in elastic filaments often drives conformational changes. We explore this paradigm using all-atom computations and report the formation of novel supercoiled shapes in individual carbon nanotubes (CNTs). Decreasing…
In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Recent observations of superconductivity in twisted bilayer WSe$_2$ have extended the family of moir\'e superconductors beyond twisted graphene. In WSe$_2$ two different twist angles were studied, 3.65{\deg} and 5.0{\deg}, and two seemingly…
We report the first observation of controlled, strain-induced square moire patterns in stacked graphene. By selectively displacing native wrinkles, we drive a reversible transition from the usual trigonal to square moire order. Scanning…
Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity.…