Related papers: The evaluation of directionally writhing polymers
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 importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of…
We study analytically and numerically the winding of directed polymers of length $t$ around each other or around a rod. Unconfined polymers in pure media have exponentially decaying winding angle distributions, the decay constant depending…
We numerically verify and analytically prove a winding number invariant that correctly predicts the number of edge states in one-dimensional, nearest-neighbor (between unit cells), two-band models with any complex couplings and open…
In this paper we look at the pinning of a directed polymer by a one-dimensional linear interface carrying random charges. There are two phases, localized and delocalized, depending on the inverse temperature and on the disorder bias. Using…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
Topological invariants such as winding numbers and linking numbers appear as charges of topological solitons in diverse nonlinear physical systems described by a unit vector field defined on two and three dimensional manifolds. While the…
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…
In this work, we combine coarse-grained Brownian dynamics simulations and mean-field theory to study supercoiling dynamics, as well as the steady-state profiles of twist and writhe, in an open DNA polymer where one of the free ends is…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
In this expository note we present an elementary direct rigorous definition and the simplest properties of the winding number. This definition is simpler than the one given in some textbooks. We show how to compute the winding number…
The relaxation dynamics of a polymer wound around a fixed obstacle constitutes a fundamental instance of polymer with twist and torque and it is of relevance also for DNA denaturation dynamics. We investigate it by simulations and Langevin…
We perform simulations to numerically study the writhe distribution of a stiff polymer. We compare with analytic results of Bouchiat and Mezard (PRL 80 1556- (1998); cond-mat/9706050).
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 generalized winding number is an essential part of the geometry processing toolkit, allowing to quantify how much a given point is inside a surface, even when the surface has boundaries and noise. We propose a new universal method to…
Directed paths have been used extensively in the scientific literature as a model of a linear polymer. Such paths models in particular the conformational entropy of a linear polymer and the effects it has on the free energy. These directed…