Writhing Geometry at Finite Temperature: Random Walks and Geometric phases for Stiff Polymers

Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here we ask if there exist local geometric features that may be used as a read-out of the underlying topology of generic polymers. We perform molecular simulations of knotted and linked semiflexbile polymers and study four geometric measures to predict topological entanglements: local curvature, local density, local 1D writhe and non-local 3D writhe. We discover that local curvature is a poor p...

For a directed polymer in a random medium lying on an infinite cylinder, that is in 1+1 dimensions with finite width and periodic boundary conditions on the transverse direction, the winding number is simply the algebraic number of turns the polymer does around the cylinder. This paper presents exact expressions of the fluctuations of this winding number due to, first, the thermal noise of the system and, second, the different realizations of the disorder in the medium.

The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the...

The conformational and electronic properties of conducting flexible random and self-avoiding walk polymer chains are under investigation. A Hamiltonian for conjugated flexible polymers is introduced and its physical consequences are presented. One important result is that the electronic degrees of freedom greatly affect the conformational statistics of the walks and vice versa. The electronic degrees of freedom extend the size of the chain. The end-to-end distance behaves as ...

We present a method for solving the Worm Like Chain (WLC) model for twisting semiflexible polymers to any desired accuracy. We show that the WLC free energy is a periodic function of the applied twist with period 4 pi. We develop an analogy between WLC elasticity and the geometric phase of a spin half system. These analogies are used to predict elastic properties of twist-storing polymers. We graphically display the elastic response of a single molecule to an applied torque. ...

The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that thermal fluctuations play an important role in determining molecular elastic properties, but a full theoretical treatment of the problem of twist elasticity of fluctuating ribbons using the simplest worm like chain model (WLC) remains elusi...

The relaxation of initially straight semiflexible polymers has been discussed mainly with respect to the longest relaxation time. The biologically relevant non-equilibrium dynamics on shorter times is comparatively poorly understood, partly because "initially straight" can be realized in manifold ways. Combining Brownian dynamics simulations and systematic theory, we demonstrate how different experimental preparations give rise to specific short-time and universal long-time d...

We investigate the statistical mechanics of long developable ribbons of finite width and very small thickness. The constraint of isometric deformations in these ribbon-like structures that follows from the geometric separation of scales introduces a coupling between bending and torsional degrees of freedom. Using analytical techniques and Monte Carlo simulations, we find that the tangent-tangent correlation functions always exhibits an oscillatory decay at any finite temperat...

This paper is extended and broadly generalized version of earlier published rapid communication, Phys.Rev.E, Vol.58, R 5213 (1998). It also elaborates on some problems which were left unsolved or just mentioned in Physics Reports Vol.298, 251 (1998). Applications of the obtained results include (but not limited to) polymer physics, classical and quantum chaos, fractional Hall effect, dynamics of textures in liquid crystals and 2+1 gravity. The paper presents some self contain...

We study the effects of thermal fluctuations on elastic rings. Analytical expressions are derived for correlation functions of Euler angles, mean square distance between points on the ring contour, radius of gyration, and probability distribution of writhe fluctuations. Since fluctuation amplitudes diverge in the limit of vanishing twist rigidity, twist elasticity is essential for the description of fluctuating rings. We find a crossover from a small scale regime in which the...