The evaluation of directionally writhing polymers

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 directional measure of the linking of two curves, which can be shown to be invariant to the set of continuous deformations vanishing at the polymer's end-point and which forbid it from passing through itself. This measure is shown to be the appropriate constraint required to evaluate the geometrical properties of a constrained DNA molecule. Using the net winding measure we define a model of an open ended constrained DNA molecule which combines the necessary constraint of self-avoidance with being analytically tractable. This model builds upon the local models of Bouchiat and Mézard (2000). In particular, we present a new derivation of the polar writhe expression, which detects both the local winding of the curve and non local winding between different sections of the curve. We then show that this expression correctly tracks the net twisting of a DNA molecule subject to rotation at the endpoints, unlike other definitions used in the literature.