CONFIGURATIONAL TRANSITIONS IN FOURIER SERIES-REPRESENTED DNA SUPERCOILS

A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational mot ions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The va n der Waals' term prevents the self-contact of distant chain segments and also mimics attractive forces thought to stabilize the association of closely spaced charged rods. The finite Fourier series-derived pol ymer formulation is an alternative to the piecewise B-spline curves us ed in past work to describe the motion of smoothly deformed supercoile d DNA in terms of a limited number of independent variables. This stud y focuses on two large-scale configurational events: the interconversi on between circular and figure-8 forms at a relatively low level of su percoiling, and the transformation between branched and interwound str uctures at a higher superhelical density.