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 motions of intermediate-length
chains. The polymer is modeled as an ideal elastic rod subject to long-range
van der Waals' interactions. The van 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 polymer formulation is an alternative to the piecewise
B-spline curves used in past work to describe the motion of
smoothly deformed supercoiled DNA in terms of a limited number of
independent variables. This study focuses on two large-scale configurational
events: the interconversion between circular and figure-8 forms at a relatively
low level of supercoiling, and the transformation between branched and
interwound structures at a higher superhelical density.
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