Effect of interaction shape on the condensed DNA toroid

Details Effect of interaction shape on the condensed DNA toroid Effect of interaction shape on the condensed DNA toroid

2007-01-30

arxiv.org/abs/cond-mat/0701738v1

J. Chem. Phys. 128 (2008) 134906

Physics

Condensed Matter

Soft Condensed Matter

5 pages (double column), 1 table and 3 figures (colour)

Scientific paper

We investigate how different microscopic interactions between semiflexible chain segments can qualitatively alter the physical properties of the condensed toroid. We propose a general form of the Hamiltonian of the toroid and discuss its analytic properties. For different interactions, the theory predicts different scaling behaviours of the mean toroidal and cross sectional radii, $r_c$ and $r_{cross}$, as functions of the contour length L: $(r_c, r_{cross}) \sim L^{\nu(N_c)}$ with $\nu=(1/5, 2/5)$ for the van der Waals type, $\nu=(-1/3, 2/3)$ for the Coulomb type, $\nu=(-1, 1)$ for the delta function type attractions in the asymptotic limit. For the toroids with finite winding number $N_c=100 \sim 400$, we find $\nu \simeq 0$ for the Yukawa interaction with screening parameter $\kappa=0.5 \sim 1.0$, and $\nu=0.1 \sim 0.13$ for the van der Waals type interactions. These findings could provide possible explanation for the experimentally well known observation $\nu \simeq 0$ of the condensed DNA toroids. Conformational transitions are also discussed.

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