Effect of interaction shape on the condensed DNA toroid.pdfVIP

OIQP-06-14 Effect of interaction shape on the condensed DNA toroid 7 0 0 Y. Ishimoto1 and N. Kikuchi2,3 2 n 1 Okayama Institute for Quantum Physics, 1-9-1 Kyouyama, Okayama 700-0015, Japan a 2 Institut f¨ur Physik, Johannes Gutenberg-Universit¨at Mainz, Staudinger Weg 7, D-55099 Mainz, Germany J 3 Fachbereich Physik, Martin-Luther-Universit¨at Halle-Wittenberg, D-06099 Halle, Germany(a) 0 3 ] PACS 82.35.Lr – Physical properties of polymers t f PACS 87.10.+e – General theory and mathematical aspects o PACS 87.14.Gg – DNA, RNA s . t Abstract. - We investigate how different microscopic interactions between semiflexible chain seg- a ments can qualitatively alter the physical properties of the condensed toroid. We propose a general m 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, rc d ν (Nc ) 1 2 and r , as functions of the contour length L: (r , r ) ∼ L with ν = ( , ) for the van n cross 1 2 c cross 5 5 o der Waals type, ν = (−3 , 3 ) for the Coulomb type, ν = (−1, 1) for the delta function type at- c tractions in the asymptotic limit. For the toroids with finite winding number Nc = 100 ∼ 400, we [ find ν ≃ 0 for the Yukawa interaction with screening parameter κ = 0.5 ∼ 1.0, and ν = 0.1 ∼ 0.13 for the van der Waals type interactions. These findings could provide possible explanation for 1 v the experimentally well known observation ν ≃ 0 of the condensed DNA toroids. Conformational 8 transi