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UBC Theses and Dissertations

Coarse-grained molecular dynamics simulations of DNA representing bases as ellipsoids Morriss-Andrews, Herbert Alexander


We conducted a study of various physical and geometric properties of single and double stranded DNA by developing a coarse-grained computational model. To represent the steric shapes of the bases more accurately, we modelled their interactions using the ellipsoidal RE² potential [18]. The bond, angle and dihedral potentials describing the DNA backbone are parametrized using statistics we gathered from atomistic simulations, and the RE² interaction parameters were likewise obtained from all-atom data. We find reasonable agreement of the dependence of the persistence length on ionic concentration with polymer theory [44]. We also observed the collapse of single stranded DNA by checking the radius of gyration as we lowered the temperature. Our simulations show a very strong dependence of helical twist and stacking interactions on the strength of the RE² potential, although increasing the twist frustrates all other potentials. The dependence of twist and stacking on ionic concentration and temperature was also analyzed. Our DNA also exhibits the correct right-handed chirality, with the chiral symmetry broken by the dihedral potentials. The model also gives clear major and minor grooves. Our methodical approach to the parametrization and analysis provides insight into the effect of the parameters in a coarse-grained model on the properties observed in the simulated DNA.

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