Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Multiscale Modeling of DNA Bending Dynamics

The propagation of bend and shear waves through DNA is investigated using a geometrically exact nonlinear elastic rod model and all atom molecular dynamics simulations. The rod model allows for shear, extension/compression, bend and twist thus enabling us to study the dynamics of all types of elastic deformations. It is formulated using DNA helical parameters (roll, tilt, twist, shift, slide, rise) so that results can readily be compared to all atom simulations. For the case of an intrinsically straight, untwisted rod, numeric and approximate analytic solutions demonstrate that the propagation of planar bend or shear disturbances of finite wavelength require bend, shear and extension/compression deformations. The wavelength of the extension/compression wave is half the wavelength the bend or shear wave. For the case of an intrinsically straight, twisted rod, planar bend-shear motion is investigated numerically (left) and compared to a similar motion in a 600ps molecular dynamics simulations of 158 basepairs of DNA. The molecular dynamics simulations indicate that DNA (right, 125 ps shown) supports the propagation of mechanical disturbances as predicted by elastic rod theory. This work was conducted at the Center for Computational Sciences at Tulane and Xavier Universities with support form the DOE (DE-FG02-01ER63119).

Thomas C. Bishop1,2
Ricardo Cortez1
Oleksander Zhmudsky1

Center for Computational Sciences at Tulane1 and Xavier2 Universities

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