Computer simulation of DNA orientation and deformation in a shear flow field

The structure and orientation of semiflexible chain molecules in a shear flow field were studied by Brownian dynamics simulation. Molecules in the size range 200 nm to 1 mu m were modeled as chains of spherical subunits with parameters chosen to mimic the size and persistence length of B-DNA. The analysis of the steady-state orientation showed a rather broad and asymmetric distribution. The simulations also showed that the orientation of the largest main axis of the moment of inertia tensor is significantly higher compared to the orientation obtained from averaging over the individual bonds in the molecules, the latter procedure being the relevant case when comparing with, e. g., linear dichroism experiments.