COMPUTER-SIMULATION OF DNA ORIENTATION AND DEFORMATION IN A SHEAR-FLOW FIELD

The structure and orientation of semiflexible chain molecules in a she ar 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 len gth of B-DNA. The analysis of the steady-state orientation showed a ra ther broad and asymmetric distribution. The simulations also showed th at the orientation of the largest main axis of the moment of inertia t ensor is significantly higher compared to the orientation obtained fro m averaging over the individual bonds in the molecules, the latter pro cedure being the relevant case when comparing with, e. g., linear dich roism experiments.