Bead models of segmentally flexible macromolecules

Abstract

Bead model methods developed for complex rigid macromolecules are extended to obtain diffusion coefficients for macromolecules with segmental flexibility. A suitable arrangement of beads is used to represent each segment and to account for hydrodynamic interactions between segments. Bead expressions for the set of three-dimensional tensors relating frictional drag forces and torques on one segment to translational and rotational motions of another are obtained and compared with previous expressions that neglected intersegmental hydrodynamic interactions. By specifying the nature of the flexible attachments, this set can be used to obtain the frictional resistance and diffusion tensors characterizing the body’s degrees of freedom. As an example, a bent rod is considered with a central bending region that is either rigid or swivel jointed. Although intersegmental interactions are seen to increase the translational diffusion coefficient as expected from hydrodynamic shielding, the rotational diffusion coefficients for the rigid bent rod show a more complex behavior with the interactions decreasing end-over-end motion at small bending angles and increasing it at large angles. For the flexible rod, these interactions generally increase the end-over-end motions of each rodhalf.