Prediction of hydrodynamic parameters from 3D structures

Abstract

The performance of different expressions for the hydrodynamic interaction tensor in the prediction of translational and rotational friction coefficients and intrinsic viscosities of a broad spectrum of different models consisting of two unequal spheres, varying from separated to completely overlapping, was tested in a systematic manner. The emphasis of the investigation was laid on checking the efficiency of different averages of the bead radii, when used in combination with the interaction tensor of Rotne and Prager for overlapping equal beads, as an ad hoc expression in treating unequal spheres. It was found that only averages based on the arithmetic means of bead volumes or bead surfaces perform well in all cases studied. An analysis of our results favors the use of the average based on the bead surfaces. Computations carried out with various bead models of the enzyme aldolase demonstrate the success of our approach in impeding the occurrence of erratic results.