Improved Calculation of Rotational Diffusion and Intrinsic Viscosity of Bead Models for Macromolecules and Nanoparticles

Abstract

The conventional Kirkwood-Riseman calculation of the hydrodynamic properties of bead models gives abnormal results for rotational quantities and the intrinsic viscosities for models with a few beads or when one bead is dominant. The reason is that beads are treated as point sources of friction. This can be remedied by introducing terms that are neglected in the conventional treatment of orders 0 and -3 in interbead distances. An alternative strategy is the cubic substitution in which each bead is replaced by a cubic array of minibeads. These procedures require a computational overload that, in the case of the intrinsic viscosity, can be avoided using an estimate of the correction due to the nonzero volume of the beads. We have found how such a correction can be estimated from the geometry of the model, and its application yields results that are within the range of typical experimental errors.

Equilibrium structure and fluctuations of suspensions of colloidal dumbbells

“…The infinite-dilution (single-particle) self-diffusion coefficients of a dumbbell particle were calculated previously using the shell-bead model (SHM) [30][31][32][33][34]. In this method, the particle surface is represented by a number of mini-beads which act as sources of hydrodynamic friction, where no-slip boundary conditions are assumed.…”

Assessing the two-body diffusion tensor calculated by the bead models

“…19,28,30 Our bead models with scaling greatly improved the accuracy of the rotational tensor block and the whole tensor. The term 0.031(4π R 2 /(N + 12)) 1/2 in the fitted formula of the scaling factor shown in Fig.…”

Chameleon behaviour of a-synuclein : brownian dynamics simulations of protein aggregation

“…3.2 also requires translational and rotational mobility tensors. These were determined using the HYDRO++ program [198,199] designed to calculate the translational and rotational diffusivity matrices, D = k B T µ, of rigid objects consisting of multiple beads. We followed the approach taken by…”

“…the HYDRO++ package; [198,199] are next inserted in Eq. (3.15) to solve for λ q , and the time step is completed by adding the constraint contribution, i.e.…”