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Updated: Feb 6, 2026

A Microfluidic-based Hydrodynamic Trap for Single Particles
Published on: January 21, 2011
GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules
Pawel J Zuk1, Bogdan Cichocki2, Piotr Szymczak2
1Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland; Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey.
Abstract:
Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.
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