AI Article Synopsis
- Two main challenges in hydrodynamic bead modeling are dealing with bead overlaps and needing volume corrections for intrinsic viscosity calculations.
- A new method based on the generalized Rotne-Prager-Yamakawa approximation effectively tackles these problems.
- The method is tested on various molecular shapes and real protein structures, showing superior performance compared to other computational techniques.
Article 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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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127458 | PMC |
| http://dx.doi.org/10.1016/j.bpj.2018.07.015 | DOI Listing |
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