Two-dimensional grid optimization for sedimentation velocity analysis in the analytical ultracentrifuge

European Biophysics Journal : EBJ
Haram KimBorries Demeler

Abstract

Sedimentation velocity experiments performed in the analytical ultracentrifuge are modeled using finite-element solutions of the Lamm equation. During modeling, three fundamental parameters are optimized: the sedimentation coefficients, the diffusion coefficients, and the partial concentrations of all solutes present in a mixture. A general modeling approach consists of fitting the partial concentrations of solutes defined in a two-dimensional grid of sedimentation and diffusion coefficient combinations that cover the range of possible solutes for a given mixture. An increasing number of grid points increase the resolution of the model produced by the subsequent analysis, with denser grids giving rise to a very large system of equations. Here, we evaluate the efficiency and resolution of several regular grids and show that traditionally defined grids tend to provide inadequate coverage in one region of the grid, while at the same time being computationally wasteful in other sections of the grid. We describe a rapid and systematic approach for generating efficient two-dimensional analysis grids that balance optimal information content and model resolution for a given signal-to-noise ratio with improved calculation efficiency. Th...Continue Reading

Citations

Sep 16, 2018·European Biophysics Journal : EBJ·Olwyn ByronTrushar R Patel
Nov 26, 2020·European Biophysics Journal : EBJ·Marielle StoutjesdykBorries Demeler

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