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Multi-speed sedimentation velocity implementation in UltraScan-III

  • Gary E. Gorbet
  • Subhashree Mohapatra
  • Borries Demeler
Methods Paper

Abstract

A framework for the global analysis of multi-speed analytical ultracentrifugation sedimentation velocity experiments is presented. We discuss extensions to the adaptive space–time finite element fitting methods implemented in UltraScan-III to model sedimentation velocity experiments where a single run is performed at multiple rotor speeds, and describe extensions in the optimization routines used for fitting experimental data collected at arbitrary multi-speed profiles. Our implementation considers factors such as speed dependent rotor stretching, the resulting radial shifting of the finite element solution’s boundary conditions, and changes in the associated time-invariant noise. We also address the calculation of acceleration rates and acceleration zones from existing radial acceleration and time records, as well as utilization of the time state object available at high temporal resolution from the new Beckman Optima AUC instrument. Analysis methods in UltraScan-III support unconstrained models that extract reliable information for both the sedimentation and the diffusion coefficients. These methods do not rely on any assumptions and allow for arbitrary variations in both sedimentation and diffusion transport. We have adapted these routines for the multi-speed case, and developed optimized and general grid based fitting methods to handle changes in the information content of the simulation matrix for different speed steps. New graphical simulation tools are presented that assist the investigator to estimate suitable grid metrics and evaluate information content based on edit profiles for individual experiments.

Keywords

Analytical ultracentrifugation Finite element modelling Multi-speed analysis 

Notes

Acknowledgements

This work was supported by NIH grant GM120600 and NSF grants NSF-ACI-1339649 (to BD). Supercomputer calculations were performed on Comet at the San Diego Supercomputing Center (support through NSF/XSEDE grant TG-MCB070039 N to BD) and on Lonestar-5 at the Texas Advanced Computing Center (supported through UT grant TG457201 to BD). We thank Beckman-Coulter, Indianapolis, for the use of an Optima AUC instrument, and Eric von Seggern (Beckman-Coulter, Fort Collins) for excellent technical assistance with the time state development.

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Copyright information

© European Biophysical Societies' Association 2018

Authors and Affiliations

  1. 1.University of Texas Health Science CenterSan AntonioUSA

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