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

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dc.contributor.authorKim, Haram
dc.contributor.authorBrookes, Emre
dc.contributor.authorCao, Weiming
dc.contributor.authorDemeler, Borries
dc.date.accessioned2021-09-22T19:08:21Z
dc.date.available2021-09-22T19:08:21Z
dc.date.issued2018
dc.descriptionAccepted author manuscripten_US
dc.description.abstractSedimentation 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. These findings are general and apply to one- and two-dimensional grids, although they no longer represent regular grids. We provide a recipe for an improved grid-point spacing in both directions which eliminates unnecessary points, while at the same time providing a more uniform resolution that can be scaled based on the stochastic noise in the experimental data.en_US
dc.description.peer-reviewYesen_US
dc.identifier.citationKim, H., Brookes, E., Cao, W., & Demeler, B. (2018). Two-dimensional grid optimization for sedimentation velocity analysis in the analytical ultracentrifuge. European Biophysics Journal, 47(7), 837-844. https://doi.org/10.1007/s00249-018-1309-zen_US
dc.identifier.urihttps://hdl.handle.net/10133/6031
dc.language.isoen_USen_US
dc.publisherSpringeren_US
dc.publisher.departmentDepartment of Chemistry and Biochemistryen_US
dc.publisher.facultyArts and Scienceen_US
dc.publisher.institutionCornell Universityen_US
dc.publisher.institutionUniversity of Texas Health Science Center at San Antonioen_US
dc.publisher.institutionUniversity of Texas at San Antonioen_US
dc.publisher.institutionUniversity of Lethbridgeen_US
dc.publisher.urlhttps://doi.org/10.1007/s00249-018-1309-zen_US
dc.subjectComputational biophysicsen_US
dc.subjectAnalytical ultracentrifugationen_US
dc.subjectNumerical optimizationen_US
dc.subjectVelocity analysis
dc.subjectTwo-dimensional grids
dc.subject.lcshHydrodynamics
dc.subject.lcshHigh performance computing
dc.subject.lcshCentrifuges
dc.titleTwo-dimensional grid optimization for sedimentation velocity analysis in the analytical ultracentrifugeen_US
dc.typeArticleen_US
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