17th International Symposium on Analytical Ultracentrifugation and Hydrodynamics

Faculty of Medical Sciences, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
Biophysics of Structure and Mechanism (Impact Factor: 2.22). 03/2009; 39(3):345-6. DOI: 10.1007/s00249-009-0406-4
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    • "Since the invention of the analytical ultracentrifuge by Svedberg [1], the technique of analytical ultracentrifugation (AUC) has been a classical - and, thanks to advances in instrumentation and analysis software, it is still a most modern - technique for characterization of macromolecules and nanoparticles in solution. The reader may grasp the recent importance of this field in monographs [2-4] and thematic issues of other journals [5-7]. "
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    ABSTRACT: We have devised a protocol for the Brownian dynamics simulation of an analytical ultracentrifugation experiment that allows for an accurate and efficient prediction of the time-dependent concentration profiles, c(r, t) in the ultracentrifuge cell. The procedure accounts for the back-diffusion, described as a Brownian motion that superimposes to the centrifugal drift, and considers the sector-shaped geometry of the cell and the boundaries imposed by the meniscus and bottom. Simulations are carried out for four molecules covering a wide range of the ratio of sedimentation and diffusion coefficients. The evaluation is done by extracting the molecular parameters that were initially employed in the simulation by analyzing the profiles with an independent tool, the well-proved SEDFIT software. The code of simulation algorithm has been parallelized in order to take advantage of current multi-core computers. Our Brownian dynamics simulation procedure may be considered as an alternative to other predictors based in numerical solutions of the Lamm equation, and its efficiency could make it useful in the most relevant, inverse problem, which is that of extracting the molecular parameters from experimentally determined concentration profiles.
    Full-text · Article · Mar 2011 · BMC Biophysics