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Open Access Research article

Brownian dynamics simulation of analytical ultracentrifugation experiments

AI Díez, A Ortega and J Garcia de la Tore*

  • * Corresponding author: J Garcia de la Tore jgt@um.es

Author Affiliations

Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain

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BMC Biophysics 2011, 4:6  doi:10.1186/2046-1682-4-6

Published: 2 March 2011

Abstract

Background

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.

Results

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.

Conclusions

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.