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Brownian dynamics simulation of analytical ultracentrifugation experiments

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-diff...

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Detalles Bibliográficos
Autores principales: Díez, AI, Ortega, A, Garcia de la Tore, J
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098213/
https://www.ncbi.nlm.nih.gov/pubmed/21596001
http://dx.doi.org/10.1186/2046-1682-4-6
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author Díez, AI
Ortega, A
Garcia de la Tore, J
author_facet Díez, AI
Ortega, A
Garcia de la Tore, J
author_sort Díez, AI
collection PubMed
description 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.
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spelling pubmed-30982132011-05-23 Brownian dynamics simulation of analytical ultracentrifugation experiments Díez, AI Ortega, A Garcia de la Tore, J BMC Biophys Research Article 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. BioMed Central 2011-03-02 /pmc/articles/PMC3098213/ /pubmed/21596001 http://dx.doi.org/10.1186/2046-1682-4-6 Text en Copyright ©2011 Diez et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Díez, AI
Ortega, A
Garcia de la Tore, J
Brownian dynamics simulation of analytical ultracentrifugation experiments
title Brownian dynamics simulation of analytical ultracentrifugation experiments
title_full Brownian dynamics simulation of analytical ultracentrifugation experiments
title_fullStr Brownian dynamics simulation of analytical ultracentrifugation experiments
title_full_unstemmed Brownian dynamics simulation of analytical ultracentrifugation experiments
title_short Brownian dynamics simulation of analytical ultracentrifugation experiments
title_sort brownian dynamics simulation of analytical ultracentrifugation experiments
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098213/
https://www.ncbi.nlm.nih.gov/pubmed/21596001
http://dx.doi.org/10.1186/2046-1682-4-6
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