Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments

The diffusion of tracer particles in 3D macromolecular crowded media has been studied using two methodologies, simulation and experimental, with the aim of comparing their results. Firstly, the diffusion of a tracer in an obstructed 3D lattice with mobile and big size obstacles has been analyzed thr...

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Authors: Vilaseca i Font, Eudald, Pastor, Isabel, Isvoran, Adriana, Madurga Díez, Sergio, Garcés, Josep Lluís, Mas i Pujadas, Francesc
Format: article
Status:Versión aceptada para publicación
Publication Date:2011
Country:España
Institution:Universidad de Barcelona
Repository:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/109046
Online Access:https://hdl.handle.net/2445/109046
Access Level:Open access
Keyword:Mètode de Montecarlo
Difusió
Macromolècules
Fluorescència
Monte Carlo method
Diffusion
Macromolecules
Fluorescence
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spelling Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experimentsVilaseca i Font, EudaldPastor, IsabelIsvoran, AdrianaMadurga Díez, SergioGarcés, Josep LluísMas i Pujadas, FrancescMètode de MontecarloDifusióMacromolèculesFluorescènciaMonte Carlo methodDiffusionMacromoleculesFluorescenceThe diffusion of tracer particles in 3D macromolecular crowded media has been studied using two methodologies, simulation and experimental, with the aim of comparing their results. Firstly, the diffusion of a tracer in an obstructed 3D lattice with mobile and big size obstacles has been analyzed through a Monte Carlo (MC) simulation procedure. Secondly, Fluorescence Recovery after Photobleaching (FRAP) experiments have been carried out to study the diffusion of a model protein (alpha-chymotrypsin) in in vitro crowded solution where two type of Dextran molecules are used as crowder agents. To facilitate the comparison the relative size between the tracer and the crowder is the same in both studies. The results indicate a qualitative agreement between the diffusional behaviors observed in the two studies. The dependence of the anomalous diffusion exponent and the limiting diffusion coefficient with the obstacle size and excluded volume shows, in both cases, a similar tendency. The introduction of a reduced mobility parameter in the simulation model accounting for the short range tracer-obstacle interactions allows to obtain a quantitative agreement between the limiting diffusion coefficient values yielded by both procedures. The simulation-experiment quantitative agreement for the anomalous diffusion exponent requires further improvements. As far as we know, this is the first reported work where both techniques are used in parallel to study the diffusion in macromolecular crowded media.Springer Verlag2011info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionapplication/pdfhttps://hdl.handle.net/2445/109046Articles publicats en revistes (Ciència dels Materials i Química Física)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésVersió postprint del document publicat a: https://doi.org/10.1007/s00214-010-0840-5Theoretical Chemistry Accounts, 2011, vol. 128, num. 4, p. 795-805https://doi.org/10.1007/s00214-010-0840-5(c) Springer Verlag, 2011info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1090462026-05-27T06:46:51Z
dc.title.none.fl_str_mv Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments
title Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments
spellingShingle Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments
Vilaseca i Font, Eudald
Mètode de Montecarlo
Difusió
Macromolècules
Fluorescència
Monte Carlo method
Diffusion
Macromolecules
Fluorescence
title_short Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments
title_full Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments
title_fullStr Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments
title_full_unstemmed Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments
title_sort Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments
dc.creator.none.fl_str_mv Vilaseca i Font, Eudald
Pastor, Isabel
Isvoran, Adriana
Madurga Díez, Sergio
Garcés, Josep Lluís
Mas i Pujadas, Francesc
author Vilaseca i Font, Eudald
author_facet Vilaseca i Font, Eudald
Pastor, Isabel
Isvoran, Adriana
Madurga Díez, Sergio
Garcés, Josep Lluís
Mas i Pujadas, Francesc
author_role author
author2 Pastor, Isabel
Isvoran, Adriana
Madurga Díez, Sergio
Garcés, Josep Lluís
Mas i Pujadas, Francesc
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Mètode de Montecarlo
Difusió
Macromolècules
Fluorescència
Monte Carlo method
Diffusion
Macromolecules
Fluorescence
topic Mètode de Montecarlo
Difusió
Macromolècules
Fluorescència
Monte Carlo method
Diffusion
Macromolecules
Fluorescence
description The diffusion of tracer particles in 3D macromolecular crowded media has been studied using two methodologies, simulation and experimental, with the aim of comparing their results. Firstly, the diffusion of a tracer in an obstructed 3D lattice with mobile and big size obstacles has been analyzed through a Monte Carlo (MC) simulation procedure. Secondly, Fluorescence Recovery after Photobleaching (FRAP) experiments have been carried out to study the diffusion of a model protein (alpha-chymotrypsin) in in vitro crowded solution where two type of Dextran molecules are used as crowder agents. To facilitate the comparison the relative size between the tracer and the crowder is the same in both studies. The results indicate a qualitative agreement between the diffusional behaviors observed in the two studies. The dependence of the anomalous diffusion exponent and the limiting diffusion coefficient with the obstacle size and excluded volume shows, in both cases, a similar tendency. The introduction of a reduced mobility parameter in the simulation model accounting for the short range tracer-obstacle interactions allows to obtain a quantitative agreement between the limiting diffusion coefficient values yielded by both procedures. The simulation-experiment quantitative agreement for the anomalous diffusion exponent requires further improvements. As far as we know, this is the first reported work where both techniques are used in parallel to study the diffusion in macromolecular crowded media.
publishDate 2011
dc.date.none.fl_str_mv 2011
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/109046
url https://hdl.handle.net/2445/109046
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Versió postprint del document publicat a: https://doi.org/10.1007/s00214-010-0840-5
Theoretical Chemistry Accounts, 2011, vol. 128, num. 4, p. 795-805
https://doi.org/10.1007/s00214-010-0840-5
dc.rights.none.fl_str_mv (c) Springer Verlag, 2011
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) Springer Verlag, 2011
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Verlag
publisher.none.fl_str_mv Springer Verlag
dc.source.none.fl_str_mv Articles publicats en revistes (Ciència dels Materials i Química Física)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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