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Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries

Chemical reactions inside cells are generally considered to happen within fixed-size compartments. However, cells and their compartments are highly dynamic. Thus, such stringent geometrical assumptions may not reflect biophysical reality, and can highly bias conclusions from simulation studies. In t...

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Detalles Bibliográficos
Autores principales: Ghosh, Atiyo, Marquez-Lago, Tatiana T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521929/
https://www.ncbi.nlm.nih.gov/pubmed/26230406
http://dx.doi.org/10.1371/journal.pone.0133401
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author Ghosh, Atiyo
Marquez-Lago, Tatiana T.
author_facet Ghosh, Atiyo
Marquez-Lago, Tatiana T.
author_sort Ghosh, Atiyo
collection PubMed
description Chemical reactions inside cells are generally considered to happen within fixed-size compartments. However, cells and their compartments are highly dynamic. Thus, such stringent geometrical assumptions may not reflect biophysical reality, and can highly bias conclusions from simulation studies. In this work, we present an intuitive algorithm for particle-based diffusion in and on moving boundaries, for both point particles and spherical particles. We first benchmark our proposed stochastic method against solutions of partial differential equations in appropriate scenarios, and further demonstrate that moving boundaries can give rise to super-diffusive motion as well as time-inhomogeneous reaction rates. Finally, we conduct a numerical experiment representing photobleaching of diffusing fluorescent proteins in dividing Saccharomyces cerevisiae cells to demonstrate that moving boundaries might cause important effects neglected in previously published studies of cell compartmentalization.
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spelling pubmed-45219292015-08-06 Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries Ghosh, Atiyo Marquez-Lago, Tatiana T. PLoS One Research Article Chemical reactions inside cells are generally considered to happen within fixed-size compartments. However, cells and their compartments are highly dynamic. Thus, such stringent geometrical assumptions may not reflect biophysical reality, and can highly bias conclusions from simulation studies. In this work, we present an intuitive algorithm for particle-based diffusion in and on moving boundaries, for both point particles and spherical particles. We first benchmark our proposed stochastic method against solutions of partial differential equations in appropriate scenarios, and further demonstrate that moving boundaries can give rise to super-diffusive motion as well as time-inhomogeneous reaction rates. Finally, we conduct a numerical experiment representing photobleaching of diffusing fluorescent proteins in dividing Saccharomyces cerevisiae cells to demonstrate that moving boundaries might cause important effects neglected in previously published studies of cell compartmentalization. Public Library of Science 2015-07-31 /pmc/articles/PMC4521929/ /pubmed/26230406 http://dx.doi.org/10.1371/journal.pone.0133401 Text en © 2015 Ghosh, Marquez-Lago http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Ghosh, Atiyo
Marquez-Lago, Tatiana T.
Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries
title Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries
title_full Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries
title_fullStr Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries
title_full_unstemmed Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries
title_short Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries
title_sort simulating stochastic reaction-diffusion systems on and within moving boundaries
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521929/
https://www.ncbi.nlm.nih.gov/pubmed/26230406
http://dx.doi.org/10.1371/journal.pone.0133401
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