Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.

Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational met...

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Autores principales:	Mohammad Azimi, Yousef Jamali, Mohammad R K Mofrad
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bf0a49c079ca47939ccea0fe0df1a599
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spelling	oai:doaj.org-article:bf0a49c079ca47939ccea0fe0df1a5992021-11-04T06:07:53ZAccounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.1932-620310.1371/journal.pone.0025306https://doaj.org/article/bf0a49c079ca47939ccea0fe0df1a5992011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21966493/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational method for modeling the diffusion of molecules and macromolecules in three-dimensional solutions using agent based modeling. This method allows for realistic modeling of a system of particles with different properties such as size, diffusion coefficients, and affinity as well as the environment properties such as viscosity and geometry. Simulations using these movement probabilities yield behavior that mimics natural diffusion. Using this modeling framework, we simulate the effects of molecular crowding on effective diffusion and have validated the results of our model using Langevin dynamics simulations and note that they are in good agreement with previous experimental data. Furthermore, we investigate an extension of this framework where single discrete cells can contain multiple particles of varying size in an effort to highlight errors that can arise from discretization that lead to the unnatural behavior of particles undergoing diffusion. Subsequently, we explore various algorithms that differ in how they handle the movement of multiple particles per cell and suggest an algorithm that properly accommodates multiple particles of various sizes per cell that can replicate the natural behavior of these particles diffusing. Finally, we use the present modeling framework to investigate the effect of structural geometry on the directionality of diffusion in the cell cytoskeleton with the observation that parallel orientation in the structural geometry of actin filaments of filopodia and the branched structure of lamellipodia can give directionality to diffusion at the filopodia-lamellipodia interface.Mohammad AzimiYousef JamaliMohammad R K MofradPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e25306 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mohammad Azimi Yousef Jamali Mohammad R K Mofrad Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.
description	Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational method for modeling the diffusion of molecules and macromolecules in three-dimensional solutions using agent based modeling. This method allows for realistic modeling of a system of particles with different properties such as size, diffusion coefficients, and affinity as well as the environment properties such as viscosity and geometry. Simulations using these movement probabilities yield behavior that mimics natural diffusion. Using this modeling framework, we simulate the effects of molecular crowding on effective diffusion and have validated the results of our model using Langevin dynamics simulations and note that they are in good agreement with previous experimental data. Furthermore, we investigate an extension of this framework where single discrete cells can contain multiple particles of varying size in an effort to highlight errors that can arise from discretization that lead to the unnatural behavior of particles undergoing diffusion. Subsequently, we explore various algorithms that differ in how they handle the movement of multiple particles per cell and suggest an algorithm that properly accommodates multiple particles of various sizes per cell that can replicate the natural behavior of these particles diffusing. Finally, we use the present modeling framework to investigate the effect of structural geometry on the directionality of diffusion in the cell cytoskeleton with the observation that parallel orientation in the structural geometry of actin filaments of filopodia and the branched structure of lamellipodia can give directionality to diffusion at the filopodia-lamellipodia interface.
format	article
author	Mohammad Azimi Yousef Jamali Mohammad R K Mofrad
author_facet	Mohammad Azimi Yousef Jamali Mohammad R K Mofrad
author_sort	Mohammad Azimi
title	Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.
title_short	Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.
title_full	Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.
title_fullStr	Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.
title_full_unstemmed	Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.
title_sort	accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/bf0a49c079ca47939ccea0fe0df1a599
work_keys_str_mv	AT mohammadazimi accountingfordiffusioninagentbasedmodelsofreactiondiffusionsystemswithapplicationtocytoskeletaldiffusion AT yousefjamali accountingfordiffusioninagentbasedmodelsofreactiondiffusionsystemswithapplicationtocytoskeletaldiffusion AT mohammadrkmofrad accountingfordiffusioninagentbasedmodelsofreactiondiffusionsystemswithapplicationtocytoskeletaldiffusion
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Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion.

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