Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments

Abstract Fluorescence correlation spectroscopy (FCS) methods are powerful tools for unveiling the dynamical organization of cells. For simple cases, such as molecules passively moving in a homogeneous media, FCS analysis yields analytical functions that can be fitted to the experimental data to reco...

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Autores principales: Mocskos, Esteban Eduardo, Levi, Valeria
Publicado: 2015
Materias:
cells
cytology
diffusion
fluorescence microscopy
Monte Carlo method
Cells
Diffusion
Microscopy, Fluorescence
Monte Carlo Method
Acceso en línea:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00063495_v108_n11_p2613_Angiolini
http://hdl.handle.net/20.500.12110/paper_00063495_v108_n11_p2613_Angiolini
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id paper:paper_00063495_v108_n11_p2613_Angiolini
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spelling paper:paper_00063495_v108_n11_p2613_Angiolini2023-06-08T14:31:14Z Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments Mocskos, Esteban Eduardo Levi, Valeria cells cytology diffusion fluorescence microscopy Monte Carlo method Cells Diffusion Microscopy, Fluorescence Monte Carlo Method Abstract Fluorescence correlation spectroscopy (FCS) methods are powerful tools for unveiling the dynamical organization of cells. For simple cases, such as molecules passively moving in a homogeneous media, FCS analysis yields analytical functions that can be fitted to the experimental data to recover the phenomenological rate parameters. Unfortunately, many dynamical processes in cells do not follow these simple models, and in many instances it is not possible to obtain an analytical function through a theoretical analysis of a more complex model. In such cases, experimental analysis can be combined with Monte Carlo simulations to aid in interpretation of the data. In response to this need, we developed a method called FERNET (Fluorescence Emission Recipes and Numerical routines Toolkit) based on Monte Carlo simulations and the MCell-Blender platform, which was designed to treat the reaction-diffusion problem under realistic scenarios. This method enables us to set complex geometries of the simulation space, distribute molecules among different compartments, and define interspecies reactions with selected kinetic constants, diffusion coefficients, and species brightness. We apply this method to simulate single- and multiple-point FCS, photon-counting histogram analysis, raster image correlation spectroscopy, and two-color fluorescence cross-correlation spectroscopy. We believe that this new program could be very useful for predicting and understanding the output of fluorescence microscopy experiments. © 2015 Biophysical Society. Fil:Mocskos, E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Levi, V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2015 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00063495_v108_n11_p2613_Angiolini http://hdl.handle.net/20.500.12110/paper_00063495_v108_n11_p2613_Angiolini
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic cells
cytology
diffusion
fluorescence microscopy
Monte Carlo method
Cells
Diffusion
Microscopy, Fluorescence
Monte Carlo Method
spellingShingle cells
cytology
diffusion
fluorescence microscopy
Monte Carlo method
Cells
Diffusion
Microscopy, Fluorescence
Monte Carlo Method
Mocskos, Esteban Eduardo
Levi, Valeria
Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments
topic_facet cells
cytology
diffusion
fluorescence microscopy
Monte Carlo method
Cells
Diffusion
Microscopy, Fluorescence
Monte Carlo Method
description Abstract Fluorescence correlation spectroscopy (FCS) methods are powerful tools for unveiling the dynamical organization of cells. For simple cases, such as molecules passively moving in a homogeneous media, FCS analysis yields analytical functions that can be fitted to the experimental data to recover the phenomenological rate parameters. Unfortunately, many dynamical processes in cells do not follow these simple models, and in many instances it is not possible to obtain an analytical function through a theoretical analysis of a more complex model. In such cases, experimental analysis can be combined with Monte Carlo simulations to aid in interpretation of the data. In response to this need, we developed a method called FERNET (Fluorescence Emission Recipes and Numerical routines Toolkit) based on Monte Carlo simulations and the MCell-Blender platform, which was designed to treat the reaction-diffusion problem under realistic scenarios. This method enables us to set complex geometries of the simulation space, distribute molecules among different compartments, and define interspecies reactions with selected kinetic constants, diffusion coefficients, and species brightness. We apply this method to simulate single- and multiple-point FCS, photon-counting histogram analysis, raster image correlation spectroscopy, and two-color fluorescence cross-correlation spectroscopy. We believe that this new program could be very useful for predicting and understanding the output of fluorescence microscopy experiments. © 2015 Biophysical Society.
author Mocskos, Esteban Eduardo
Levi, Valeria
author_facet Mocskos, Esteban Eduardo
Levi, Valeria
author_sort Mocskos, Esteban Eduardo
title Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments
title_short Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments
title_full Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments
title_fullStr Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments
title_full_unstemmed Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments
title_sort exploring the dynamics of cell processes through simulations of fluorescence microscopy experiments
publishDate 2015
url https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00063495_v108_n11_p2613_Angiolini
http://hdl.handle.net/20.500.12110/paper_00063495_v108_n11_p2613_Angiolini
work_keys_str_mv AT mocskosestebaneduardo exploringthedynamicsofcellprocessesthroughsimulationsoffluorescencemicroscopyexperiments
AT levivaleria exploringthedynamicsofcellprocessesthroughsimulationsoffluorescencemicroscopyexperiments
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