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Single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data

The analysis of single molecule imaging experiments is complicated by the stochastic nature of single molecule events, by instrument noise and by the limited information which can be gathered about any individual molecule observed. Consequently, it is important to cross check experimental results us...

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Detalles Bibliográficos
Autor principal: Mashanov, Gregory I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233692/
https://www.ncbi.nlm.nih.gov/pubmed/25008080
http://dx.doi.org/10.1098/rsif.2014.0442
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author Mashanov, Gregory I.
author_facet Mashanov, Gregory I.
author_sort Mashanov, Gregory I.
collection PubMed
description The analysis of single molecule imaging experiments is complicated by the stochastic nature of single molecule events, by instrument noise and by the limited information which can be gathered about any individual molecule observed. Consequently, it is important to cross check experimental results using a model simulating single molecule dynamics (e.g. movements and binding events) in a virtual cell-like environment. The output of such a model should match the real data format allowing researchers to compare simulated results with the real experiments. The proposed model exploits the advantages of ‘object-oriented’ computing. First of all, the ability to create and manipulate a number of classes, each containing an arbitrary number of single molecule objects. These classes may include objects moving within the ‘cytoplasm’; objects moving at the ‘plasma membrane’; and static objects located inside the ‘body’. The objects of a given class can interact with each other and/or with the objects of other classes according to their physical and chemical properties. Each model run generates a sequence of images, each containing summed images of all fluorescent objects emitting light under given illumination conditions with realistic levels of noise and emission fluctuations. The model accurately reproduces reported single molecule experiments and predicts the outcome of future experiments.
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spelling pubmed-42336922014-11-21 Single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data Mashanov, Gregory I. J R Soc Interface Research Articles The analysis of single molecule imaging experiments is complicated by the stochastic nature of single molecule events, by instrument noise and by the limited information which can be gathered about any individual molecule observed. Consequently, it is important to cross check experimental results using a model simulating single molecule dynamics (e.g. movements and binding events) in a virtual cell-like environment. The output of such a model should match the real data format allowing researchers to compare simulated results with the real experiments. The proposed model exploits the advantages of ‘object-oriented’ computing. First of all, the ability to create and manipulate a number of classes, each containing an arbitrary number of single molecule objects. These classes may include objects moving within the ‘cytoplasm’; objects moving at the ‘plasma membrane’; and static objects located inside the ‘body’. The objects of a given class can interact with each other and/or with the objects of other classes according to their physical and chemical properties. Each model run generates a sequence of images, each containing summed images of all fluorescent objects emitting light under given illumination conditions with realistic levels of noise and emission fluctuations. The model accurately reproduces reported single molecule experiments and predicts the outcome of future experiments. The Royal Society 2014-09-06 /pmc/articles/PMC4233692/ /pubmed/25008080 http://dx.doi.org/10.1098/rsif.2014.0442 Text en http://creativecommons.org/licenses/by/3.0/ © 2014 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.
spellingShingle Research Articles
Mashanov, Gregory I.
Single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data
title Single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data
title_full Single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data
title_fullStr Single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data
title_full_unstemmed Single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data
title_short Single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data
title_sort single molecule dynamics in a virtual cell: a three-dimensional model that produces simulated fluorescence video-imaging data
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233692/
https://www.ncbi.nlm.nih.gov/pubmed/25008080
http://dx.doi.org/10.1098/rsif.2014.0442
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