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Detailed Simulations of Cell Biology with Smoldyn 2.1
Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Co...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837389/ https://www.ncbi.nlm.nih.gov/pubmed/20300644 http://dx.doi.org/10.1371/journal.pcbi.1000705 |
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author | Andrews, Steven S. Addy, Nathan J. Brent, Roger Arkin, Adam P. |
author_facet | Andrews, Steven S. Addy, Nathan J. Brent, Roger Arkin, Adam P. |
author_sort | Andrews, Steven S. |
collection | PubMed |
description | Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells. |
format | Text |
id | pubmed-2837389 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-28373892010-03-17 Detailed Simulations of Cell Biology with Smoldyn 2.1 Andrews, Steven S. Addy, Nathan J. Brent, Roger Arkin, Adam P. PLoS Comput Biol Research Article Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells. Public Library of Science 2010-03-12 /pmc/articles/PMC2837389/ /pubmed/20300644 http://dx.doi.org/10.1371/journal.pcbi.1000705 Text en Andrews et al. 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 Andrews, Steven S. Addy, Nathan J. Brent, Roger Arkin, Adam P. Detailed Simulations of Cell Biology with Smoldyn 2.1 |
title | Detailed Simulations of Cell Biology with Smoldyn 2.1 |
title_full | Detailed Simulations of Cell Biology with Smoldyn 2.1 |
title_fullStr | Detailed Simulations of Cell Biology with Smoldyn 2.1 |
title_full_unstemmed | Detailed Simulations of Cell Biology with Smoldyn 2.1 |
title_short | Detailed Simulations of Cell Biology with Smoldyn 2.1 |
title_sort | detailed simulations of cell biology with smoldyn 2.1 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837389/ https://www.ncbi.nlm.nih.gov/pubmed/20300644 http://dx.doi.org/10.1371/journal.pcbi.1000705 |
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