MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies
Abstract The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the coarse-grained model and the vertex model, its high computa...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-02-01
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| Series: | npj Systems Biology and Applications |
| Online Access: | https://doi.org/10.1038/s41540-023-00265-w |
| _version_ | 1797864347184136192 |
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| author | Xiangyu Kuang Guoye Guan Chao Tang Lei Zhang |
| author_facet | Xiangyu Kuang Guoye Guan Chao Tang Lei Zhang |
| author_sort | Xiangyu Kuang |
| collection | DOAJ |
| description | Abstract The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the coarse-grained model and the vertex model, its high computational cost caused by three-dimensional spatial discretization hampered its application and scalability, especially for multicellular organisms. Recently, we built a phase field model coupled with in vivo imaging data to accurately reconstruct the embryonic morphogenesis of Caenorhabditis elegans from 1- to 8-cell stages. In this work, we propose an improved phase field model by using the stabilized numerical scheme and modified volume constriction. Then we present a scalable phase-field framework, MorphoSim, which is 100 times more efficient than the previous one and can simulate over 100 mechanically interacting cells. Finally, we demonstrate how MorphoSim can be successfully applied to reproduce the assembly, self-repairing, and dissociation of a synthetic artificial multicellular system - the synNotch system. |
| first_indexed | 2024-04-09T22:50:18Z |
| format | Article |
| id | doaj.art-4c88d50fa771437bb5f845b3b17329bf |
| institution | Directory Open Access Journal |
| issn | 2056-7189 |
| language | English |
| last_indexed | 2024-04-09T22:50:18Z |
| publishDate | 2023-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Systems Biology and Applications |
| spelling | doaj.art-4c88d50fa771437bb5f845b3b17329bf2023-03-22T11:39:07ZengNature Portfolionpj Systems Biology and Applications2056-71892023-02-019111110.1038/s41540-023-00265-wMorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologiesXiangyu Kuang0Guoye Guan1Chao Tang2Lei Zhang3Center for Quantitative Biology, Peking UniversityCenter for Quantitative Biology, Peking UniversityCenter for Quantitative Biology, Peking UniversityCenter for Quantitative Biology, Peking UniversityAbstract The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the coarse-grained model and the vertex model, its high computational cost caused by three-dimensional spatial discretization hampered its application and scalability, especially for multicellular organisms. Recently, we built a phase field model coupled with in vivo imaging data to accurately reconstruct the embryonic morphogenesis of Caenorhabditis elegans from 1- to 8-cell stages. In this work, we propose an improved phase field model by using the stabilized numerical scheme and modified volume constriction. Then we present a scalable phase-field framework, MorphoSim, which is 100 times more efficient than the previous one and can simulate over 100 mechanically interacting cells. Finally, we demonstrate how MorphoSim can be successfully applied to reproduce the assembly, self-repairing, and dissociation of a synthetic artificial multicellular system - the synNotch system.https://doi.org/10.1038/s41540-023-00265-w |
| spellingShingle | Xiangyu Kuang Guoye Guan Chao Tang Lei Zhang MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies npj Systems Biology and Applications |
| title | MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies |
| title_full | MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies |
| title_fullStr | MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies |
| title_full_unstemmed | MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies |
| title_short | MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies |
| title_sort | morphosim an efficient and scalable phase field framework for accurately simulating multicellular morphologies |
| url | https://doi.org/10.1038/s41540-023-00265-w |
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