ArticleNature computational science2024
SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization.
Article in Nature computational science, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Mechanics of compression-driven morphogenesis.Development (Cambridge, England) · 2026Review
- Biophysics of lumen morphogenesis.Development (Cambridge, England) · 2026Review
- Multicellular simulations with shape and volume constraints using optimal transport.Science advances · 2026Article
- Advancing mechanobiology from single molecules to complex cellular systems.Nature nanotechnology · 2026Review
- Mitochondrial mechanics nucleates axonal jamming and swelling.bioRxiv : the preprint server for biology · 2026Article
- Article
- Leveraging experimental vasculature data for high-resolution brain tumor simulations.Biophysical journal · 2026Article
- Anisotropic Cellular Forces Drive Hexagonal-to-Tetragonal Tiling Transitions in the Drosophila Eye.Development, growth & differentiation · 2026Article
- Emergent stable tissue shapes from the regulatory feedback between morphogens and cell growth.Journal of theoretical biology · 2026Article
- How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis.Soft matter · 2026Article
- Who's afraid of synthetic data? Hybrid approaches to deliver medical digital twins.Informatics in medicine unlocked · 2026Article
- Modeling of viscous frictional force in multicellular morphogenesis.Biophysics and physicobiology · 2026Article
- Spatially-smoothed quantification improves cell typing in imaging mass cytometry datasets.bioRxiv : the preprint server for biology · 2025Article
- AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential.NPJ digital medicine · 2025Review
- Active foam dynamics of tissue spheroid fusion.Nature communications · 2025Article
- Modeling bulk mechanical effects in a planar cellular monolayer.Physical review. E · 2025Article
- Capturing nematic order on tissue surfaces of arbitrary geometry.Nature communications · 2025Article
- Emergent Stable Tissue Shapes from the Regulatory Feedback between Morphogens and Cell Growth.bioRxiv : the preprint server for biology · 2025Article
- Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell.PLoS computational biology · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
The three-dimensional (3D) organization of cells determines tissue function and integrity, and changes markedly in development and disease. Cell-based simulations have long been used to define the underlying mechanical principles. However, high computational costs have so far limited simulations to either simplified cell geometries or small tissue patches. Here, we present SimuCell3D, an efficient open-source program to simulate large tissues in three dimensions with subcellular resolution, growth, proliferation, extracellular matrix, fluid cavities, nuclei and non-uniform mechanical properties, as found in polarized epithelia. Spheroids, vesicles, sheets, tubes and other tissue geometries can readily be imported from microscopy images and simulated to infer biomechanical parameters. Doing so, we show that 3D cell shapes in layered and pseudostratified epithelia are largely governed by a competition between surface tension and intercellular adhesion. SimuCell3D enables the large-scale in silico study of 3D tissue organization in development and disease at a great level of detail.
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