PalaCell2D: A framework for detailed tissue morphogenesis

@article{Conradin2021PalaCell2DAF,
  title={PalaCell2D: A framework for detailed tissue morphogenesis},
  author={Rapha{\"e}l Conradin and Christophe Coreixas and Jonas Latt and Bastien Chopard},
  journal={bioRxiv},
  year={2021}
}
In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues. As compared to in vivo experiments, computer based frameworks dedicated to tissue modeling allow us to easily test different hypotheses, and to quantify the impact of various biophysically relevant parameters. Here, we propose a formalism based on a detailed… 
1 Citations
3D Organisation of Cells in Pseudostratified Epithelia
TLDR
A recently developed new perspective on epithelial cell organisation is reviewed and the complex 3D cell neighbour relationships in pseudostratified epithelia are introduced as punakoids, paving the way for the development of data-driven 3D simulation frameworks that will be invaluable in the simulation of epithelial dynamics in development and disease.

References

SHOWING 1-10 OF 60 REFERENCES
SIMULATION TECHNIQUES FOR MECHANO-CHEMICAL INTERACTIONS IN MORPHOGENESIS
TLDR
This thesis focuses on the continuous formulation of a model for embryonic long bone development and the emergence of novel phenomena such as salt-and-pepper pattern formation and cell clustering, and investigates the behaviour of Turing-like receptor-ligand signalling systems on growing cellular tissue.
A model for individual and collective cell movement in Dictyostelium discoideum.
  • E. Palsson, H. Othmer
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2000
TLDR
A biologically realistic model for motile D. discoideum cells that can generate active forces, that interact via surface molecules, and that can detect and respond to chemotactic signals is described.
LBIBCell: a cell-based simulation environment for morphogenetic problems
TLDR
An open-source software framework for morphogenetic problems that offers core functionalities for the tissue and signalling models, and great flexibility to add custom extensions and biologically motivated processes.
Numerical Modelling of Confluent Cell Monolayers : Study of Tissue Mechanics and Morphogenesis
TLDR
The numerical model of confluent cell monolayers that was developed in order to study the interplay between cell biophysical properties and tissue mechanics and morphology was extended to the 3D space and presented its application for further studies of tissue folding.
Implementing vertex dynamics models of cell populations in biology within a consistent computational framework.
Influence of proliferation on the motions of epithelial monolayers invading adherent strips.
TLDR
It is shown that confined to adherent strips, and on the time scale of a day or two, monolayers move with a characteristic front speed independent of proliferation, but that the motion is accompanied by persistent velocity waves, only in the absence of cell divisions.
Cell topology, geometry, and morphogenesis in proliferating epithelia.
A Sub-Cellular Viscoelastic Model for Cell Population Mechanics
TLDR
A single-cell-based model representing the cross section of a typical tissue that enables one to isolate the effects of biomechanical properties of individual cells and the communication between cells and their microenvironment while simultaneously allowing for the formation of clusters or sheets of cells that act together as one complex tissue.
Influence of cell mechanics and proliferation on the buckling of simulated tissues using a vertex model
TLDR
This work uses a 2D vertex model of circular cross-sections of cell monolayers to investigate how cell mechanical properties and proliferation affect the shape of in-silico growing tissues and shows that increasing the cells’ contractility and the intercellular adhesion reduces tissue buckling.
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