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Simulating 3D Cell Shape with the Cellular Potts Model

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Mechanobiology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2600))

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Abstract

Computer simulations have become a widely used method for the field of mechanobiology. An important question is whether one can predict the shape and forces of cells as a function of the extracellular environment. Different types of models have been described before to simulate cell and tissue shapes in structured environments. In this chapter, we give a brief overview of commonly used models and then describe the Cellular Potts Model, a lattice-based modelling framework, in more detail. We provide a hands-on guide on how to build a model that simulates the shape of a single cell on a micropattern in three dimensions in different open source software packages using the Cellular Potts framework. A simulation is set up with an initial configuration of generalized cells that change shape and position due to an energy function that incorporates cellular volume and surface area constraints as well as interaction energies between the generalized cells.

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Acknowledgments

This research has been funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy via the Excellence Cluster 3D Matter Made to Order (EXC-2082/1 – 390761711). USS is a member of the Interdisciplinary Center for Scientific Computing (IWR) at Heidelberg.

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Authors and Affiliations

  1. Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany

    Rabea Link & Ulrich S. Schwarz

  2. BioQuant, Heidelberg University, Heidelberg, Germany

    Rabea Link & Ulrich S. Schwarz

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  1. Ulrich S. Schwarz
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Correspondence to Ulrich S. Schwarz .

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Editors and Affiliations

  1. Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

    Ronen Zaidel-Bar

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Link, R., Schwarz, U.S. (2023). Simulating 3D Cell Shape with the Cellular Potts Model. In: Zaidel-Bar, R. (eds) Mechanobiology. Methods in Molecular Biology, vol 2600. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2851-5_22

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  • DOI: https://doi.org/10.1007/978-1-0716-2851-5_22

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2850-8

  • Online ISBN: 978-1-0716-2851-5

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