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Improving the realism of the cellular Potts model in simulations of biological cells

Author

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  • Ouchi, Noriyuki Bob
  • Glazier, James A.
  • Rieu, Jean-Paul
  • Upadhyaya, Arpita
  • Sawada, Yasuji

Abstract

Because the extended or cellular large-Q Potts model (CPM) captures effectively the global features of tissue rearrangement experiments, including cell sorting and tissue engulfment, it has become a common technique for cell level simulation of tissues. However, it omits three key elements of real cells, their fixed membrane area, their attractive binding and the dissipation of making and breaking membrane contacts. In this paper, we modify the Hamiltonian to use negative surface energies, constrained surface area and a spin flip energy threshold to improve the correspondence to reality. We find that the new model correctly predicts several dynamical behaviors of cells which the original CPM does not, including the hierarchy of diffusion constants.

Suggested Citation

  • Ouchi, Noriyuki Bob & Glazier, James A. & Rieu, Jean-Paul & Upadhyaya, Arpita & Sawada, Yasuji, 2003. "Improving the realism of the cellular Potts model in simulations of biological cells," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 329(3), pages 451-458.
    • Handle: RePEc:eee:phsmap:v:329:y:2003:i:3:p:451-458
    DOI: 10.1016/S0378-4371(03)00574-0
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    Citations

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    Cited by:

    1. Moreno, Felipe & Davis, Sergio & Loyola, Claudia & Peralta, Joaquín, 2018. "Ordered metastable states in the Potts model and their connection with the superheated solid state," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 509(C), pages 361-368.
    2. Thomas, Gilberto L. & Mironov, Vladimir & Nagy-Mehez, Agnes & Mombach, José C.M., 2014. "Dynamics of cell aggregates fusion: Experiments and simulations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 395(C), pages 247-254.
    3. Elisabeth G Rens & Leah Edelstein-Keshet, 2019. "From energy to cellular forces in the Cellular Potts Model: An algorithmic approach," PLOS Computational Biology, Public Library of Science, vol. 15(12), pages 1-23, December.
    4. Anja Voss-Böhme, 2012. "Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-14, September.
    5. Richard J Beck & Dario I Bijker & Joost B Beltman, 2020. "Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data," PLOS Computational Biology, Public Library of Science, vol. 16(7), pages 1-25, July.

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