Model Portfolio

[germannp]

For illustration we could implement some published models:

• Nissen, S. B., Perera, M., Gonzalez, J. M., Morgani, S. M., Jensen, M. H., Sneppen, K., … Trusina, A. (2017). Four simple rules that are sufficient to generate the mammalian blastocyst, 1–30. https://doi.org/https://doi.org/10.1371/journal. pbio.2000737
• Allena, R., Scianna, M., & Preziosi, L. (2016). A Cellular Potts Model of single cell migration in presence of durotaxis. Mathematical Biosciences. https://doi.org/10.1016/j.mbs.2016.02.011
• Niculescu, I., Textor, J., & de Boer, R. J. (2015). Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration. PLOS Computational Biology, 11(10), e1004280. https://doi.org/10.1371/journal.pcbi.1004280
• Polymer chain for DNA compartmentalization

[mmarinriera]

• Epithelial invagination by apical cell contraction.

[germannp]

• Sandersius, S. a, Chuai, M., Weijer, C. J., & Newman, T. J. (2011). A “chemotactic dipole” mechanism for large-scale vortex motion during primitive streak formation in the chick embryo. Physical Biology, 8(4), 45008. https://doi.org/10.1088/1478-3975/8/4/045008

[germannp]

• Planar cell polarity of epithelial cells in curved sheets. Would require additional angle for PCP polarity in the plan normal to the apical-basal polarity and then an XY model for those, i.e. U_PCP = - Σp_i . p_j.