SMART Nanopillars Simulation Data

This repository includes all of the meshes and the main results data associated with the manuscript "Nanoscale curvature of the plasma membrane regulates mechanoadaptation through nuclear deformation and rupture". The associated code is in an additional repository linked to Github.

The data is organized into 8 zip folders.  For those containing meshes, the folders within each subfolder describe properties of the mesh and contain the mesh in a single file, "spreadCell_mesh.h5" for use in simulations. Each mesh folder also contains "cells.pvd" (domain markers defined on each tetrahedron of the mesh), "facets.pvd" (domain markers defined on each triangle of the mesh), and "curvatures.xdmf" (curvature values at each point on the mesh), which can all be readily viewed in Paraview. Average concentrations over time are summarized in "npy-files" folders, which contain organized sets of .npy files containing average concentrations of each molecule for each simulation in numpy arrays. These can be loaded in "mech_figs.ipynb" within the main repository. The final zip folder contains simulation data from the case in which a nucleus is deformed by 2.8 microns with alpha_0 (stretch sensitivity) = 5, as shown in Movie 10 and used for calculations in Movies 11-12 and Figure 5.

Note that this new version (v2, Mar 2025) uses different diffusion coefficients for YAP/TAZ in the nucleus (4 microns sq per second) vs. in the cytosol (80 microns sq per second), as indicated by "newdiff".

In summary, the folders are:

- "nanopillars_baseline": meshes for tests on different nanopillar and flat substrates shown in Fig 1-2 and Movies 1-6- "nanopillars_movenuc": meshes for tests shifting the nucleus upward, shown in Fig S2- "nanopillars_indent": different degrees of indentation tested in Figs 3-5 and Movies 7-12- "npy-files-nanopillars-newdiff": baseline tests in Figs 1-2, Movies 1-6- "npy-files-nanopillars-movenuc-newdiff": vertical shifts of nucleus tested in Fig S2- "npy-files-nanopillars-indent-newdiff": different nuclear indentations tested in Fig 4, Movies 7-10- "npy-files-nanopillars-rupture-newdiff": nuclear rupture tests shown in Fig 5, Movies 11 and 12- "simulation_results_2.8indent": simulation results for 2.8 microns nuclear indentation (no nuclear rupture), shown in Movie 10 and used for calculations in Movies 11-12 and Figure 5.