Mathematical analysis to test how lamellar bilayers fit within different bicontinuous cubic space groups
- FATSLiM.yml contains the conda environment to run the FATSLiM membrane thickness calculation
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Data were generated with the following command:
- python geometric_analysis.py -s gyroid schwarz primitive -n 10000 -o pore2pore
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This produces probability density distributions for each of the three space groups using 10,000 samples.
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The hard-coded parameters for this analysis are:
- n, grid size of 100 by 100 by 100 for the discretized nodal approximations
- box, 9.4 nm -- experimental unit cell size
- struct_tol, 0.01 -- tolerance for discretized points on surface
- guess, 4.6 nm -- initial guess for the pore-to-pore distance from bilayer simulation
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The kernel density estimation used to smooth the distribution was a Gaussian kernel.
- Bandwidth was determined by 10-fold cross-validation -- 0.1 for every space group