Physical and geometric determinants of transport in feto-placental microvascular networks: Supplementary Datasets
2019-12-20T04:48:13Z (GMT) by
The raw geometric data of Specimen 1 is given in the files Specimen1_Vasculature.stl and Specimen1_Villi.stl. The geometries can be previewed in 3D by clicking on the file names. Further raw villous geometries are available upon request.
The files with "N_" in the filename are for computation of the advective-diffusive transport at varying inlet-outlet pressure drops. To evaluate these files, first one must run the flow study, after that the transport study, as the latter uses solutions of the former.
The files with "Nmax_" in their fine name are for calculation of the transport capacity, which is purely a diffusion problem. These files can be evaluated simply by running the transport study.
The simulations in files "...N_HIGHRES" and "Nmax_HIGHRES" underly Fig. 4, Fig. S3 and Fig. 5A&B. In particular, the geometry is sliced into nine distinct capillaries shown in Fig. 4. To evaluate the fluxes of individual capillaries correctly (and to account for solute concentration boundary layers, should they arise) the pre-programmed mesh settings are at a high resolution: Mesh1 (Stokes problem) has approx. 3mio tetrahedral elements, Mesh 2 (Transport problem) approx. 60mio tetrahedral elements. See details in the supplementary information.
The simulations in files "...N_original" and "Nmax_original" (8 in total) underly Figs 2 & 3. The purpose of these files is to calculate transport across an entire network, which is why they do not require as high a resolution: The Stokes meshes have approximately 300k tetrahedral elements and the transport meshes between 3mio and 12mio elements.
All Comsol files which do not include "with_solutions" in their file name are saved with compact history, and all meshes and solutions are cleared. For easier reproducibility, the two files marked "with_solutions" contain meshes and solutions, so in order to reproduce the blue curves in Fig. 2 and most of the results of the supplementary information, one can directly evaluate the solutions stored in the "with_solutions" files.
Code that creates Fig. 5 is contained in "Fig5-dicrete-network-model_figshare.zip". To produce all the subparts of Fig. 5, run the Mathematica file "Fig5-discrete_network_model.nb" from top to bottom (Evaluation->Evaluate Notebook). It requires an instllation of Matlab and a link between Mathematica and Matlab to be established via MatLink (http://matlink.org/).