DOI: 10.5281/zenodo.7038939
title: Time-averaged simulations results for bi-phasic blood flow simulations in realistic microvascular networks for multi-capillary dilation scenarios mimicking pericyte ablation

description: Documentation to reproduce in silico analyses related to the manuscript<br> <strong>Pericyte remodelling is deficient in the aged brain and contributes to impaired capillary flow and structure</strong> by Andrée-Anne Berthiaume, Franca Schmid, Stefan Stamenkovic, Vanessa Coelho-Santos, Cara D. Nielson, Bruno Weber, Mark W. Majesky and Andy Y. Shih Published in<br> Nature Communications (doi: 10.1038/s41467-022-33464-w) All simulations are performed based on the in silico blood flow model with discrete red blood cell (RBC) tracking as described in Schmid et al., 2017, PLoS Comp Biol (doi: 10.1371/journal.pcbi.1005392). The bi-phasic blood flow simulations have been performed in two realistic microvascular networks from the somatosensory cortex of the mouse first published in Blinder et al., 2013, Nature Neuroscience (doi: 10.1038/nn.3426). For further information and instructions please contact Franca Schmid (franca.schmid@unibe.ch, orcid.org/0000-0002-0689-9366). <br> <strong>Simulation results:</strong> All time-averaged simulation results are saved as vascular graphs building on the python library igraph and stored as python pickle files (Python 2.7). For each simulation two files are available: <em>verticesDict.pkl</em> and <em>edgesDict.pkl</em>containing all vertex and edge specific data, respectively. A summary of the vertex and edge attributes is provided below. The folder <em>Baseline</em> contains the simulation results for microvascular network 1 (MVN1) and MVN2 for the reference simulation, i.e. without any dilation. Folder <em>Dilated</em> contains the simulation results mimicking the four pericyte ablation scenarios. Subfolders <em>dc_x.x</em> contain the simulation results for the different diameter changes. Note that, folder <em>dc_0.0</em> contains no new simulation results but is a dummy folder containing the information about the vessels to be dilated for the different dilation scenarios (namely edge attribute: <em>toDilate</em> and <em>base_capillary</em>). <strong>Reproducing figure 8:</strong> Panels a-c: created by illustrating the simulation results with the open source software Paraview (v5.7.0).<br> Panels d-f & h: can be generated by executing make_all_figures.py in Python 2.7 within the provided folder structure.<br> Panel g: can be generated by executing make_figure_8g.py after installation of the the vgm-framework (further information see below). <br> Output: All created Figures are saved in the folder <em>Figures</em>. The associated source data is available in Excel format in the folder <em>SourceData</em>. <strong>Edge attributes:</strong> diameter: vessel diameter [µm]<br> mainAV: 1 if ascending venule main branch, 0 otherwise<br> connectivity: vertex tuple to define location of edge<br> flow: flow rate [µm<sup>3</sup>/ms]<br> mainDA: 1 if descending arteriole main branch, 0 otherwise<br> nkind: 0: pial artery, 1: pial vein, 2: descending arteriole, 3: ascending venule, 4: capillary<br> htt: tube hematocrit [-]<br> toDilate: 1 if vessel is dilated for the current dilation scenario, 0 otherwise<br> base_capillary: 1 if vessel is the base capillary of the current dilation scenario, 0 otherwise <strong>Vertex attributes:</strong> index: vertex index<br> pressure: pressure [mmHg]<br> nkind: 0: pial artery, 1: pial vein, 2: descending arteriole, 3: ascending venule, 4: capillary<br> coords: vertex coordinates x,y,z [µm]<br> pBC: pressure boundary conditions at inflow vertices [mmHg], None at internal nodes <strong>Obtaining simulation results:</strong><br> General: Running bi-phasic blood flow simulations requires setting-up the vgm-framework available at: https://github.com/Franculino/vgm.git (v.1.0). vgm is written in Python 2.7 and builds on standard python libraries. vgm has been used on macOS, Ubuntu and Windows Systems. Installation time &lt; 5min. Further details available within the vgm README. Runtime depends on the network size, the chosen blood flow model and the initial conditions (e.g. ~8hrs for a Restart simulation of MVN1 with the bi-phasic blood flow model, see Restarty.py). scripts/Test.py provides an example how a simulation can be initiated. A Demo case is provided (details see below). Output: sampledict_BackUp_xx.pkl The bi-phasic blood flow model can be applied on all kind of microvascular graphs. Specific for current application: Simulations are a restart on the statistical steady state of the baseline cases. All relevant pre-processing functions for the current study are available in scripts/find_stroke_locations.py. Further details are available from the definition of the different functions. The simulations are initiated with scripts/Restart.py. To obtain the time-averaged simulation results scripts/01_put_together_sampledicts.py and scripts/02_convergenceDiscrete.py need to be executed. This results in the file G_averaged.pkl that is used for further analyses. Demo: Contains a small hexagonal microvascular network to test the code. 1) Run Test.py to start the simulation 2) Run 01_put_together_sampledicts.py 3) Run 02_convergenceDiscrete.py to obtain time-averaged results (<em>G_averaged.pkl</em>)