diff --git a/README.md b/README.md index 77995b2..4575bfc 100644 --- a/README.md +++ b/README.md @@ -25,6 +25,39 @@ and consists in a phase-field model for tumor angiogenesis. The model is based o ### Parameters We provide typical parameters for simulations in [`input_file`](https://github.com/phydev/angio/blob/master/input_file). +See the description of each paramter in the table bellow and the mapping with experimental data in [Supplementary material](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-018-27034-8/MediaObjects/41598_2018_27034_MOESM1_ESM.pdf). + + +| Reference value | Variable | Description | +|-----------------|-----------------------|----------------------------------------| +| 4.00 | cell_radius | Radius of individual cells | +| 100.0 | diffusion_const | Diffusion constant for VEGF | +| 1.00 | interface_width | Width of the phase-field interface | +| 0.30 | vegf_p | VEGF concentration for maximum proliferation | +| 0.09 | vegf_c | VEGF concentration for branching | +| 20.0 | diff_oxy_length | Diffusion length for oxygen | +| 6.25 | vegf_rate | Rate of VEGF uptake by cells | +| 1.00 | vegf_source_conc | Concentration of VEGF at source | +| 1.00 | prolif_rate | Rate of proliferation of endothelial cells | +| 5.00 | vessel_radius | Initial radius of blood vessels | +| 150000 | total_time_step | Total time steps for simulation | +| 0.0010 | dt | Time step size | +| 800.00 | chi_chemiotactic_resp | Chemotactic response of endothelial cells | +| 100, 100, 50, 1, 1, 1 | Lx_Ly_Lz_dx_dy_dz | Simulation domain size and grid spacing | +| -754333222 | random_seed | Seed for random number generation - must be negative | +| 20 | number_of_boundary_points | Number of boundary points to keep track | +| 10000 | source_max | Maximum number of VEGF source points | +| 0.01 | vegf_grad_min | Threshold for VEGF gradient | +| 0.03 | vegf_max | Maximum VEGF concentration | +| 2.00 | depletion_weight | Energy cost to avoid overlap between vessels and hypoxic cells | +| 2000 | output_period | Time period between outputting results | +| 40000 | extra_steps | Additional time steps for simulation | +| 4000 | max_number_of_tip_cells | Maximum number of tip cells allowed | +| T | thinning_FT | Flag for using thinning algorithm | +| F | periodic_FT | Flag for using periodic boundary conditions | +| F | flow_FT | Flag for computing the blood flow | + + Beware that the input file `inp001` is solely used to run the docker image with Github actions. The parameters were changed to produce a short simulation with small grid, few iterations, and no sources of VEGF. Please do __not__ base future studies on this file. @@ -32,7 +65,7 @@ Beware that the input file `inp001` is solely used to run the docker image with In the folder `tools` we have scripts to postprocess the data generated with the simulations. The documentation for each script is found [here](https://github.com/phydev/angio/blob/master/tools/about.md). -### Publications: +### Publications M. Moreira-Soares, R. Coimbra, L. Rebelo, J. Carvalho & R. D. M. Travasso. [Angiogenic Factors produced by Hypoxic Cells are a leading driver of Anastomoses in Sprouting Angiogenesis–a computational study](https://www.nature.com/articles/s41598-018-27034-8). Scientific Reports 8, 8726 (2018)