Code to reproduce the results from Mathematical modeling of radiation-augmented T-cell extravasation
- Install CMake. In Windows make sure installer adds it to PATH.
- Run terminal / cmd / PowerShell and activate your Python environment (for Anaconda use Anaconda prompt).
- Go to Git root (this directory).
- Type
pip install ./engine/
All of them are real numbers (double / float).
When passed to constructor, they are converted from {unit} and stored in (unit).
- eq_bond_len: equilibrium bond length {nm} (μm)
- spring_const: spring constant {dyn/cm} (kg/s^2)
- binding_rate_0: multiplicative constant in binding rate, it doesn't include receptor density {μm^2/s} (μm^2/s)
- rec_dens: density of bond receptors on the surface {1/μm^2} (1/μm^2)
- react_compl_slip: reactive compliance for binding rate and slip part of rupture rate {Å} (μm)
- rup_rate_0_slip: multiplicative constant in slip part of rupture rate {1/s} (1/s)
- react_compl_catch: reactive compliance for catch part of rupture rate {Å} (μm)
- rup_rate_0_catch: multiplicative constant in catch part of rupture rate {1/s} (1/s)
Again, all of them are real, { } and ( ) as above.
- r_cell: cell (sphere) radius {μm} (μm)
- visc: fluid viscosity {g/(cm s)} (kg/(μm s))
- temp: temperature {K} (K)
- dens_diff: density difference between cell and fluid (cell is more dense) {g/cm^3} (kg/μm^3)
- f_rep_0: repulsive force coefficient {N} ((kg μm)/s^2)
- tau: reciprocal length scale of repulsive force {Å} (Å)
All real, no unit conversion.
- shear_rate: shear rate in 1/s
- rot: sphere's rotation from initial position in radians
- h: height above endothelium (surface) in μm