Code to reproduce the results from Mathematical modeling of radiation-augmented T-cell extravasation

Installation

1. Install CMake. In Windows make sure installer adds it to PATH.
2. Run terminal / cmd / PowerShell and activate your Python environment (for Anaconda use Anaconda prompt).
3. Go to Git root (this directory).
4. Type pip install ./engine/

Parameters of bond types:

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)

Parameters of model

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)

Parameters of simulation

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