FibriNet
Mechanochemical simulation framework for fibrin clot degradation coupling WLC mechanics with Gillespie kinetics
FibriNet is a mechanochemical simulation framework for fibrin clot degradation that couples nonlinear fiber mechanics (worm-like chain model) with stochastic cleavage events (Gillespie algorithm).
This work is supported by the NIH grant 2R15HL148842-02 under the supervision of Dr. Brittany Bannish at the University of Central Oklahoma.
Key Results
- Non-monotonic clearance: Mean clearance time vs applied strain (70 sims: 7 strains × 10 realizations)
- Percolation failure: Connectivity loss occurs at ~20–50% lysis
- Optimal strain: Fastest network failure near ε ≈ 0.05
Methodology
The model represents fibrin networks as interconnected nodes connected by nonlinear springs following worm-like chain (WLC) mechanics. Enzyme cleavage is modeled as a stochastic process using the Gillespie algorithm, coupling mechanical stress with biochemical degradation.
Technical Details
- Language: Python
- Mechanics: Worm-like chain (WLC) model
- Kinetics: Gillespie algorithm for stochastic cleavage
- Application: Computational biology, biophysics, biomechanics