Fig. 2: Stochastic reaction-diffusion-dynamics model of fibrin clot contraction.

a The SRDDM requires the initial input available from experiment (distributions of the fibrin fiber lengths and diameters, density of 3- and 4-degree nodes, platelet count, platelet size, etc.) to describe the fibrin clot structure and shape and geometry of spatial arrangements of different components. The SRDDM couples the kinematics (cyclic extension-retraction of filopodia protrusions), kinetics (formation-dissociation of bonds between platelet filopodia and fibrin fibers), mass transport (translocation of fibrin fibers and platelets), and mechanics (interaction between platelets and fibrin fibers, bending of fibrin fibers, fibrin densification, associations of platelets). Kinetics and transport are described using the stochastic reaction-diffusion formalism, whereas mechanics is described using the Langevin dynamics (Methods). The model parameters also include the number of filopodia per platelet, speed of filopodium extension-retraction, the on- and off-rates for formation and dissociation of non-covalent bonds between platelets and fibrin fibers, as well as the mechanical force field, which includes stretching and bending rigidities of fibrin fibers, filopodium length and diameter, filopodium traction force (list of parameters is in Supplementary Table 1). b Initial configuration of the 120 µm × 120 µm × 120 µm fibrin clot reconstructed as described in Methods. Small orange spheres with thin orange protrusions represent platelets with filopodia inside the 3D fibrin network represented by thin blue lines converging at 3- and 4-degree nodes. There is a total of ~780 platelets in a fibrin network formed by ~5.1 × 10⁴ fibrin fibers; there is a total of ~3.4 × 10⁴ nodes, of which ~2.9 × 10⁴ are 3-degree nodes and ~5.5 × 10³ are 4-degree nodes. Each platelet has 8 filopodia extending and contracting in random directions at each time point. c A close-up view of the fibrin network depicting the fibrin fibers of different lengths and diameters (see Supplementary Fig. 1) forming the 3-degree and 4-degree nodes (indicated by the arrows). d A 40 µm cross-section of the central portion of fibrin clot (from panel b) showing the initial distribution of platelets (orange spheres) in the fibrin network (transparent cylinders).