We first perform a stress relaxation test to show how the network relaxes over a timescale of order seconds. The homogeneous meshwork and bundle-embedded meshwork relax on a similar timescale. These movies show 5 seconds of simulation time on a domain of size 2 microns, which is smaller than the domain we actually collect data on.
The rheological studies in our paper are performed with SAOS rheology. Here are examples for a homogeneous meshwork and bundle-embedded meshwork. These movies show 5 seconds of simulation time on a domain of size 2 microns, which is smaller than the domain we actually collect data on. The maximum strain here is 0.2 (for visualization purposes), which is significantly outside the linear regime.
We now add Brownian fluctuations (semiflexible bending fluctuations and translational and rotational diffusion) and look at the same network of filaments. We set the turnover time to 2.5 s (about 60% of the bundling time) and the persistence length to lp=17 μm (corresponding to actin filaments). Here is a movie comparing deterministic filaments (at left) with Brownian filaments (at right) with frequency ω=1 Hz and full hydrodynamic interactions. While the Brownian dynamics are faster, there isn't much difference in the morphologies. Decreasing to lp=1.7 μm, we see a substantial difference in the morphologies, as the Brownian bending fluctuations become visible to the naked eye, while the deterministic filaments remain pretty straight. We give a side-by-side movie movie comparing Brownian fibers with lp=1.7 μm, but with intra-fiber hydro on the left and full hydro on the right. There isn't much difference visually between the two, other than perhaps less bundling with hydrodynamics (something we also saw deterministically).