Active nematics director and flow field data

We conduct our experiments on the microtubule-kinesin active nematic system pioneered in Sanchez et al. 2012. The long rod-like MTs are bundled together via depletion interactions and are driven out of equilibrium by the action of kinesin-streptavidin motor protein complexes, which are units that induce relative motion utilizing ATP
as the energy source. Depletion forces also aid in driving the MT bundles to form bundles to the oil-water
fluid interface, where they execute self-sustained bending and buckling instabilities. The system is extensile,
which means that active stresses cause the MT bundles to extend in length and contract in width.

To investigate the dynamics of defects in 2D flat space, we prepare the active nematic in a flow-cell setup
where the entire pool of ingredients is confined in a 2D sealed cell roughly 10 cm2 in area and 100 μm in
thickness. The lower surface of the cell is subjected to hydrophobic treatment (using Aquapel) and the
upper surface to hydrophilic treatment (using polyacrylamide coating) to enhance wetting by the respective
fluid phases. A fluorinated oil (HFE-7500 with surfactant E2K0660) forms the oil-phase, and the active MT
suspension forms the water-phase. We obtained purified tubulin monomers and kinesin–streptavidin motor
protein complexes from the Dogic Group at Brandeis University. The polymerization of tubulin to
MTs is performed in our lab before mixing with other biomaterials as per the protocols described in previous
works. The final active mix has 20% MTs by volume aided with 144μM ATP. The entire flow
cell is sealed by epoxy resin and centrifuged at 1000 RPM to accelerate the depletion mechanism to the
interface.

We use confocal fluorescence microscopy for visualization. The MTs are labeled with AlexaFlour 647 dye
and illuminated at 633 nm; the excitation and emission peaks are at 651 nm and 667 nm, respectively. After
sample preparation and centrifugation, we wait for 15-20 minutes to allow for uniform depletion, and then
image at a constant framerate till the activity ceases. Typically, the MTs stay active for 6+ hours. Imaging
is done using 10× and 20× objectives to focus on regions with area on the order of mm2, away from the
edges of the flow cell. The imaging process results in a time series of 8-bit grayscale images, which are stored
as the raw data.

For more information, see "Physically-informed data-driven modeling of active nematics" by Golden et al.