Table 1 Parameters of the model.
From: Spatiotemporal development of coexisting wave domains of Rho activity in the cell cortex
Notation | Description | Value |
|---|---|---|
\({D}_{A}\) | Diffusion coefficient of active Rho | \(\frac{0.001}{3}\left(\frac{\upmu{\text{m}}^{2}}{\text{s}}\right)\) |
\({D}_{I}\) | Diffusion coefficient of inactive Rho | \(\frac{0.1}{3}\left(\frac{\upmu {\text{m}}^{2}}{\text{s}}\right)\) |
\({k}_{0}\) | Basal activation rate of Rho | \([0, 0.3]\) \(\left(\frac{1}{\text{s}}\right)\) |
\(\gamma\) | Rate constant of autocatalytic activation of Rho | \(1\left(\frac{1}{\text{s}}\right)\) |
\({A}_{0}\) | Parameter controlling the sensitivity of positive feedback of Rho to the concentration of active Rho | \(0.4 {G}_{T}\) |
\({s}_{1}\) | Basal deactivation rate of Rho | \(0.5\left(\frac{1}{\text{s}}\right)\) |
\({s}_{2}\) | Rate constant of negative feedback from F-actin on Rho | \(\left[0, 1.3\right]\left(\frac{1}{\text{s}}\right)\) |
\({F}_{0}\) | Parameter controlling the sensitivity of negative feedback of Rho to the concentration of F-actin | \(0.5{ G}_{T}\) |
\({k}_{n}\) | Rate constant of F-actin polymerization | \(0.1\left(\frac{1}{\text{s}}\right)\) |
\({k}_{s}\) | Rate constant of F-actin depolymerization | \(0.025\left(\frac{1}{\text{s}}\right)\) |
\({\alpha }_{\text{1,2}}\) | Magnitude of noise | \([{10}^{-15},3] \left(\frac{\text{mol}}{\text{L s}}\right)\) |
\(\Delta t\) | Temporal step of finite difference scheme | \(0.001\), \({10}^{-5}\) au (\(1.8\times {10}^{-3}\) s, \(1.8\times {10}^{-5}\) s) |
\(h\) | Spatial step of finite difference scheme | \(h=0.02\) au (0.3186 μm) |
\({\tau }_{sc}^{1}\) | Temporal scaling factor for starfish experiment (see Supplemental Text for scaling method) | \(\text{0.83}\) s |
\({\tau }_{sc}^{2}\) | Temporal scaling factor for frog experiment | \(\text{1.56}\) s |
\({r}_{sc}\) | Spatial scaling factor | \(15.93\) microns |
\(d\) | Size of the simulation domain | 4–14 au |
\(\frac{d}{dt}{a}_{l}(t)\) | Threshold value for the slope of pattern amplitude in log scale defining the duration of the low-activity stage | \(0.001\frac{1}{au \; of \; time}\) \((0.0083\frac{1}{\text{s}} )\) |
\({T}_{g}\) | Duration of the low-activity stage | 500–2471 s |
\({w}_{c}\) | Size of the convolution window for calculating wave vector directions | 5 pixels |
\({\tau }_{c}\) | Time lag between frames for calculating wave vector directions | 8 au (6.64 s) |
\({T}_{av}\) | Time averaging window for calculating wave vector directions | 300 au (249 s) |
\({C}_{cr}\) | Threshold value for the circular standard deviation of wave vector directions defining the coherence distance | \(0.4\) |
\({\theta }_{m}\) | Threshold value for the difference in mean values of wave vector directions defining the regions for merging | 0.5 radians |
\({l}_{cr}\) | Threshold value for the length of the interface between neighboring domains defining the regions for merging | 10% of \(\sqrt{\text{the \; area \; of \; the \; smaler domain}}\) |
