Formation of polarity convergences underlying shoot outgrowths

All parameters relate to either equations specified here or in Abley et al., 2013.

* In the simulations used to generate Figure 7C and Figure 7—figure supplement 1C, γ_Aux = 0.9 µm²/A_u.s, ρ_Aux = 1.3 × 10⁻⁴ A_u/µm².s and µ_Aux = 0.02/s. Also, in some simulations, at tissue boundaries or centres of polarity convergence, auxin production, degradation and influx auxin permeability rates may vary from the background rates. Modulation of the influx auxin permeability rate is used to simulate elevated rates of auxin import. In Figure 9C, the auxin production rate in the bottom-most row of cells = 2 × 10⁻⁴ A_u/µm².s, and the auxin degradation rate in the top most row of cells = 0.07/s. In Figure 9D, and at the beginning of the simulation used to generate Figure 10C and D the auxin production rate in the bottom-most row of cells = 2 × 10⁻⁴A_u/µm².s. Throughout both simulations, in the top-most row, the auxin degradation rate = 0.015/s and the auxin influx permeability = 4.5 µm/s. In the simulation used to generate Figure 10C and D, changes in auxin production occur during the simulation and are described below. In this simulation, in the cell that forms the centre of convergence, the inwards permeation of auxin = 37.5 µm/s and the auxin degradation rate = 0.15/s. In Figure 16C and D, the proximo-distal polarity field is established as described for Figure 9D. In the three cells with elevated auxin production, the auxin production rate is 1.4 × 10⁻³A_u/µm².s. In the cell with elevated auxin import and removal (Figure 16D), the auxin degradation rate = 0.1 /s and the auxin influx permeability = 37.5 µm/s. In the simulations used to generate Figure 10—figure supplement 1A and B, parameter values are as for Figures 9D and 10D, respectively except Ψ_PIN = 80 µm²/A_u.s and γ_Aux = 0.85 µm²/A_u.s. Here, c, the concentration of A* at which half of the PINs are activated = 0.22 A_u/µm and the hill coefficient, h = 2.

* For cells with hexagonal geometries, each cell edge has a length of 10 µm.

^† Value given is that used in simulations used to generate Figure 7.B and Figure 7—figure supplement 1B. In all other simulations, C_PIN = 0.

‡ Values apply to simulations used to generate Figure 7B (ɛ_PIN) and Figure 7—figure supplement 1B, and Figure 7E (ɛ_Aux). All other simulations are initialised without noise addition.

^§ The value given for the auxin production rate applies to simulations used to generate Figures 9A,B, 10A, B and 16A,B. In the simulation used to generate Figure 7B and Figure 7—figure supplement 1B, ρ = 0.0025 A_u/µm².s and in the simulation used to generate Figure 7E, ρ = 0.002 A_u/µm².s.

^# The value given for, α, the flux-dependent promotion of PIN allocation to cell edges, applies to simulations used to generate Figures 9A,B, 10A,B and 16A,B. In the simulation used to generate Figure 7B, α = 4 × 10⁻³ and in the simulation used to generate Figure 7E, α = 3.2 × 10⁻³.

^¶ In the simulation used to generate Figures 7B, Figure 7—figure supplement 1B and 7E, P_max = 0.04A_u /µm.

* For cells with hexagonal geometries, each cell edge has a length of 10 µm.

^† Values given for the initial concentration of PIN1 at cell edge compartments, and the limit for noise addition to this concentration, are those used in simulations used to generate Figure 7A and Figure 7—figure supplement 1A. In all other simulations, C_PIN and ɛ_PIN = 0. The value given for ɛ_Aux applies only to Figure 7D, in all other simulations, ɛ_Aux = 0.

^‡ Value given for the production rate of auxin applies to the simulations used to generate Figures 7D, 8A, B, 11H, 14D and 16E,F. In the simulation used to generate Figure 7A and Figure 7—figure supplement 1A, ρ = 0.0025 A_u /µm².s.