Figure 3.

Notation for our computational domains. (a) First, the domain is treated without a buried channel. The molecular interior Ω_i has an active site Γ_a and a non-reactive boundary Γ_s. (b) When the domain is treated as a buried channel, the molecular interior Ω_i is bounded by Γ_s ⋃ Γ_c ⋃ Γ_a. The active site Γ_a can be accessed from the exterior region Ω_e by passing through the buried channel region Ω_c. Access to Ω_c is through the mouth of the channel Γ_m which may represent a gating mechanism. Both domain types sit inside a large sphere with boundary Γ_e. (c) Inside the channel, the reaction coordinate axis (shown here as a dashed line) is described by the coordinate x ranging from x = 0 (at the active site Γ_a) to the x = L (at the channel entrance Γ_m). The cross-sectional region at a particular x is called σ(x) with area denoted by ∣σ(x)∣.