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Table 2 Reactions of the transport model

From: URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

 

Reaction

Description

Cellular location

(R1)

∅→ μ 1 V

Creation of cargo

Cell body

(R2–R5)

V ⇌ σ d σ b V k , d

Binding of V to microtubule

All domains

(R6,R7)

V k ⇌ σ dk σ kd V d

Reversal of direction

Microtubule

(R8)

V→ μ 2 ∅

Degradation of V

All domains

  1. Model of active transport of a cargo species V that is transported on microtubule filaments in a direction determined by the orientation of the fibers (as modeled by a velocity field) and the current motor protein bound to the fiber (kinesin or dynein).