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

BMC Systems Biology

Table 2 Reactions of the transport model

	Reaction	Description	Cellular location
(R1)	$\emptyset \to μ_{1} V$	Creation of cargo	Cell body
(R2–R5)	$V \overset{σ_{b}}{\underset{σ_{d}}{⇌}} V^{k, d}$	Binding of V to microtubule	All domains
(R6,R7)	$V^{k} \overset{σ_{kd}}{\underset{σ_{dk}}{⇌}} V^{d}$	Reversal of direction	Microtubule
(R8)	$V \to μ_{2} \emptyset$	Degradation of V	All domains

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).

ISSN: 1752-0509