. Author manuscript; available in PMC: 2020 Mar 14.

Published in final edited form as: J Phys Chem B. 2019 Mar 5;123(10):2217–2234. doi: 10.1021/acs.jpcb.8b10946

Table 13:

Spatial gene expression reactions and propensities

	reaction	Propensity
1.	$G_{i} \overset{k_{g e n e}^{+}}{\to} G_{i + 1}$	$α_{1} = k_{g e n e}^{+} [i \leq 2]$
2.	$G_{i} \overset{k_{g e n e}^{-}}{\to} G_{i - 1}$	$α_{2} = k_{g e n e}^{-} [i \geq 1]$
3.	$G_{i} \overset{k_{r}}{\to} G_{i} + R N A_{n u c}$	$α_{3} = k_{r} [i \geq 1]$
4.	$R N A_{n u c} \overset{γ_{n u c}}{\to} \emptyset$	$α_{4} = γ_{n u c} [R N A_{n u c}]$
5.	$R N A_{n u c} \overset{k_{t r a n s}}{\to} R N A_{c y t}$	$α_{5} = k_{t r a n s} [R N A_{n u c}]$
6.	$R N A_{c y t} \overset{γ_{c y t}}{\to} \emptyset$	$α_{6} = γ_{c y t} [R N A_{c y t}]$

The gene is considered as one species with 4 different states G_i, i = 0, … , 3.

Parameters’ units are sec⁻¹.