Standard compartment-based morphogen gradient model

standard compartment-based model for morphogen gradient modelling

Description

Signaling molecules (A) are produced locally, and morphogen molecules (B) are produced from A. Diffusion corresponds to two chains of chemical reactions (picture).

Contained entities

reaction diffusion master equation	$\frac{\partial p}{\partial t} (𝐧, 𝐦, t) = (𝒟 + ℛ) p (𝐧, 𝐦, t)$
	$𝒟$ represents diffusion operator
	$ℛ$ represents reaction operator
	$p (𝐧, 𝐦, t)$ represents joint probability

stationary reaction-diffusion master equation	$0 = (𝒟 + ℛ) ϕ (𝐧, 𝐦)$
	$𝒟$ represents diffusion operator
	$ℛ$ represents reaction operator
	$ϕ$ represents stationary distribution

steady state equations	$\begin{matrix} (\frac{D_{A}}{h^{2}} S - k_{2} I) \overline{𝐀} = - k_{1} 𝐞_{1} (\frac{D_{B}}{h^{2}} S - k_{3} I) \overline{𝐁} = - k_{2} \overline{𝐀} \end{matrix}$
	$D_{A}$ represents diffusion coefficient a
	$D_{B}$ represents diffusion coefficient b
	$S$ represents matrix S
	$\frac{D_{A}}{h^{2}}$ represents jump rate of a
	$\frac{D_{B}}{h^{2}}$ represents jump rate of b
	${\overline{A}}_{i}$ represents average number of molecules of signal
	${\overline{B}}_{i}$ represents average number of molecules of morphogen
	$h$ represents length
	$k_{1}$ represents reaction rate constant
	$k_{2}$ represents reaction rate constant
	$k_{3}$ represents reaction rate constant

product of Poisson distributions	$ϕ (𝐧, 𝐦) = \exp [- \sum_{i = 1}^{K} ({\bar{A}}_{i} + {\bar{B}}_{i})] \prod_{i = 1}^{K} \frac{{\bar{A}}_{i}^{n_{i}} {\bar{B}}_{i}^{m_{i}}}{n_{i}! m_{i}!}$
	$\overline{A}$ represents average number of molecules of signal
	$\overline{B}$ represents average number of molecules of morphogen
	$ϕ (𝕟, 𝕞)$ represents stationary distribution

Assumptions

a produced in first compartment, reaction diffusion system

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