Generalized compartment based morphogen gradient model (generalized compartment-based model for morphogen gradient modelling)

Community: MathModDB

mathematical model

Available identifiers

MaRDI QIDQ6775434 FDOQ6775434

Description

Assuming that molecules of species A diffuse significantly faster than those of species B, a larger compartment size for A is chosen.

Contained entities

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

generalized compartment reaction	$A_{j} \overset{k_{2} / γ}{\to} B_{i}, j = 1, 2, \dots, K_{A}$
	$A$ represents signal
	$B$ represents morphogen
	$γ$ represents compartment length ratio

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

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

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

stationary multi grid reaction diffusion master equation	$0 = (\tilde{𝒟} + \tilde{ℛ}) p (𝕟, 𝕞, t)$
	$\tilde{𝒟}$ represents generalized diffusion operator
	$\tilde{ℛ}$ represents generalized reaction operator
	$p (𝕟, 𝕞, t)$ represents joint probability

generalized steady state equations	$\begin{matrix} (\frac{D_{A}}{h_{A}^{2}} S_{A} - k_{2} I_{A}) \overline{𝐀} & = & - k_{1} 𝐞_{1} \\ (\frac{D_{B}}{h_{B}^{2}} S_{B} - k_{3} I_{B}) \overline{𝐁} & = & - \frac{k_{2}}{γ} M \overline{𝐀} \end{matrix}$
	$D_{A}$ represents diffusion coefficient a
	$D_{B}$ represents diffusion coefficient b
	$S$ represents matrix S
	${\overline{A}}_{i}$ represents average number of molecules of signal
	${\overline{B}}_{i}$ represents average number of molecules of morphogen
	$M$ represents matrix M

Assumptions

a produced in first compartment, reaction diffusion system

References

Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling

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