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However, the techniques used therein are build on mass action kinetics and rational functions and explicitly use mass conservation relations.
The first step is to identify state variables for which the QSS assumption holds, and the mass conservation relations in the model.
This is because mass conservation relations are often present in the system which cause some variables to be linear combinations of others.
A complete mechanistic model of the exemplified network would comprise 77 ODEs of which three can be eliminated due to mass conservation relations.
Mechanisms giving rise to negative correlations are, for example, coparticipation in the same reaction (cf. Figure 1E), mass conservation relations [ 6] or opposing regulatory effects.
If there are mass conservation relations reducing the rank of the Jacobian matrix to r< n, a critical fragment S k i 1, …, i k j 1, …, j k of order k< r is required to detect possible oscillations in an ODE model (4) of a biochemical mechanism (1).
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Since our toy model only represents a small part of a larger system, missing exchange reaction for cofactors would create a false mass conservation relation that compromises correlation calculation.
The mass conservation relation under the steady-state conditions (d X i /d t = 0) reduces to the expression: (3) where S is the stoichiometric matrix (m rows and n columns), v is the vector of n metabolic fluxes and b is the vector representing m transport fluxes.
Thus, the final net flux of c1 and c2 can be expressed as J1 = J d 1 + J c and J2 = J d 2: (3) J 1 = − M 1 ∇ μ 1 0 + M 1 β ∇ ϕ J 2 = − M 2 ∇ μ 2 0. The evolution of each field variable c1 and c2 is governed by Cahn-Hilliard nonlinear diffusion equation and combined with mass conservation relation ∂ c1/∂ t = −∇· J1, ∂ c2/∂ t = −∇· J2.
In addition to mass conservation and energy balance relations, conditions at the migrating interface ("contact conditions") are required to predict the values of the variables at a sharp interface.
When translating, based on various experimental and theoretical findings, this mass conservation proposition into diffraction mass density relations, the latter are remarkably well confirmed by independent experimental data from various sources.
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