Quasi-steady-state analysis example - Revision history

Elena.kutumova@biouml.org at 03:48, 16 March 2022

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Elena.kutumova@biouml.org at 02:12, 16 March 2022

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Elena.kutumova@biouml.org at 09:37, 14 March 2022

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Elena.kutumova@biouml.org at 10:04, 11 March 2022

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Elena.kutumova@biouml.org at 10:03, 11 March 2022

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Elena.kutumova@biouml.org: Created page with "Description of the quasy-steady-state approximation method is done in the section "Quasi-Steady-State Analysis". Below we use the notation given there. As an example cons..."

2019-03-11T11:23:51Z

Created page with "Description of the quasy-steady-state approximation method is done in the section "Quasi-Steady-State Analysis". Below we use the notation given there. As an example cons..."

New page

Description of the quasy-steady-state approximation method is done in the section "[[Quasi-Steady-State Analysis]]". Below we use the notation given there.

As an example consider the simplest enzyme reaction

[[File:qssa_formula_1.png]]

which involves an enzyme ''E'' binding to a substrate ''S'' to form a complex ''ES'' and its dissociation into a product ''P'' and the enzyme ''E''.

Let us find the conditions under which the concentration of the complex ''ES'' is quasi-stationary in time ''t'' = 0. To do this, we consider the expressions

[[File:qssa_formula_2.png]]

which result in the following derivatives

[[File:qssa_formula_3.png]]

Next, we find the formulas for ''δtES'' and ''rES'':

[[File:qssa_formula_4.png]]

Thus, the complex ''ES'' is in quasi-steady state at ''t'' = 0 only when ''δtES'' << 1, i.e.

[[File:qssa_formula_5.png]]

@@ Line 4: / Line 4: @@
 ==Reproducing a test case in BioUML==
-To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
+To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analyses</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
 After double click on ''Quasi-Steady-State Analysis'', a new tab with analysis opens.

@@ Line 1: / Line 1: @@
 Description of the quasy-steady-state approximation method is done in the section "[[Quasi-Steady-State Analysis]]". Below we use the notation given there.
 ==Reproducing a test case in BioUML==
 To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
-After double click on ''Quasi-Steady-State Analysis'', a new tab with analysis opens (Figure 1).
+After double click on ''Quasi-Steady-State Analysis'', a new tab with analysis opens.
 Set the following analysis settings:
@@ Line 16: / Line 15: @@
 *'''Completion time''' = 0.01
 *'''Time increment''' = 0.001
 After you click the <b>Run</b> button and the calculations are finished, you can see the result table, including ranges of fast dynamics of diagram entities.
@@ Line 46: / Line 47: @@
 [[File:qssa_formula_5.png]]

@@ Line 2: / Line 2: @@
 ==Reproducing a test case in BioUML==
 To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.
-After double click on ''Quasi-Steady-State Analysis'', a new tab with analysis opens.
+After double click on ''Quasi-Steady-State Analysis'', a new tab with analysis opens (Figure 1).
 Set the following analysis settings:

@@ Line 1: / Line 1: @@
 Description of the quasy-steady-state approximation method is done in the section "[[Quasi-Steady-State Analysis]]". Below we use the notation given there.
-==Reproducing a test case==
+==Reproducing a test case in BioUML==
 To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.

@@ Line 1: / Line 1: @@
 Description of the quasy-steady-state approximation method is done in the section "[[Quasi-Steady-State Analysis]]". Below we use the notation given there.
-==Reproducing a test case in BioUML==
+==Reproducing a test case==
 To reproduce a test case below in the [[BioUML]] workbench, go to the <b>Analysis</b> tab in the navigation pane and follow to ''analyses'' > ''Methods'' > ''Differential algebraic equations''.