Difference between revisions of "Quasi-steady-state analysis example"
| (4 intermediate revisions by one user not shown) | |||
| Line 1: | Line 1: | ||
| + | <font size="3"> | ||
Description of the quasy-steady-state approximation method is done in the section "[[Quasi-Steady-State Analysis]]". Below we use the notation given there. | 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 in BioUML== | ||
| − | To reproduce a test case below in the [[BioUML]] workbench, go to the <b> | + | 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. | After double click on ''Quasi-Steady-State Analysis'', a new tab with analysis opens. | ||
| Line 14: | Line 15: | ||
*'''Completion time''' = 0.01 | *'''Completion time''' = 0.01 | ||
*'''Time increment''' = 0.001 | *'''Time increment''' = 0.001 | ||
| + | |||
| + | <br>[[File:qssa_figure_1.png]]<br><br> | ||
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. | 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 44: | Line 47: | ||
[[File:qssa_formula_5.png]] | [[File:qssa_formula_5.png]] | ||
| + | |||
| + | </font> | ||
Latest revision as of 10:48, 16 March 2022
Description of the quasy-steady-state approximation method is done in the section "Quasi-Steady-State Analysis". Below we use the notation given there.
[edit] Reproducing a test case in BioUML
To reproduce a test case below in the BioUML workbench, go to the Analyses 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.
Set the following analysis settings:
- Input diagram = data/Examples/DAE models/Data/Diagrams/Simplest_enzyme_reaction
- Result table = data/Collaboration/Demo/Data/Temp/Quasi-Steady-State Analysis results
- Initial time = 0.0
- Completion time = 0.01
- Time increment = 0.001
After you click the Run button and the calculations are finished, you can see the result table, including ranges of fast dynamics of diagram entities.
Ready analysis results can be found in the table:
data/Examples/DAE models/Data/Quasi-Steady-State Analysis results
[edit] Description of the test case
As an example we consider the simplest enzyme reaction
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
which result in the following derivatives
Next, we find the formulas for δtES and rES:
Thus, the complex ES is in quasi-steady state at t = 0 only when δtES << 1, i.e.
