Difference between revisions of "Serine out"
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==Parameters with uncertainty== | ==Parameters with uncertainty== | ||
| − | *The transport rates have been modelled using mass action kinetics (i.e., as non-saturable, non-enzymatic reactions). No information is available about the uncertainty of these parameters. As these parameters are strictly positive, they are sampled using a log-normal distribution as are and values. The means of <math>K_{1}</math> are set to the value reported in Turnaev (2006) et al. <ref name="Turnaev_2006"></ref> for the fixed-parameter model. The reaction is presumed to be at equilibrium, such that <math>K_{eq} = 1</math> and <math>K_{1} = K_{2}</math>. The sampling of the parameters are done in a way so that it ranges between <math>[0.001\times mean \quad 1000 \times mean ]</math> to allow a large exploration of the parameter space. | + | *The transport rates have been modelled using mass action kinetics (i.e., as non-saturable, non-enzymatic reactions). No information is available about the uncertainty of these parameters. As these parameters are strictly positive, they are sampled using a log-normal distribution as are and values. The means of <math>K_{1}</math> are set to the value reported in Turnaev (2006) et al. <ref name="Turnaev_2006"></ref> for the fixed-parameter model. The reaction is presumed to be at equilibrium, such that <math>K_{eq} = 1</math> and <math>K_{1} = K_{2}</math>. The sampling of the parameters are done in a way so that it ranges between <math>[0.001\times mean \quad 1000 \times mean ]</math> to allow a large exploration of the parameter space. We use the '''Range rule''' to calculate the mean and standard deviation from maximum and minimum value. For both <math>K_{1}</math> and <math>K_{2}</math> the minimum and maximum value lies between 0.0000103 and 10.3. So the mean is 5.16 and standard deviation would be 2.57499. |
{|class="wikitable" | {|class="wikitable" | ||
! Parameter | ! Parameter | ||
| Line 40: | Line 40: | ||
|- | |- | ||
|<math>K_{1}</math> | |<math>K_{1}</math> | ||
| − | | | + | |5.16 \pm 2.57 |
|rowspan="2"| | |rowspan="2"| | ||
|rowspan="2"| | |rowspan="2"| | ||
|- | |- | ||
|<math>K_{2}</math> | |<math>K_{2}</math> | ||
| − | | | + | |5.16 \pm 2.57 |
|} | |} | ||
==References== | ==References== | ||
<references/> | <references/> | ||
Revision as of 17:14, 23 May 2014
This reaction describes the utilization of the endproduct Serine in other pathways.
Contents
Reaction equation
Rate equation
Simple reversible mass action rate law is used.
![v = K_{1} * [Serine] - K_{2} * [Serine_{out}]](/wiki/images/math/e/6/b/e6b7d292763cb679cbd1de648b4b0ddf.png)
Parameters
- For Transport reactions it is presumed to be at equilibrium, such that
and 
.
| Parameter | Value | Units | Organism | Remarks |
|---|---|---|---|---|
|
0.0103 [1] | 
|
Escherichia coli | |
|
0.0103 |
|
Parameters with uncertainty
- The transport rates have been modelled using mass action kinetics (i.e., as non-saturable, non-enzymatic reactions). No information is available about the uncertainty of these parameters. As these parameters are strictly positive, they are sampled using a log-normal distribution as are and values. The means of are set to the value reported in Turnaev (2006) et al. [1] for the fixed-parameter model. The reaction is presumed to be at equilibrium, such that and . The sampling of the parameters are done in a way so that it ranges between
![[0.001\times mean \quad 1000 \times mean ]](/wiki/images/math/7/0/5/70565b13097c64cb12ee455eb2006ee7.png)
to allow a large exploration of the parameter space. We use the Range rule to calculate the mean and standard deviation from maximum and minimum value. For both and the minimum and maximum value lies between 0.0000103 and 10.3. So the mean is 5.16 and standard deviation would be 2.57499.
| Parameter | Value | Organism | Remarks |
|---|---|---|---|
|
|
5.16 \pm 2.57 | ||
|
|
5.16 \pm 2.57 |
