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Team:Groningen/Modelling/24 August 2013
From 2013.igem.org
(Created page with "<p>After closer inspection, the k5 calculation was still wrong as it didn't take the feedback into account. k5 is now determined by; k5_lower_bound + X - Y. </p> <p>Where X= Ta*x...") |
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<p>After closer inspection, the k5 calculation was still wrong as it didn't take the feedback into account. k5 is now determined by; k5_lower_bound + X - Y. </p> | <p>After closer inspection, the k5 calculation was still wrong as it didn't take the feedback into account. k5 is now determined by; k5_lower_bound + X - Y. </p> | ||
| - | <p>Where X= Ta*x1*x2 + x1*T0 and Y | + | <p>Where X= Ta*x1*x2 + x1*T0 and Y =x3(VP+TM1+TD0).</p> |
<p>Where x2 determines the increase in receptor activity when a stimulatory ligand is bound (Ta) with respect to an unbound receptor (T0). x1 is a scaling factor that ensures that the maximum increase for k5 is within some predetermined range. x3 is also a scaling factor, which ensures that the negative feedback determined by VP, TM1 and TD0 concentrations can potentially compensate for the positive increase.</p> | <p>Where x2 determines the increase in receptor activity when a stimulatory ligand is bound (Ta) with respect to an unbound receptor (T0). x1 is a scaling factor that ensures that the maximum increase for k5 is within some predetermined range. x3 is also a scaling factor, which ensures that the negative feedback determined by VP, TM1 and TD0 concentrations can potentially compensate for the positive increase.</p> | ||
<p>The error function strived to minimize the difference between k5 values when 0 attractant was present, with respect to when 10+ attractant is present. The idea is that the increase in receptor activity by stimulatory ligands is then, over time, fully compensated for by the negative feedback, as is the case in the real chemotaxis system. </p> | <p>The error function strived to minimize the difference between k5 values when 0 attractant was present, with respect to when 10+ attractant is present. The idea is that the increase in receptor activity by stimulatory ligands is then, over time, fully compensated for by the negative feedback, as is the case in the real chemotaxis system. </p> | ||
Revision as of 22:27, 24 August 2013
After closer inspection, the k5 calculation was still wrong as it didn't take the feedback into account. k5 is now determined by; k5_lower_bound + X - Y.
Where X= Ta*x1*x2 + x1*T0 and Y =x3(VP+TM1+TD0).
Where x2 determines the increase in receptor activity when a stimulatory ligand is bound (Ta) with respect to an unbound receptor (T0). x1 is a scaling factor that ensures that the maximum increase for k5 is within some predetermined range. x3 is also a scaling factor, which ensures that the negative feedback determined by VP, TM1 and TD0 concentrations can potentially compensate for the positive increase.
The error function strived to minimize the difference between k5 values when 0 attractant was present, with respect to when 10+ attractant is present. The idea is that the increase in receptor activity by stimulatory ligands is then, over time, fully compensated for by the negative feedback, as is the case in the real chemotaxis system.
