Team:KULeuven/Modeling

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<div id="modeling_submenu"><a href="https://2011.igem.org/Team:KULeuven/Modeling" style="color:#000; border-bottom:2px solid #000;">overview</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://2011.igem.org/Team:KULeuven/Freeze">Freeze</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://2011.igem.org/Team:KULeuven/Antifreeze">Antifreeze</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://2011.igem.org/Team:KULeuven/Death">Cell Death</a></div>
<div id="modeling_submenu"><a href="https://2011.igem.org/Team:KULeuven/Modeling" style="color:#000; border-bottom:2px solid #000;">overview</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://2011.igem.org/Team:KULeuven/Freeze">Freeze</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://2011.igem.org/Team:KULeuven/Antifreeze">Antifreeze</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://2011.igem.org/Team:KULeuven/Death">Cell Death</a></div>
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<h3>Modeling Overview</h3>
<h3>Modeling Overview</h3>

Revision as of 13:32, 15 September 2011

KULeuven iGEM 2011

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overview     Freeze     Antifreeze     Cell Death


Modeling Overview


1. Description of the whole system

To make predictions for are plasmid transformed E.coli, a structured segregated model is designed in Simbiology. A graphical representation of the model was build in the block diagram editor . Afterwards reaction equations and parameters were added. We designed one model for the whole system and 3 models for 3 subsystems. The 3 subsystems are antifreeze, freeze and cell death. For more information about these 3 subsystems, we refer to the extended project description and the 3 modelling pages: freeze, antifreeze and cell death.


2. Full Model

There are in total 5 different kinetic equations we used in the model Transcription equation For most promoters, hill kinetics is used, it is a way of quantitatively describing cooperative binding processes, it was developed for hemoglobin in 1913. A Hill coefficient (n) is a measure for the cooperativity. Translation equation RNA degradation Protein degration Assimiliation

3. Simulation tests

In the table below the parameters for our full model are displayed. However it was hard to find accurate parameters, because databases for kinetic parameters are limiting.

PARAMETER TABLE

Name Value Comments References
row 1, cell 1 row 1, cell 2
row 2, cell 1 row 2, cell 2

The parameters used in this model are:

Parameter Description Value Unit Reference
Active LacI concentration (LacI which is not inactivated by IPTG) NA molecules
per cell
Notation convention
IPTG concentration NA molecules
per cell
Notation convention
Inactived LacI concentration NA molecules
per cell
Notation convention
Total LacI concentration TBD molecules
per cell
Steady state for equation
T7 RNA polymerase (emitter, T7') concentration NA molecules
per cell
Notation convention
mRNA associated with T7' concentration NA molecules
per cell
Notation convention
T7 RNA polymerase (auto-amplification, T7'') concentration NA molecules
per cell
Notation convention
mRNA associated with T7'' concentration NA molecules
per cell
Notation convention
GFP concentration NA molecules
per cell
Notation convention
mRNA associated with GFP concentration NA molecules
per cell
Notation convention
RFP concentration NA molecules
per cell
Notation convention
mRNA associated with RFP concentration NA molecules
per cell
Notation convention
Maximal production rate of pVeg promoter (constitutive) 0.02 molecules.s-1
or pops
Estimated, see the justification
Maximal production rate of pLac promoter 0.02 molecules.s-1
or pops
Estimated, see the justification
Maximal production rate of pT7 promoter 0.02 molecules.s-1
or pops
Estimated, see the justification
Dissociation constant for IPTG to LacI 1200 molecules
per cell
Aberdeen 2009 wiki
Dissociation constant for LacI to LacO (pLac) 700 molecules
per cell
Aberdeen 2009 wiki
Dissociation constant for T7 RNA polymerase to pT7 10 molecules
per cell
We used the classic assumption 1nM=1 molecule per cell and [1]
Translation rate of proteins 0.9 s-1 Estimated, see the justification
Dilution rate in exponential phase 2.88x10-4 s-1 Calculated with a 40 min generation time. See explanation
Degradation rate of mRNA 2.88x10-3 s-1 Uri Alon (To Be Confirmed)
Degradation rate of GFP 10-4 s-1 BioNumbers
Degradation rate of RFP 10-4 s-1 Estimated equal to GFP degradation rate
Delay due to T7 RNA polymerase production and maturation 300 s [2]
Delay due to GFP production and maturation 360 s BioNumbers
Delay due to RFP production and maturation 360 s Estimated equal to GFP delay (similar molecules)
Delay due to mRNA production 30 s BioNumbers with an approximation: all our contructs are around 1-2kb

References

  1. Cytoplasmic expression of a reporter gene by co-delivery of T7 RNA polymerase and T7 promoter sequence with cationic liposomes, X Gao and L Huang, accessible here
  2. Molecular Biology for Masters by Dr. G. R. Kantharaj, accessible here