Team:Groningen/Modelling/Characterization

From 2009.igem.org

(Difference between revisions)
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                           time:[60,600,1200,2400,3600]}},
                           time:[60,600,1200,2400,3600]}},
                   Singh2008: // We assume 5g/L wet cells were used... (at 1100kg/m^3)
                   Singh2008: // We assume 5g/L wet cells were used... (at 1100kg/m^3)
-
                   {constants:{Vc:(0.004545455),Vs:(1-(0.004545455)),pro:0,ars2T:0},AsT:0.467154987e-6,
+
                   {constants:{Vc:(0.004545455),Vs:(1-(0.004545455)),pro:0,ars2T:0,proF:16.605e-9},AsT:0.467154987e-6,
                     data:{AsexT:[0.467154987e-6,0.419211538e-6,0.391262322e-6,0.378368845e-6,
                     data:{AsexT:[0.467154987e-6,0.419211538e-6,0.391262322e-6,0.378368845e-6,
                                 0.361791516e-6,0.332907991e-6,0.320748614e-6],
                                 0.361791516e-6,0.332907991e-6,0.320748614e-6],
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                           time:[44928,83520,132192,171036]}},*/
                           time:[44928,83520,132192,171036]}},*/
                   Kostal2004fig3A:  //  fig 3A
                   Kostal2004fig3A:  //  fig 3A
-
                   {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0},time:Infinity,
+
                   {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0,proK:16.605e-9},time:Infinity,
                     data:{AsinT:[28.71e-6,78.87e-6,144.21e-6,377.19e-6,490.38e-6,617.76e-6,649.11e-6],
                     data:{AsinT:[28.71e-6,78.87e-6,144.21e-6,377.19e-6,490.38e-6,617.76e-6,649.11e-6],
                           AsT:[0.4e-6,1e-6,2e-6,5e-6,20e-6,50e-6,100e-6]}},
                           AsT:[0.4e-6,1e-6,2e-6,5e-6,20e-6,50e-6,100e-6]}},
                   Kostal2004fig3B:  //fig 3B
                   Kostal2004fig3B:  //fig 3B
-
                   {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0},AsT:20e-6,
+
                   {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0,proK:16.605e-9},AsT:20e-6,
                     data:{AsinT:[2.25e-4,3.47e-4,4.19e-4,3.93e-4,4.19e-4,4.82e-4,4.82e-4,4.95e-4],
                     data:{AsinT:[2.25e-4,3.47e-4,4.19e-4,3.93e-4,4.19e-4,4.82e-4,4.82e-4,4.95e-4],
-
                           time:[582,1212,1890,2514,3144,3828,4260,6036]}}};   
+
                           time:[582,1212,1890,2514,3144,3828,4260,6036]}}};
 +
                  pSB1A2con:    //  concentration mode this is our first icps measerment wild type
 +
                  {constants:{Vc:0.000808081,Vs:(1-0.000808081),ars2T:0},time:Infinity,
 +
                    data:{AsinT:[0.167289553e-6,0.185086314e-6,0.398647446e-6,0.473393842e-6],
 +
                          AsT:[10e-6,20e-6,50e-6,100e-6]}},
 +
                  pSB1A2time:  //  concentration mode this is our first icps measerment wild type
 +
                  {constants:{Vc:0.002320346,Vs:(1-0.002320346),ars2T:0},AsT:20e-6,
 +
                    data:{AsinT:[0.153306384e-6,0.194188086e-6,0.265731066e-6,0.306612768e-6,0.480360003],
 +
                          time:[0,600,1200,2400,3600]}}};
 +
                  pArsRRFPcon:  /* here the cell only contains extra RFP behind the the extra ArsR promotors.
 +
                                    We incorporate this in our model by pretending RFP=GVP (1st icps)*/
 +
                  {constants:{Vc:0.001272727,Vs:(1-0.001272727)},time:Infinity,
 +
                    data:{AsinT:[0.173785371e-6,0.353176722e-6,0.369994661e-6,0.437266418],
 +
                          AsT:[10e-6,20e-6,50e-6,100e-6]}},
 +
                  pArsRRFPtime:  /* here the cell only contains extra RFP behind the the extra ArsR promotors.
 +
                                    We incorporate this in our model by pretending RFP=GVP (1st icps)*/
 +
                  {constants:{Vc:0.003333333,Vs:(1-0.003333333)},AsT:20e-6,
 +
                    data:{AsinT:[0.176187934e-6,0.308328884e-6,0.102776295e-6,0.293646556e-6,0.455152162],
 +
                          time:[0,600,1200,2400,3600]}}};   
var varsToMutate = ['v5_K5','v5','k8_K7','k8','tauBbeta4','beta4','tauR_tauB','beta1_beta4'];
var varsToMutate = ['v5_K5','v5','k8_K7','k8','tauBbeta4','beta4','tauR_tauB','beta1_beta4'];

Revision as of 14:06, 12 October 2009

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TODO: Talk about the devices we have and in what way we want to characterize them.

Uptake measurements

Sampling scheme
Time (min)
0 10 20 40 60
As(III)exT(0)
(µM) 		0 x
10 x x x x x
20 x
50 x
100 x

To efficiently look at both time and concentration dependent processes we took samples as in the table on the right. Below we list all results, which have been used for fitting all necessary parameters.

TODO: List results. Take conversion from nmol/mg and mg/ml to µM and Vc/Vs into account.

best cur gradient solved
v5/K5
v5
K5
k8/K7
k8
K7
tauBbeta4
tauB
beta4
tauR
beta1
E

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