Team:Paris Saclay/simulation

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{{Team:Paris_Saclay/incl_debut_generique}}
{{Team:Paris_Saclay/incl_debut_generique}}
='''simulation.hsim'''=
='''simulation.hsim'''=
-
<p>title="FNR regulator simulation";
+
title="FNR regulator simulation scenario 2";
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 +
molecule mfnr;
-
molecule Pfnr;//fnr promotor
+
molecule FNRi;
-
molecule Ise,ClpXP;//Ise: iron-sulfur cluster assembly proteins : enzyme of dimerisation ; ClpXP: ATP dependent protease that induces degradation for all protein
+
molecule FNRa;
-
molecule QFeFNRa,apoFNR,DFeFNRi;//3 states of FNR: activated, without Fe (inactivated), and inactivated
+
molecule o2;
-
molecule GPV,PV;//GPV green protein gene, PV green protein
+
molecule ClpXP;
-
molecule GPR,PR;//GPR red protein gene, PR red protein
+
molecule proteinase1,proteinase2,proteinase3;
-
molecule QFeFNRa_GPR_binded,QFeFNRa_GPV_binded;//molecule FNR binds on mRNA from GPR and GPV
+
molecule GPV;
-
molecule rep;//complexe of 4 FNRs, prevent production of red protein
+
molecule PV (0,200,0);//color set :green
 +
molecule GPR;
 +
molecule PR (200,0,0); //color set : red
-
metabolite o2;//declare the o2 as a cytosolic molecule leads to be treated as an homogeneous population
+
molecule GPR_binded;
 +
molecule FNRa_binded_GPR;
 +
molecule FNRa_binded_PV;
-
//size in 10nm unit
+
molecule repression_red_protein;
-
size(Pfnr)=0.01;
+
molecule FNRa_binded;
-
size(Ise)=0.5;
+
 
 +
 
 +
//size : 10nm as unit
 +
 
 +
 
 +
size(mfnr)=0.1;
size(ClpXP)=0.5;
size(ClpXP)=0.5;
-
size(QFeFNRa)=2;
+
size(FNRa)=0.6;
 +
 
 +
size(FNRi)=0.3;
 +
 
 +
size(o2)=0.01;
 +
 
 +
size(FNRa_binded)=1.2;
 +
 
 +
size(proteinase1)=0.5;
 +
 
 +
size(proteinase2)=0.5;
 +
 
 +
size(proteinase3)=0.5;
-
size(apoFNR)=1;
 
-
size(DFeFNRi)=2;
 
size(GPV)=0.01;
size(GPV)=0.01;
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size(PR)=1;
size(PR)=1;
-
size(QFeFNRa_GPR_binded)=2.01;
+
size(GPR_binded)=0.02;
-
size(QFeFNRa_GPV_binded)=2.01;
+
size(FNRa_binded_GPR)=1.3;
-
size(rep)=4.02;
+
size(FNRa_binded_PV)=2.3;
 +
size(repression_red_protein)=4;
-
//speed
 
-
speed(Pfnr)=0;
+
// speed : probability to move to a distance of 10 nm
-
speed(Ise)=0.5;
 
-
speed(ClpXP)=0.5;
 
-
speed(QFeFNRa)=0.3;
+
speed(mfnr)=0.1;
-
speed(DFeFNRi)=0.3;
+
speed(ClpXP)=0.5;
-
speed(apoFNR)=0.3;
+
speed(FNRa)=0.3;
-
speed(GPV)=0;
+
speed(FNRi)=0.3;
 +
 
 +
speed(GPV)=01;
speed(PV)=0.3;
speed(PV)=0.3;
-
speed(GPR)=0;
+
speed(GPR)=0.1;
speed(PR)=0.3;
speed(PR)=0.3;
-
speed(QFeFNRa_GPR_binded)=0;
+
speed(o2)=0.8;
-
speed(QFeFNRa_GPV_binded)=0;
+
speed(FNRa_binded)=0.1;
-
speed(rep)=0;
+
speed(FNRa_binded_GPR)=0.1;
 +
speed(repression_red_protein)=0.01;
 +
speed(GPR_binded)=0.1;
-
//reactions
+
speed(FNRa_binded_PV) = 0.1;
-
//translating Pfnr to FNR
+
//maximum of number of link
-
Pfnr -> Pfnr + apoFNR [0.1];//fnr mRNA generates steagyly apoFNR(inactived)
 
 +
maxlinks (GPR) = FNRa_binded(1);
 +
maxlinks (GPV) = FNRa_binded(1);
-
//dimerisation
 
-
apoFNR + Ise -> QFeFNRa + Ise[0.8];//production of 4Fe-FNR by Ise is steady
+
//rules
 +
//translation fnr to FNR inactived
-
//oxydation
+
mfnr -> mfnr + FNRi [0.001];
-
QFeFNRa + o2 -> DFeFNRi +o2 [0.8];//aerobically, oxygen inactivates FNR
 
-
DFeFNRi + Ise -> QFeFNRa + Ise [0.5];//but cell continues to reactivate it steadly
 
 +
//2 FNRi bind
 +
FNRi + FNRi -> FNRa [0.5];
-
DFeFNRi + o2 -> apoFNR +o2 [0.6];//return to apoFNR
 
 +
//to many FNRa will reduce FNR production
-
//degradation FNR
+
FNRa + mfnr -> FNRa*mfnr [0.1];
-
apoFNR + ClpXP -> ClpXP [0.05];
+
FNRa*mfnr -> FNRa + mfnr [0.1];
-
DFeFNRi + ClpXP -> ClpXP [0.05];
 
-
QFeFNRa + ClpXP -> ClpXP [0.05];
 
 +
//deactivation FNR
 +
FNRa + o2 -> FNRi + FNRi [0.9];
-
//activation/inactivation of green gene
+
//degradation FNR
-
QFeFNRa + GPV -> QFeFNRa_GPV_binded [0.8];//association
+
FNRi + ClpXP -> ClpXP [0.05];
-
QFeFNRa_GPV_binded -> QFeFNRa + GPV [0.4];//dissociation
+
FNRa + proteinase1 -> proteinase1 [0.05];//taux de dissociation est different
-
QFeFNRa_GPV_binded -> PV + QFeFNRa_GPV_binded [0.3];//production of green protein
 
 +
//green reporter protein  production
-
//green protein degradation
+
FNRa + FNRa -> FNRa_binded [0.5];
-
PV + ClpXP -> ClpXP [0.05];
+
FNRa_binded -> FNRa + FNRa [0.001];
-
//repression of red gene
+
FNRa_binded + GPV -> FNRa_binded_PV [0.1];
-
QFeFNRa + GPR -> QFeFNRa_GPR_binded [0.8];
+
FNRa_binded_PV -> FNRa_binded + GPV[0.001];
-
QFeFNRa_GPR_binded -> QFeFNRa + GPR [0.1];
+
FNRa_binded_PV -> PV + FNRa_binded_PV[0.05];
-
QFeFNRa_GPR_binded + QFeFNRa_GPR_binded -> rep [0.5];
 
-
rep -> QFeFNRa_GPR_binded + QFeFNRa_GPR_binded [0.05];
 
 +
//red protein repression with 4 FNR activated
-
//expression the red gene in aerobic condition
+
FNRa_binded + GPR -> FNRa_binded_GPR [0.8];
-
GPR -> GPR + PR [0.3];//production of red protein
+
FNRa_binded_GPR + FNRa_binded_GPR -> repression_red_protein [0.5];
-
QFeFNRa_GPR_binded -> QFeFNRa_GPR_binded + PR [0.1];
+
repression_red_protein -> FNRa_binded_GPR + FNRa_binded_GPR [0.00001];
 +
FNRa_binded_GPR -> FNRa_binded + GPR[0.0001];
-
//degradation of red protein
+
//production of red protein when aerobic
-
PR + ClpXP -> ClpXP [0.05];
+
GPR + GPR -> GPR_binded[0.05];
 +
GPR_binded -> GPR_binded + PR [0.05];
 +
GPR_binded -> GPR + GPR[0.001];
-
//initialtion
 
 +
//degradation of protein
 +
PR + proteinase2 -> proteinase2 [0.1];
-
init(100,Pfnr);
+
PV + proteinase3 -> proteinase3 [0.1];
-
init(100,Ise);
 
-
init(100,ClpXP);
 
-
init(100,QFeFNRa);
+
//initialtion of paremeters
-
init(100,DFeFNRi);
+
init(10,mfnr);
-
init(100,apoFNR);
+
init(100,ClpXP);
init(100,GPV);
init(100,GPV);
-
 
-
init(10,PV);
 
init(100,GPR);
init(100,GPR);
-
init(10,PR);
+
init(1000,o2);
-
 
+
-
init(10,o2);
+
-
 
+
-
init(10,QFeFNRa_GPR_binded);
+
-
 
+
-
init(10,QFeFNRa_GPV_binded);
+
-
init(10,rep);
+
init(100,proteinase1);
 +
init(100,proteinase2);
 +
init(100,proteinase3);
 +
<big>[https://2013.igem.org/Team:Paris_Saclay/Modeling/FNR Back] </big>
{{Team:Paris_Saclay/incl_fin}}
{{Team:Paris_Saclay/incl_fin}}

Latest revision as of 01:49, 5 October 2013

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simulation.hsim

title="FNR regulator simulation scenario 2";


geometry = 200:50; // size of E.coli in unit of 10nm 200 : 50=2:0.5 µm


//molecules list


molecule mfnr;

molecule FNRi;

molecule FNRa;

molecule o2;

molecule ClpXP;

molecule proteinase1,proteinase2,proteinase3;

molecule GPV;

molecule PV (0,200,0);//color set :green

molecule GPR;

molecule PR (200,0,0); //color set : red

molecule GPR_binded;

molecule FNRa_binded_GPR;

molecule FNRa_binded_PV;

molecule repression_red_protein;

molecule FNRa_binded;


//size : 10nm as unit


size(mfnr)=0.1;

size(ClpXP)=0.5;

size(FNRa)=0.6;

size(FNRi)=0.3;

size(o2)=0.01;

size(FNRa_binded)=1.2;

size(proteinase1)=0.5;

size(proteinase2)=0.5;

size(proteinase3)=0.5;


size(GPV)=0.01;

size(PV)=1;

size(GPR)=0.01;

size(PR)=1;

size(GPR_binded)=0.02;

size(FNRa_binded_GPR)=1.3;

size(FNRa_binded_PV)=2.3;

size(repression_red_protein)=4;


// speed : probability to move to a distance of 10 nm


speed(mfnr)=0.1;

speed(ClpXP)=0.5;

speed(FNRa)=0.3;

speed(FNRi)=0.3;

speed(GPV)=01;

speed(PV)=0.3;

speed(GPR)=0.1;

speed(PR)=0.3;

speed(o2)=0.8;

speed(FNRa_binded)=0.1;

speed(FNRa_binded_GPR)=0.1;

speed(repression_red_protein)=0.01;

speed(GPR_binded)=0.1;

speed(FNRa_binded_PV) = 0.1;


//maximum of number of link


maxlinks (GPR) = FNRa_binded(1);

maxlinks (GPV) = FNRa_binded(1);


//rules


//translation fnr to FNR inactived

mfnr -> mfnr + FNRi [0.001];


//2 FNRi bind

FNRi + FNRi -> FNRa [0.5];


//to many FNRa will reduce FNR production

FNRa + mfnr -> FNRa*mfnr [0.1];

FNRa*mfnr -> FNRa + mfnr [0.1];


//deactivation FNR

FNRa + o2 -> FNRi + FNRi [0.9];


//degradation FNR

FNRi + ClpXP -> ClpXP [0.05];

FNRa + proteinase1 -> proteinase1 [0.05];//taux de dissociation est different


//green reporter protein production

FNRa + FNRa -> FNRa_binded [0.5];

FNRa_binded -> FNRa + FNRa [0.001];


FNRa_binded + GPV -> FNRa_binded_PV [0.1];

FNRa_binded_PV -> FNRa_binded + GPV[0.001];

FNRa_binded_PV -> PV + FNRa_binded_PV[0.05];


//red protein repression with 4 FNR activated


FNRa_binded + GPR -> FNRa_binded_GPR [0.8];

FNRa_binded_GPR + FNRa_binded_GPR -> repression_red_protein [0.5];

repression_red_protein -> FNRa_binded_GPR + FNRa_binded_GPR [0.00001];

FNRa_binded_GPR -> FNRa_binded + GPR[0.0001];


//production of red protein when aerobic

GPR + GPR -> GPR_binded[0.05];

GPR_binded -> GPR_binded + PR [0.05];

GPR_binded -> GPR + GPR[0.001];


//degradation of protein

PR + proteinase2 -> proteinase2 [0.1];

PV + proteinase3 -> proteinase3 [0.1];


//initialtion of paremeters

init(10,mfnr);

init(100,ClpXP);

init(100,GPV);

init(100,GPR);

init(1000,o2);

init(100,proteinase1);

init(100,proteinase2);

init(100,proteinase3);

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