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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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@@ Line 1: / Line 1: @@
 {{Team:Paris_Saclay/incl_debut_generique}}
 ='''simulation.hsim'''=
-<p>title="FNR regulator simulation";
+title="FNR regulator simulation scenario 2";
-<br>
 geometry = 200:50; // size of E.coli in unit of 10nm 200 : 50=2:0.5 µm
-<br>
 //molecules list
-<br>
-molecule Pfnr;//fnr promotor<br>
-molecule Ise,ClpXP;//Ise: iron-sulfur cluster assembly proteins : enzyme of dimerisation ; ClpXP: ATP dependent protease that induces degradation for all protein<br>
-molecule QFeFNRa,apoFNR,DFeFNRi;//3 states of FNR: activated, without Fe (inactivated), and inactivated<br>
-molecule GPV,PV;//GPV green protein gene, PV green protein<br>
+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;
-molecule GPR,PR;//GPR red protein gene, PR red protein<br>
-molecule QFeFNRa_GPR_binded,QFeFNRa_GPV_binded;//molecule FNR binds on mRNA from GPR and GPV<br>
-molecule rep;//complexe of 4 FNRs, prevent production of red protein<br>
+//size : 10nm as unit
+size(mfnr)=0.1;
-metabolite o2;//declare the o2 as a cytosolic molecule leads to be treated as an homogeneous population<br>
+size(ClpXP)=0.5;
+size(FNRa)=0.6;
+size(FNRi)=0.3;
-//size in 10nm unit<br>
+size(o2)=0.01;
-size(Pfnr)=0.01;<br>
+size(FNRa_binded)=1.2;
-<br>
-size(Ise)=0.5;
-size(ClpXP)=0.5;<br>
+size(proteinase1)=0.5;
-size(QFeFNRa)=2;<br>
+size(proteinase2)=0.5;
-size(apoFNR)=1;<br>
+size(proteinase3)=0.5;
-size(DFeFNRi)=2;<br>
-size(GPV)=0.01;<br>
-size(PV)=1;<br>
+size(GPV)=0.01;
-size(GPR)=0.01;<br>
+size(PV)=1;
-size(PR)=1;<br>
+size(GPR)=0.01;
-size(QFeFNRa_GPR_binded)=2.01;<br>
+size(PR)=1;
-size(QFeFNRa_GPV_binded)=2.01;<br>
+size(GPR_binded)=0.02;
-size(rep)=4.02;<br>
+size(FNRa_binded_GPR)=1.3;
+size(FNRa_binded_PV)=2.3;
+size(repression_red_protein)=4;
-//speed <br>
-speed(Pfnr)=0;<br>
-speed(Ise)=0.5;<br>
+// speed : probability to move to a distance of 10 nm
-speed(ClpXP)=0.5;<br>
-speed(QFeFNRa)=0.3;<br>
-speed(DFeFNRi)=0.3;<br>
+speed(mfnr)=0.1;
-speed(apoFNR)=0.3;<br>
+speed(ClpXP)=0.5;
-speed(GPV)=0;<br>
+speed(FNRa)=0.3;
-speed(PV)=0.3;<br>
+speed(FNRi)=0.3;
-speed(GPR)=0;<br>
+speed(GPV)=01;
-speed(PR)=0.3;<br>
+speed(PV)=0.3;
-speed(QFeFNRa_GPR_binded)=0;<br>
+speed(GPR)=0.1;
-speed(QFeFNRa_GPV_binded)=0;<br>
+speed(PR)=0.3;
-speed(rep)=0;<br>
+speed(o2)=0.8;
+speed(FNRa_binded)=0.1;
+speed(FNRa_binded_GPR)=0.1;
-//reactions<br>
+speed(repression_red_protein)=0.01;
+speed(GPR_binded)=0.1;
+speed(FNRa_binded_PV) = 0.1;
-//translating Pfnr to FNR<br>
-Pfnr -> Pfnr + apoFNR [0.1];//fnr mRNA generates steagyly apoFNR(inactived)<br>
+//maximum of number of link
-//dimerisation <br>
+maxlinks (GPR) = FNRa_binded(1);
-apoFNR + Ise -> QFeFNRa + Ise[0.8];//production of 4Fe-FNR by Ise is steady<br>
+maxlinks (GPV) = FNRa_binded(1);
+//rules
-//oxydation<br>
-QFeFNRa + o2 -> DFeFNRi +o2 [0.8];//aerobically, oxygen inactivates FNR<br>
+//translation fnr to FNR inactived
-DFeFNRi + Ise -> QFeFNRa + Ise [0.5];//but cell continues to reactivate it steadly<br>
+mfnr -> mfnr + FNRi [0.001];
-DFeFNRi + o2 -> apoFNR +o2 [0.6];//return to apoFNR<br>
+//2 FNRi bind
+FNRi + FNRi -> FNRa [0.5];
-//degradation FNR<br>
-apoFNR + ClpXP -> ClpXP [0.05];<br>
+//to many FNRa will reduce FNR production
-DFeFNRi + ClpXP -> ClpXP [0.05];<br>
+FNRa + mfnr -> FNRa*mfnr [0.1];
-QFeFNRa + ClpXP -> ClpXP [0.05];<br>
+FNRa*mfnr -> FNRa + mfnr [0.1];
+//deactivation FNR
+FNRa + o2 -> FNRi + FNRi [0.9];
-//activation/inactivation of green gene<br>
-QFeFNRa + GPV -> QFeFNRa_GPV_binded [0.8];//association<br>
-QFeFNRa_GPV_binded -> QFeFNRa + GPV [0.4];//dissociation<br>
-QFeFNRa_GPV_binded -> PV + QFeFNRa_GPV_binded [0.3];//production of green protein<br>
+//degradation FNR
+FNRi + ClpXP -> ClpXP [0.05];
+FNRa + proteinase1 -> proteinase1 [0.05];//taux de dissociation est different
-//green protein degradation<br>
-PV + ClpXP -> ClpXP [0.05];<br>
+//green reporter protein  production
+FNRa + FNRa -> FNRa_binded [0.5];
-//repression of red gene<br>
+FNRa_binded -> FNRa + FNRa [0.001];
-QFeFNRa + GPR -> QFeFNRa_GPR_binded [0.8];<br>
-QFeFNRa_GPR_binded -> QFeFNRa + GPR [0.1];<br>
-QFeFNRa_GPR_binded + QFeFNRa_GPR_binded -> rep [0.5];<br>
+FNRa_binded + GPV -> FNRa_binded_PV [0.1];
-rep -> QFeFNRa_GPR_binded + QFeFNRa_GPR_binded [0.05];<br>
+FNRa_binded_PV -> FNRa_binded + GPV[0.001];
+FNRa_binded_PV -> PV + FNRa_binded_PV[0.05];
-//expression the red gene in aerobic condition<br>
-GPR -> GPR + PR [0.3];//production of red protein<br>
+//red protein repression with 4 FNR activated
-QFeFNRa_GPR_binded -> QFeFNRa_GPR_binded + PR [0.1];<br>
+FNRa_binded + GPR -> FNRa_binded_GPR [0.8];
+FNRa_binded_GPR + FNRa_binded_GPR -> repression_red_protein [0.5];
-//degradation of red protein<br>
+repression_red_protein -> FNRa_binded_GPR + FNRa_binded_GPR [0.00001];
-PR + ClpXP -> ClpXP [0.05];<br>
+FNRa_binded_GPR -> FNRa_binded + GPR[0.0001];
+//production of red protein when aerobic
-//initialtion<br>
+GPR + GPR -> GPR_binded[0.05];
+GPR_binded -> GPR_binded + PR [0.05];
+GPR_binded -> GPR + GPR[0.001];
-init(100,Pfnr);<br>
-init(100,Ise);<br>
+//degradation of protein
-init(100,ClpXP);<br>
+PR + proteinase2 -> proteinase2 [0.1];
-init(100,QFeFNRa);<br>
+PV + proteinase3 -> proteinase3 [0.1];
-init(100,DFeFNRi);<br>
-init(100,apoFNR);<br>
-init(100,GPV);<br>
+//initialtion of paremeters
-init(10,PV);<br>
+init(10,mfnr);
-init(100,GPR);<br>
+init(100,ClpXP);
-init(10,PR);<br>
+init(100,GPV);
-init(10,o2);<br>
+init(100,GPR);
-init(10,QFeFNRa_GPR_binded);<br>
+init(1000,o2);
-init(10,QFeFNRa_GPV_binded);<br>
+init(100,proteinase1);
-init(10,rep);<br>
+init(100,proteinase2);
-</p>
+init(100,proteinase3);
+<big>[https://2013.igem.org/Team:Paris_Saclay/Modeling/FNR Back] </big>
 {{Team:Paris_Saclay/incl_fin}}

Team:Paris Saclay/simulation

From 2013.igem.org

Latest revision as of 01:49, 5 October 2013

simulation.hsim