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);

molecule GPR;

molecule PR (200,0,0);

molecule GPR_binded;

molecule FNRa_binded_GPR;

molecule FNRa_binded_PV;

molecule repression_red_protein;

molecule FNRa_binded;

//size in 10nm 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;

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

init(10,mfnr);

init(100,ClpXP);

init(100,GPV);

init(100,GPR);

init(1000,o2);

init(100,proteinase1);

init(100,proteinase2);

init(100,proteinase3);