func_li08

 example function: bacterial cell cycle [modelwtin(t,y), Li et al. 2008]
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&%
%Parameters values for the equations

0001 function dydt=func_li08(t,y)
0002 % example function: bacterial cell cycle [modelwtin(t,y), Li et al. 2008]
0003 %&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&%
0004 %%Parameters values for the equations
0005 
0006 ksCtrAP1=0.0083;    JiCtrACtrA=0.4;    niCtrACtrA=2;
0007 ksCtrAP2=0.073;    JaCtrACtrA=0.45;    naCtrACtrA=2;
0008 
0009 kdCtrA1=0.002;
0010 kdCtrA2=0.15;    ndCtrA2=2;
0011 JdCtrADivKP=0.55;
0012 
0013 ksGcrA=0.045;    JiGcrACtrA=0.2;    niGcrACtrA=2;
0014 
0015 kdGcrA=0.022;
0016 
0017 ksFts=0.063;    kdFts=0.035;
0018 
0019 kzringopen=0.8;    Jaopen=0.01;
0020 kzringclosed1=0.0001;    Jaclosed1=0.1;
0021 kzringclosed2=0.6;    nzringclosed2=4;
0022 JZringFts=0.78;
0023 
0024 ksDivK=0.0054;    ktransDivKP=0.0295;    ktransDivK=0.5;    kdDivK=0.002;
0025 
0026 ksI=0.08;    kdI=0.04;
0027 
0028 ksCcrM=0.072;    kdCcrM=0.07;
0029 
0030 
0031 kaDnaA=0.0165;    JiDnaAGcrA=0.5;    niDnaAGcrA=2;
0032 kdDnaA=0.007;
0033 
0034 kaIni=0.01;    JaIni=1;        naIni=4;
0035 
0036 thetaCtrA=0.2;    nthetaCtrA=4;
0037 thetaDnaA=0.6;    nthetaDnaA=4;
0038 thetaGcrA=0.45;    nthetaGcrA=4;
0039 thetaCori=0.0002;    nthetaCori=1;
0040 
0041 kmcori=0.4;    Jmcori=0.95;    nmcori=4;
0042 kmccrM=0.4;    JmccrM=0.95;    nmccrM=4;
0043 kmctrA=0.4;    JmctrA=0.95;    nmctrA=4;
0044 kmfts=0.4;    Jmfts=0.95;    nmfts=4;
0045 
0046 kelong=0.95/160;
0047 nelong=4;
0048 
0049 %$end of parameters
0050 %&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&%
0051 %%Differential equations of the model
0052 %%variable map
0053 %y(1)=[CtrA]
0054 %y(2)=[GcrA]
0055 %y(3)=[DnaA]
0056 %y(4)=[Fts]
0057 %y(5)=[Zring]
0058 %y(6)=[DivK]
0059 %y(7)=[DivK~P]
0060 %y(8)=[Total DivK]
0061 %y(9)=[I] (Intermediate)]
0062 %y(10)=[CcrM]
0063 %y(11)=[hCori] (hemimethylated Cori)
0064 %y(12)=[hccrM] (hemimethylated ccrM)
0065 %y(13)=[hctrA] (hemimethylated ctrA)
0066 %y(14)=[hfts](hemimethylated fts)
0067 %y(15)=[Ini] (Initiation)
0068 %y(16)=[Elong](Elongation)
0069 %y(17)=[DNA] (Total DNA)
0070 %y(18)=Count (# of Chromosome)
0071 
0072 dydt=zeros(18,1);  
0073 
0074 dydt(1)=(ksCtrAP1*JiCtrACtrA^niCtrACtrA/(JiCtrACtrA^niCtrACtrA+y(1)^niCtrACtrA)*y(2)+ksCtrAP2*y(1)^naCtrACtrA/(JaCtrACtrA^naCtrACtrA+y(1)^naCtrACtrA))*y(13)-(kdCtrA1+kdCtrA2*y(7)^ndCtrA2/(JdCtrADivKP^ndCtrA2+y(7)^ndCtrA2))*y(1);
0075 
0076 dydt(2)=(ksGcrA*JiGcrACtrA^niGcrACtrA/(JiGcrACtrA^niGcrACtrA+y(1)^niGcrACtrA)*y(3)-kdGcrA*y(2));
0077 
0078 dydt(3)=kaDnaA*JiDnaAGcrA^niDnaAGcrA/(JiDnaAGcrA^niDnaAGcrA+y(2)^niDnaAGcrA)*y(1)*(2-y(11))-kdDnaA*y(3);
0079 
0080 dydt(4)=ksFts*y(1)*y(14)-kdFts*y(4);
0081 
0082 dydt(5)=(kzringopen*(1-y(5))/(0.01+(1-y(5)))-(kzringclosed1+kzringclosed2*(y(4)/JZringFts)^nzringclosed2)*y(5)/(0.05+y(5)));
0083 
0084 dydt(6)=(ksDivK*y(1)+ktransDivKP*y(7)-ktransDivK*(1-y(5))*y(6)-kdDivK*y(6));
0085 
0086 dydt(7)=(-ktransDivKP*y(7)+ktransDivK*(1-y(5))*y(6)-kdDivK*y(7));
0087 
0088 dydt(8)=(ksDivK*y(1)-kdDivK*y(8));
0089 
0090 dydt(9)=ksI*y(12)*y(1)-kdI*y(9);
0091 
0092 dydt(10)=ksCcrM*y(9)-kdCcrM*y(10);
0093 
0094 dydt(11)=-kmcori*y(10)^nmcori/(Jmcori^nmcori+y(10)^nmcori)*y(11);
0095 
0096 dydt(12)=-kmccrM*y(10)^nmccrM/(JmccrM^nmccrM+y(10)^nmccrM)*y(12);
0097 
0098 dydt(13)=-kmctrA*y(10)^nmctrA/(JmctrA^nmctrA+y(10)^nmctrA)*y(13);
0099 
0100 dydt(14)=-kmfts*y(10)^nmfts/(Jmfts^nmfts+y(10)^nmfts)*y(14);
0101 
0102 dydt(15)=kaIni*(y(3)/thetaDnaA)^nthetaDnaA*(y(2)/thetaGcrA)^4/(JaIni^naIni+(y(1)/thetaCtrA)^nthetaCtrA+(y(3)/thetaDnaA)^nthetaDnaA+(y(2)/thetaGcrA)^nthetaGcrA+(y(11)/thetaCori)^nthetaCori);
0103 
0104 dydt(16)=kelong*y(16)^nelong/(y(16)^nelong+0.05^nelong)*y(18);
0105 
0106 dydt(17)=kelong*y(16)^nelong/(y(16)^nelong+0.05^nelong)*y(18);
0107 
0108 dydt(18)=0; %count (of chromosome - is only altered at an event
0109 
0110 %%end of equations
0111 %&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&%
0112 %%Clear the Computing
0113 end