Circadian clock model based on protein sequestration (simple version) (Kim & Forger 2012)

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Accession:145800
"… To understand the biochemical mechanisms of this timekeeping, we have developed a detailed mathematical model of the mammalian circadian clock. Our model can accurately predict diverse experimental data including the phenotypes of mutations or knockdown of clock genes as well as the time courses and relative expression of clock transcripts and proteins. Using this model, we show how a universal motif of circadian timekeeping, where repressors tightly bind activators rather than directly binding to DNA, can generate oscillations when activators and repressors are in stoichiometric balance. …"
Reference:
1 . Kim JK, Forger DB (2012) A mechanism for robust circadian timekeeping via stoichiometric balance. Mol Syst Biol 8:630 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network;
Brain Region(s)/Organism:
Cell Type(s): Suprachiasmatic nucleus (SCN) neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; XPP; MATLAB; Mathematica; SBML;
Model Concept(s): Oscillations; Simplified Models; Circadian Rhythms;
Implementer(s): Kim, Jae Kyoung [kimjack0 at kaist.ac.kr];
#ifdef SIZE_DEFINITIONS
#define N_METABS 5
#define N_ODE_METABS 0
#define N_INDEP_METABS 5
#define N_COMPARTMENTS 1
#define N_GLOBAL_PARAMS 11
#define N_KIN_PARAMS 12
#define N_REACTIONS 10
#endif // SIZE_DEFINITIONS

#ifdef TIME
#define T  <set here a user name for the time variable> 
#endif // TIME

#ifdef INITIAL
x[0] = 0.102583;	//metabolite 'M': reactions
x[1] = 0.0899344;	//metabolite 'Pc': reactions
x[2] = 0.0640356;	//metabolite 'P': reactions
x[3] = 0.0622499;	//metabolite 'A': reactions
x[4] = 0.371178;	//metabolite 'R': reactions
#endif INITIAL

#ifdef FIXED
p[0] = 1;	//compartment 'Cell':fixed
p[1] = 1;	//global quantity 'ao':fixed
p[2] = 1;	//global quantity 'at':fixed
p[3] = 1;	//global quantity 'ah':fixed
p[4] = 1;	//global quantity 'bo':fixed
p[5] = 1;	//global quantity 'bt':fixed
p[6] = 1;	//global quantity 'bh':fixed
p[7] = 1e-05;	//global quantity 'kd':fixed
p[8] = 1;	//global quantity 'ro':fixed
p[9] = 0.0395;	//global quantity 'rt':fixed
p[10] = 0.2;	//global quantity 'do':fixed
p[11] = 0.2;	//global quantity 'dt':fixed
p[12] = 0.1;	//reaction 'Translation':  kinetic parameter 'k'
p[13] = 0.1;	//reaction 'Activation':  kinetic parameter 'k'
p[14] = 0.1;	//reaction 'Transcription':  kinetic parameter 'ao'
p[15] = 0.1;	//reaction 'Transcription':  kinetic parameter 'Kd'
p[16] = 0.1;	//reaction 'Degradation_M':  kinetic parameter 'k1'
p[17] = 0.1;	//reaction 'Degradation_Pc':  kinetic parameter 'k1'
p[18] = 0.1;	//reaction 'Degradation_P':  kinetic parameter 'k1'
p[19] = 0.1;	//reaction 'Transcription_two':  kinetic parameter 'ao'
p[20] = 0.1;	//reaction 'Transcription_two':  kinetic parameter 'Kd'
p[21] = 0.1;	//reaction 'Translation_two':  kinetic parameter 'k'
p[22] = 0.1;	//reaction 'Degradation_R':  kinetic parameter 'k1'
p[23] = 0.1;	//reaction 'Degradation_A':  kinetic parameter 'k1'
#endif FIXED

#ifdef ASSIGNMENT
x_c[0] = x[0]/p[0];	//concentration of metabolite 'M': reactions
x_c[1] = x[1]/p[0];	//concentration of metabolite 'Pc': reactions
x_c[2] = x[2]/p[0];	//concentration of metabolite 'P': reactions
x_c[3] = x[3]/p[0];	//concentration of metabolite 'A': reactions
x_c[4] = x[4]/p[0];	//concentration of metabolite 'R': reactions
#endif ASSIGNMENT

#ifdef  FUNCTIONS_HEADERS
double linearActivation(double param_0, double modif_0); 
double Transcription_2(double param_0, double modif_0, double modif_1, double param_1); 
#endif FUNCTIONS_HEADERS

#ifdef  FUNCTIONS
double linearActivation(double param_0, double modif_0) 	//linear activation
{return  param_0*modif_0;} 
double Transcription_2(double param_0, double modif_0, double modif_1, double param_1) 	//Transcription_2
{return  param_0*(1-modif_0/modif_1-param_1/modif_1+pow((pow((1-modif_0/modif_1-param_1/modif_1),2)+4*param_1/modif_1),0.5))/2;} 
#endif FUNCTIONS

#ifdef ODEs
dx[0] = Transcription_2(p[1], x_c[2], x_c[3], p[7])*p[0]-(p[4] * x_c[0]) *p[0];	// 
dx[1] = linearActivation(p[2], x_c[0])*p[0]-(p[5] * x_c[1]) *p[0];	// 
dx[2] = linearActivation(p[3], x_c[1])*p[0]-(p[6] * x_c[2]) *p[0];	// 
dx[3] = linearActivation(p[9], x_c[4])*p[0]-(p[11] * x_c[3]) *p[0];	// 
dx[4] = Transcription_2(p[8], x_c[2], x_c[3], p[7])*p[0]-(p[10] * x_c[4]) *p[0];	// 
#endif ODEs

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