notes.txt

//Remember to set CVODE to MAXSTATES-1 length Assume for now, for
//now that I can init states and dstates, pass that memory to the
//integrators and state 46 if in algebraic mode.

-Modification to use seperate vectors? for mito/force only, how to
 modify? -> linear vectors with state offsets (I.e. subset vectors)

-Where do the 'extra' charges from the alg model get changed

-VFO is a calculated but unused variable? -> Move to output?
 (Commented Out)

//VAD_AT
//VcnsASP

VAAT
VACO
VANT
VATPase
VCS
VFH
VHFe
Vhleak
VHNe
Vhu
VIDH
VKGDH
VMDH
VnaCa
VNO
VSDH
VSL
Vuni 

	double O1_RyR;
	double 1000_F_Acap_C_m;
	double Co;
	double Istim;
	double E_Na;
	double E_K;
	double E_Ks;
	double E_Ca;
	double INa;
	double G_Na;
	double IKs;
	double IK1;
	double G_Nab;
	double INab;
	double G_Kp;
	double IKp;
	double ICahalf;
	double ICamax;
	double PK;
	double ICaK;
	double ICa;
	double INaK;
	double INaKmax;
	double KmNai;
	double KmKo;
	double Ko;
	double Ki1AD_NaK;
	double Km1AT_NaK;
	double eta;
	double Nao;
	double Cao;
	double KmCa;
	double ksat;
//	double Fcik1;
	double KmNa;
	double G_Cab;
	double ICab;
	double IpCa;
	double Km2ATP_CaP;
	double KiADP_CaP;
	double Km1ATP_CaP;
	double KmpCa;
	double IpCamax;
	double PnsNa;
	double KmnsCa;
	double PnsK;
	double InsCa;
	double V_AM_scaler;
	double f_01;
	double f_12;
	double f_23;
	double V_AM;

	//Mitochondia
	double ATPm;
	double Cm;
	double DmuH;
	double DpH;
	double CPN;
	double NAD;
	double VCS;
	double KmOaa;
	double AcCoA;
	double KmAcCoA;
	double EtCS;
	double KCS;
	double VACO;
	double CIK;
	double KACOeq;
	double kfACO;
	double kKGDH;
	double EtKG;
	double KmKG;
	double Mg;
	double Kmg;
	double Kca;
	double KmKGNAD;
	double nKG;
	double VKGDH;
	double CoA;
	double kfSL;
	double KSLeq;
	double VSL;
	double kSDH;
	double EtSDH;
	double KmSucc;
	double KiFUM;
	double KiOxaa;
	double VSDH;
	double kfFH;
	double KFHeq;
	double VFH;
	double Kh1;
	double Kh2;
	double Kh3;
	double Kh4;
	double Koff;
	double H;
	double Kioaa;
	double KmmNAD;
	double Kmal;
	double EtMD;
	double kMDH;
	double VMDH;
	double kfAAT;
	double GLU;
	double kcnsASP;
	double KAATeq;
	double VAAT;
	double kres;
	double rhoREN;
	double Dpsio;
	double g;
	double ra;
	double rc1;
	double r1;
	double rc2;
	double rb;
	double VNO;
	double VHNe;
	double kresf;
	double FADH2;
	double FAD;
	double r2;
	double r3;
	double VFO;
	double VHFe;
	double kf1;
	double Pi;
	double pa;
	double pc1;
	double pc2;
	double VATPase;
	double Vhu;
	double gh;
	double VmDT;
	double hm;
	double VANT;
	double Vhleak;

	//Junction Paramerters & Vars
	double Kfb;
	double Krb;
	double Nfb;
	double KSR;
	double vmaxf;
	double vmaxr;
	double KmATP_SR;
	double Ki_SR;
	double Ki_prime_SR;
	double v1;
	double tauxfer;
	double tautr;
	double Jup;
	double Jrel;
	double Jtr;
	double Jxfer;

	//force Parameters
	double alpha_SL;
	double zeta;
	double FN_Ca;
	double Fnorm;
	double Force;
	double kTrop_pn;
	double LTRPNtot;
	double Ktrop_half;
	double Ntrop;
	double f_01;
	double g_01_mod;
	double f_12;
	double g_12_mod;
	double g_23_mod;
	double f_23;
	double kltrpn_plus;
	double LTRPNtot;
	double kltrpn_minus;

	//Junction Params
	double CMDNtot;
	double KmCMDN;
	double CSQNtot;
	double KmCSQN;
	double Jtrpn;
	double beta_SS;
	double beta_JSR;
	double beta_i;

	//Vuni
	double Vmuni;
	double ktrans;
	double L;
	double kact;
	double na;
	double Vuni;

	//VnaCa
	double b;
	double VmNC;
	double Kna;
	double n;
	double Knca;
	double VnaCa;

	//Mitochondia

	//Derivative Calculation Parameters
	double InsNa;
	double Vmyo;
	double Acap;
	double InsK;
	double VSS;
	double VNSR;
	double VJSR;
	double C_m;
	double kaplus;
	double kbplus;
	double kaplus;
	double kaminus;
	double kbminus;
	double kcminus;
	double fprime;
	double gprime;

	//Stimulation modes
	double time_on_Is1;
	double time_off_Is1;
	double time_on_Is2;
	double time_off_Is2;
	double pulse_amplitude;
	double shift;
	double t1;
	double t2;
	double high_freq;
	double period;
	double norm_freq;
	double high_freq_hz;
	double norm_freq_hz;
	double pulse_duration;
	double start_time_shift;
	double start_time_shift_time_on;
	double time_vclamp_on;
	double vclamp_set;
	double vclamp_hold;