#arnold11

FIX: ATPc CO2 GLUc KGc NAD NADH NADP NADPH O2 UTPc

#reactions
AGPase:
 {1.0}HeP + {1.0}ATP = $pool
  chloroplast * function_10(Vm, G1P, ATP, K1, K2, ADP, KR1, Pi, KA1, PGA, KA2, F6P, KA3, FBP)
ATP_S:
 $pool = {1.0}ATP
  chloroplast * function_4(ADP, Pi, ATP, q, Ks1, Ks2, Kp1, Vm)
F26BPc_P:
 {1.0}F26BPc = {1.0}HePc
  cytosol * function_16(Vm, F26BPc, Pic, Kr1, F6Pc, Kr2, Ks1)
F6P_TK:
 {1.0}HeP + {1.0}TP = {1.0}E4P + {1.0}PeP
  chloroplast * function_6(Vm, F6P, GAP, X5P, E4P, Ks1, Ks2, X5P, Kr1, E4P, Kr2, q)
F6Pc_K:
 {1.0}HePc + {1.0}ATPc = {1.0}F26BPc
  cytosol * function_15(Vm, F6Pc, ATPc, F26BPc, ADPc, q, Ks1, F26BPc, Kr1, DHAPc, Kr2, Ks2, ADPc, Kr3)
FBP_A:
 {2.0}TP = {1.0}FBP
  chloroplast * function_4(GAP, DHAP, FBP, q, Ks1, Ks2, Kp1, Vm)
FBPase:
 {1.0}FBP = {1.0}HeP
  chloroplast * function_5(Vm, FBP, F6P, Pi, q, Ks1, F6P, Kr1, Pi, Kr2)
FBPc_A:
 {2.0}TPc = {1.0}FBPc
  cytosol * function_4(GAPc, DHAPc, FBPc, q, Ks1, Ks2, Kp1, Vm)
FBPcase:
 {1.0}FBPc = {1.0}HePc
  cytosol * function_12(FBPc, F6Pc, Pic, q, K52a, Kp1, Kp2, Vm)
GAP_DH:
 {1.0}DPGA + {1.0}NADPH = {1.0}TP + {1.0}NADP
  chloroplast * function_3(Vm, DPGA, NADPH, K1, K2)
GCAc_Ox:
 {1.0}GCAc = {1.0}GOAc
  cytosol * function_17(GCAc, Km, V)
GCEA_DH:
 {1.0}HPRc + {1.0}NADH = {1.0}GCEAc + {1.0}NAD
  function_21(Vm, HPRc, NADH, GCEAc, NAD, q, Ks1, HPRc, Kr1)
GCEA_K:
 {1.0}ATP + {1.0}GCEA = {1.0}PGA
  chloroplast * function_20(Vm, ATP, GCEA, PGA, ADP, q, Ks1, PGA, Kr1, Ks2)
GLUcGOAc_AT:
 {1.0}GLUc + {1.0}GOAc = {1.0}KGc + {1.0}GLYc
  cytosol * function_20(Vm, GLUc, GOAc, KGc, GLYc, q, Ks1, GLYc, Kr1, Ks2)
GLYc_DC:
 {2.0}GLYc = {1.0}SERc
  cytosol * function_22(Vm, GLYc, Ks1, SERc, Kr1)
GPT_GCA:
 {1.0}GCA = {1.0}GCAc
  function_18(GCA, GCEA, Km, V, Ki)
GPT_GCAc:
 {1.0}GCAc = {1.0}GCA
  function_18(GCAc, GCEAc, Km, V, Ki)
GPT_GCEA:
 {1.0}GCEA = {1.0}GCEAc
  function_18(GCEA, GCA, Km, V, Ki)
GPT_GCEAc:
 {1.0}GCEAc = {1.0}GCEA
  function_18(GCEAc, GCAc, Km, V, Ki)
PGA_K:
 {1.0}PGA + {1.0}ATP = {1.0}DPGA
  chloroplast * function_2(Vm, PGA, ATP, Ks1, Ks2, ADP, Kr1)
PGAc_Deg:
 {1.0}PGAc = $pool
  cytosol * function_17(PGAc, Km, V)
PGCA_P:
 {1.0}PGCA = {1.0}GCA
  chloroplast * function_19(Vm, PGCA, Ks1, GCA, Kr1, Pi, Kr2)
Ru5P_K:
 {1.0}PeP + {1.0}ATP = {1.0}RuBP
  chloroplast * function_9(Vm, Ru5P, ATP, RuBP, ADP, q, Ks1, PGA, Kr1, RuBP, Kr2, Pi, Kr3, ADP, Kr41, Ks2, Kr42)
RuBisCO_CO2:
 {1.0}RuBP = {2.0}PGA
  chloroplast * function_1(Wc_min, RuBP, K, PGA, KR1, FBP, KR2, SBP, KR3, Pi, KR4, NADPH, KR5)
RuBisCO_O2:
 {1.0}RuBP = {1.0}PGA + {1.0}PGCA
  chloroplast * function_1(Wo_min, RuBP, K, PGA, KR1, FBP, KR2, SBP, KR3, Pi, KR4, NADPH, KR5)
S7P_TK:
 {1.0}TP + {1.0}S7P = {2.0}PeP
  chloroplast * function_6(Vm, GAP, S7P, X5P, R5P, Ks1, Ks2, X5P, Kr1, R5P, Kr2, q)
SBP_A:
 {1.0}TP + {1.0}E4P = {1.0}SBP
  chloroplast * function_7(Vm, DHAP, E4P, SBP, q, Ks1, Ks2)
SBPase:
 {1.0}SBP = {1.0}S7P
  chloroplast * function_8(Vm, SBP, S7P, Pi, q, Ks1, Pi, Kr1)
SERcGOAc_AT:
 {1.0}SERc + {1.0}GOAc = {1.0}HPRc + {1.0}GLYc
  function_20(Vm, SERc, GOAc, HPRc, GLYc, q, Ks1, GLYc, Kr1, Ks2)
SucPc_P:
 {1.0}SucPc = {1.0}Succ
  cytosol * function_8(Vm, SucPc, Succ, Pic, q, Ks1, Succ, Kr1)
SucPc_S:
 {1.0}HePc + {1.0}UDPGc = {1.0}SucPc
  cytosol * function_14(Vm, F6Pc, UDPGc, SucPc, UDPc, q, Ks1, FBPc, Kr1, Ks2, UDPc, Kr2, SucPc, Kr3, Succ, Kr4, Pic, Kr5)
Succ_Deg:
 {1.0}Succ = $pool
  cytosol * function_17(Succ, Km, V)
TPT_DHAP:
 {1.0}TP = {1.0}TPc
  function_11(Vm, DHAP, KA, Pic, K, Pi, KR1, PGA, KR2, GAP, KR3)
TPT_GAP:
 {1.0}TP = {1.0}TPc
  function_11(Vm, GAP, KA, Pic, K, Pi, KR1, PGA, KR2, DHAP, KR3)
TPT_PGA:
 {1.0}PGA = {1.0}PGAc
  function_11(Vm, PGA, KA, Pic, K, Pi, KR1, GAP, KR2, DHAP, KR3)
UGPase:
 {1.0}HePc + {1.0}UTPc = {1.0}UDPGc
  cytosol * function_13(G1Pc, UTPc, UDPGc, PiPic, q, Ks1, Ks2, Kp1, Kp2, Vm)


#parameters
E = 1.456965457
cA = 1.5
cAc = 1.0
cNc = 0.87
cP = 15.0
cPc = 15.0
cUc = 1.5
ATPc = 0.35
CO2 = 0.009
GLUc = 24.0
KGc = 0.4
NAD = 0.4
NADH = 0.47
NADP = 0.29
NADPH = 0.21
O2 = 0.2646
UTPc = 0.75
RuBisCO_CO2_K = 0.02
RuBisCO_CO2_KR1 = 0.84
RuBisCO_CO2_KR2 = 0.04
RuBisCO_CO2_KR3 = 0.075
RuBisCO_CO2_KR4 = 0.9
RuBisCO_CO2_KR5 = 0.07
PGA_K_Vm = 30.1408
PGA_K_Ks1 = 0.24
PGA_K_Ks2 = 0.39
PGA_K_Kr1 = 0.23
GAP_DH_Vm = 4.03948
GAP_DH_K1 = 0.004
GAP_DH_K2 = 0.1
FBP_A_q = 7.1
FBP_A_Ks1 = 0.3
FBP_A_Ks2 = 0.4
FBP_A_Kp1 = 0.02
FBP_A_Vm = 1.21889
FBPase_Vm = 0.72626
FBPase_q = 666000.0
FBPase_Ks1 = 0.033
FBPase_Kr1 = 0.7
FBPase_Kr2 = 12.0
F6P_TK_Vm = 3.12207
F6P_TK_Ks1 = 0.1
F6P_TK_Ks2 = 0.1
F6P_TK_Kr1 = 0.1
F6P_TK_Kr2 = 0.1
F6P_TK_q = 10.0
SBP_A_Vm = 1.21889
SBP_A_q = 1.017
SBP_A_Ks1 = 0.4
SBP_A_Ks2 = 0.2
SBPase_Vm = 0.324191
SBPase_q = 666000.0
SBPase_Ks1 = 0.05
SBPase_Kr1 = 12.0
S7P_TK_Vm = 3.12207
S7P_TK_Ks1 = 0.072
S7P_TK_Ks2 = 0.46
S7P_TK_Kr1 = 0.1
S7P_TK_Kr2 = 1.5
S7P_TK_q = 1.17647
Ru5P_K_Vm = 10.8348
Ru5P_K_q = 6846.0
Ru5P_K_Ks1 = 0.05
Ru5P_K_Kr1 = 2.0
Ru5P_K_Kr2 = 0.7
Ru5P_K_Kr3 = 4.0
Ru5P_K_Kr41 = 2.5
Ru5P_K_Ks2 = 0.059
Ru5P_K_Kr42 = 0.4
ATP_S_q = 5.734
ATP_S_Ks1 = 0.014
ATP_S_Ks2 = 0.3
ATP_S_Kp1 = 0.3
ATP_S_Vm = 15.0
AGPase_Vm = 0.266843
AGPase_K1 = 0.08
AGPase_K2 = 0.08
AGPase_KR1 = 10.0
AGPase_KA1 = 0.1
AGPase_KA2 = 0.02
AGPase_KA3 = 0.02
TPT_PGA_Vm = 1.24333
TPT_PGA_KA = 0.74
TPT_PGA_K = 0.25
TPT_PGA_KR1 = 0.63
TPT_PGA_KR2 = 0.075
TPT_PGA_KR3 = 0.077
TPT_GAP_Vm = 1.24333
TPT_GAP_KA = 0.74
TPT_GAP_K = 0.075
TPT_GAP_KR1 = 0.63
TPT_GAP_KR2 = 0.25
TPT_GAP_KR3 = 0.077
TPT_DHAP_Vm = 1.24333
TPT_DHAP_KA = 0.74
TPT_DHAP_K = 0.077
TPT_DHAP_KR1 = 0.63
TPT_DHAP_KR2 = 0.25
TPT_DHAP_KR3 = 0.075
FBPc_A_q = 12.0
FBPc_A_Ks1 = 0.3
FBPc_A_Ks2 = 0.4
FBPc_A_Kp1 = 0.02
FBPc_A_Vm = 0.107377
FBPcase_q = 6663.0
FBPcase_Kp1 = 0.7
FBPcase_Kp2 = 12.0
FBPcase_Vm = 0.063979
UGPase_q = 0.31
UGPase_Ks1 = 0.14
UGPase_Ks2 = 0.1
UGPase_Kp1 = 0.12
UGPase_Kp2 = 0.11
UGPase_Vm = 0.115403
SucPc_S_Vm = 0.0555034
SucPc_S_q = 10.0
SucPc_S_Ks1 = 0.8
SucPc_S_Kr1 = 0.8
SucPc_S_Ks2 = 2.4
SucPc_S_Kr2 = 0.7
SucPc_S_Kr3 = 0.4
SucPc_S_Kr4 = 50.0
SucPc_S_Kr5 = 11.0
SucPc_P_Vm = 0.555034
SucPc_P_q = 780.0
SucPc_P_Ks1 = 0.35
SucPc_P_Kr1 = 80.0
F6Pc_K_Vm = 0.100915
F6Pc_K_q = 590.0
F6Pc_K_Ks1 = 0.5
F6Pc_K_Kr1 = 0.021
F6Pc_K_Kr2 = 0.7
F6Pc_K_Ks2 = 0.5
F6Pc_K_Kr3 = 0.16
F26BPc_P_Vm = 0.0168192
F26BPc_P_Kr1 = 0.5
F26BPc_P_Kr2 = 0.1
F26BPc_P_Ks1 = 0.032
Succ_Deg_Km = 5.0
Succ_Deg_V = 2.0
PGAc_Deg_Km = 1.0
PGAc_Deg_V = 0.5
GPT_GCEAc_Km = 0.39
GPT_GCEAc_V = 5.0
GPT_GCEAc_Ki = 0.28
GPT_GCEA_Km = 0.39
GPT_GCEA_V = 5.0
GPT_GCEA_Ki = 0.28
GPT_GCA_Km = 0.2
GPT_GCA_V = 6.0
GPT_GCA_Ki = 0.22
GPT_GCAc_Km = 0.2
GPT_GCAc_V = 6.0
GPT_GCAc_Ki = 0.22
RuBisCO_O2_K = 0.02
RuBisCO_O2_KR1 = 0.84
RuBisCO_O2_KR2 = 0.04
RuBisCO_O2_KR3 = 0.075
RuBisCO_O2_KR4 = 0.9
RuBisCO_O2_KR5 = 0.07
PGCA_P_Vm = 52.4199
PGCA_P_Ks1 = 0.026
PGCA_P_Kr1 = 94.0
PGCA_P_Kr2 = 2.55
GCEA_K_Vm = 5.71579
GCEA_K_q = 300.0
GCEA_K_Ks1 = 0.21
GCEA_K_Kr1 = 0.36
GCEA_K_Ks2 = 0.25
GCAc_Ox_Km = 0.1
GCAc_Ox_V = 1.45611
SERcGOAc_AT_Vm = 3.30619
SERcGOAc_AT_q = 0.24
SERcGOAc_AT_Ks1 = 2.7
SERcGOAc_AT_Kr1 = 33.0
SERcGOAc_AT_Ks2 = 0.15
GCEA_DH_Vm = 10.0098
GCEA_DH_q = 250000.0
GCEA_DH_Ks1 = 0.09
GCEA_DH_Kr1 = 12.0
GLUcGOAc_AT_Vm = 2.74582
GLUcGOAc_AT_q = 607.0
GLUcGOAc_AT_Ks1 = 1.7
GLUcGOAc_AT_Kr1 = 2.0
GLUcGOAc_AT_Ks2 = 0.15
GLYc_DC_Vm = 2.49475
GLYc_DC_Ks1 = 6.0
GLYc_DC_Kr1 = 4.0
chloroplast = 1.0
cytosol = 1.0


#initial values
ATP = 0.68
DPGA = 0.0011
E4P = 0.05
F26BPc = 7.8e-06
FBP = 0.669999999999999
FBPc = 2.0
GCA = 0.36
GCAc = 0.36
GCEA = 0.1812
GCEAc = 0.1812
GLYc = 1.8
GOAc = 0.028
HPRc = 0.0035
HeP = 2.2
HePc = 5.8
PGA = 2.4
PGAc = 0.0
PGCA = 0.0029
PeP = 0.25
RuBP = 2.0
S7P = 2.0
SBP = 0.3
SERc = 7.5
SucPc = 0.0
Succ = 0.0
TP = 0.5
TPc = 2.3
UDPGc = 0.57


#assignment rules
!F Ru5P = PeP / (1.0 + 1.0 / 0.4 + 1.0 / 0.67)
!F Pi = cP - 2.0 * (RuBP + DPGA + FBP + SBP) - (PGA + TP + HeP + E4P + S7P + PeP + ATP + PGCA)
!F X5P = PeP / 0.67 / (1.0 + 1.0 / 0.4 + 1.0 / 0.67)
!F G1P = HeP * 0.058 / (1.0 + 1.0 / 2.3 + 0.058)
!F GAP = 0.05 * TP / (1.0 + 0.05)
!F DHAP = TP / (1.0 + 0.05)
!F G6P = HeP / (1.0 + 1.0 / 2.3 + 0.058)
!F R5P = PeP / 0.4 / (1.0 + 1.0 / 0.4 + 1.0 / 0.67)
!F K52a = 0.0025 * (1.0 + F26BPc / 7.000000e-05)
!F ADPc = cAc - ATPc
!F Wo_min = 0.24 * 2.913930914 * O2 / (O2 + 0.222 * (1.0 + CO2 / 0.0115)) * ((1.0 + RuBP / E - abs(1.0 - RuBP / E)) / 2.0)
!F UDPc = cUc - UTPc - UDPGc
!F DHAPc = TPc / (1.0 + 0.05)
!F G1Pc = HePc * 0.0584 / (1.0 + 1.0 / 2.3 + 0.0584)
!F Wc_min = 2.913930914 * CO2 / (CO2 + 0.0115 * (1.0 + O2 / 0.222)) * ((1.0 + RuBP / E - abs(1.0 - RuBP / E)) / 2.0)
!F PiPic = PiTc - Pic
!F Pic = 12000000.0 / 2.0 * (sqrt(1.0 + 4.0 * PiTc / 12000000.0) - 1.0)
!F F6Pc = HePc / 2.3 / (1.0 + 1.0 / 2.3 + 0.0584)
!F PiTc = cPc - 2.0 * (FBPc + F26BPc) - (PGAc + TPc + HePc + SucPc + ATPc + UTPc)
!F GAPc = 0.05 * TPc / (1.0 + 0.05)
!F G6Pc = HePc / (1.0 + 1.0 / 2.3 + 0.0584)
!F ADP = cA - ATP
!F F6P = HeP / 2.3 / (1.0 + 1.0 / 2.3 + 0.058)