#bray2

FIX: asp ni species_1

#reactions
motor_r1:
 {1.0}M + {1.0}Yp = {1.0}MYp
  cell * function_4_motor_r1(M, MYp, Yp, cell, ka, kappa)
motor_r2:
 {1.0}MYp + {1.0}Yp = {1.0}MYpYp
  cell * function_4_motor_r2(MYp, MYpYp, Yp, alpha, cell, ka, kappa)
motor_r3:
 {1.0}MYpYp + {1.0}Yp = {1.0}MYpYpYp
  cell * function_4_motor_r3(MYpYp, MYpYpYp, Yp, alpha, cell, ka, kappa)
motor_r4:
 {1.0}MYpYpYp + {1.0}Yp = {1.0}MYpYpYpYp
  cell * function_4_motor_r4(MYpYpYp, MYpYpYpYp, Yp, alpha, cell, ka, kappa)
phosphorylation_r1:
 {1.0}A = {1.0}Ap
  cell * Autophosphorylation(kcat, parameter_2, A)
phosphorylation_r10:
 {1.0}Bp = {1.0}B
  cell * k1 * Bp
phosphorylation_r2:
 {1.0}A = {1.0}Ap
  cell * ModAutophosphorylation(TWA, A, kcat, parameter_2)
phosphorylation_r3:
 {1.0}A = {1.0}Ap
  cell * ModAutophosphorylation(Tni_WA, A, kcat, parameter_2)
phosphorylation_r4:
 {1.0}Tasp_WA + {1.0}Yp = {1.0}Tasp_WA + {1.0}Y
  cell * k1 * Tasp_WA * Yp
phosphorylation_r5:
 {1.0}Ap + {1.0}Y = {1.0}A + {1.0}Yp
  cell * k1 * Ap * Y
phosphorylation_r6:
 {1.0}Y = {1.0}Yp
  cell * Autophosphorylation(kcat, parameter_2, Y)
phosphorylation_r7:
 {1.0}Yp = {1.0}Y
  cell * k1 * Yp
phosphorylation_r8:
 {1.0}Yp + {1.0}Z = {1.0}Y + {1.0}Z
  cell * k1 * Yp * Z
phosphorylation_r9:
 {1.0}Ap + {1.0}B = {1.0}A + {1.0}Bp
  cell * k1 * Ap * B
reaction_1:
 {1.0}TA + {1.0}asp = {1.0}Tasp_A
  cell * (k1 * TA * asp - k2 * Tasp_A)
reaction_2:
 {1.0}TW + {1.0}asp = {1.0}Tasp_W
  cell * (k1 * TW * asp - k2 * Tasp_W)
reaction_3:
 {1.0}TWA + {1.0}asp = {1.0}Tasp_WA
  cell * (k1 * TWA * asp - k2 * Tasp_WA)
regulatory_r1:
 {1.0}T + {1.0}asp = {1.0}Tasp
  cell * (k1 * T * asp - k2 * Tasp)
regulatory_r10:
 {1.0}Tasp + {1.0}A = {1.0}Tasp_A
  cell * (k1 * Tasp * A - k2 * Tasp_A)
regulatory_r11:
 {1.0}Tasp_W + {1.0}A = {1.0}Tasp_WA
  cell * (k1 * Tasp_W * A - k2 * Tasp_WA)
regulatory_r12:
 {1.0}Tasp_A + {1.0}W = {1.0}Tasp_WA
  cell * (k1 * Tasp_A * W - k2 * Tasp_WA)
regulatory_r13:
 {1.0}Tasp + {1.0}WA = {1.0}Tasp_WA
  cell * (k1 * Tasp * WA - k2 * Tasp_WA)
regulatory_r14:
 {1.0}Tni + {1.0}W = {1.0}Tni_W
  cell * (k1 * Tni * W - k2 * Tni_W)
regulatory_r15:
 {1.0}Tni + {1.0}A = {1.0}Tni_A
  cell * (k1 * Tni * A - k2 * Tni_A)
regulatory_r16:
 {1.0}Tni_W + {1.0}A = {1.0}Tni_WA
  cell * (k1 * Tni_W * A - k2 * Tni_WA)
regulatory_r17:
 {1.0}Tni_A + {1.0}W = {1.0}Tni_WA
  cell * (k1 * Tni_A * W - k2 * Tni_WA)
regulatory_r18:
 {1.0}Tni + {1.0}WA = {1.0}Tni_WA
  cell * (k1 * Tni * WA - k2 * Tni_WA)
regulatory_r2:
 {1.0}T + {1.0}ni = {1.0}Tni
  cell * (k1 * T * ni - k2 * Tni)
regulatory_r3:
 {1.0}T + {1.0}W = {1.0}TW
  cell * (k1 * T * W - k2 * TW)
regulatory_r4:
 {1.0}T + {1.0}A = {1.0}TA
  cell * (k1 * T * A - k2 * TA)
regulatory_r5:
 {1.0}W + {1.0}A = {1.0}WA
  cell * (k1 * W * A - k2 * WA)
regulatory_r6:
 {1.0}TW + {1.0}A = {1.0}TWA
  cell * (k1 * TW * A - k2 * TWA)
regulatory_r7:
 {1.0}TA + {1.0}W = {1.0}TWA
  cell * (k1 * TA * W - k2 * TWA)
regulatory_r8:
 {1.0}T + {1.0}WA = {1.0}TWA
  cell * (k1 * T * WA - k2 * TWA)
regulatory_r9:
 {1.0}Tasp + {1.0}W = {1.0}Tasp_W
  cell * (k1 * Tasp * W - k2 * Tasp_W)


#parameters
alpha = 0.14
ka = 0.1
kappa = 2.25e-07
parameter_1 = 1e-07
parameter_3 = 0.0003
asp = 0.0
ni = 0.0
species_1 = 0.1
phosphorylation_r1_kcat = 0.001
phosphorylation_r2_kcat = 75000.0
phosphorylation_r3_kcat = 200000.0
phosphorylation_r4_k1 = 100000000.0
phosphorylation_r5_k1 = 200000.0
phosphorylation_r6_kcat = 0.0
phosphorylation_r7_k1 = 0.037
phosphorylation_r8_k1 = 500000.0
phosphorylation_r9_k1 = 1000000.0
phosphorylation_r10_k1 = 1.0
regulatory_r1_k1 = 1000000.0
regulatory_r1_k2 = 1.0
regulatory_r2_k1 = 1000.0
regulatory_r2_k2 = 1.0
regulatory_r3_k1 = 100000.0
regulatory_r3_k2 = 1.0
regulatory_r4_k1 = 10000.0
regulatory_r4_k2 = 1.0
regulatory_r5_k1 = 100000.0
regulatory_r5_k2 = 1.0
regulatory_r6_k1 = 400000.0
regulatory_r6_k2 = 1.0
regulatory_r7_k1 = 400000.0
regulatory_r7_k2 = 1.0
regulatory_r8_k1 = 400000.0
regulatory_r8_k2 = 1.0
regulatory_r9_k1 = 100000.0
regulatory_r9_k2 = 1.0
regulatory_r10_k1 = 10000.0
regulatory_r10_k2 = 1.0
regulatory_r11_k1 = 400000.0
regulatory_r11_k2 = 1.0
regulatory_r12_k1 = 400000.0
regulatory_r12_k2 = 1.0
regulatory_r13_k1 = 400000.0
regulatory_r13_k2 = 1.0
regulatory_r14_k1 = 0.1
regulatory_r14_k2 = 1.0
regulatory_r15_k1 = 0.01
regulatory_r15_k2 = 1.0
regulatory_r16_k1 = 0.4
regulatory_r16_k2 = 1.0
regulatory_r17_k1 = 0.4
regulatory_r17_k2 = 1.0
regulatory_r18_k1 = 0.4
regulatory_r18_k2 = 1.0
reaction_1_k1 = 1000000.0
reaction_1_k2 = 1.0
reaction_2_k1 = 1000000.0
reaction_2_k2 = 1.0
reaction_3_k1 = 1000000.0
reaction_3_k2 = 1.0
cell = 1.41e-15


#initial values
A = 3e-06
Ap = 3.48e-08
B = 1.93e-06
Bp = 6.87e-08
M = 6.24e-09
MYp = 7.77e-10
MYpYp = 2.99e-10
MYpYpYp = 3.78e-10
MYpYpYpYp = 2.31e-09
T = 3.12e-06
TA = 4.44e-07
TW = 5.91e-07
TWA = 8.47e-07
Tasp = 0.0
Tasp_A = 0.0
Tasp_W = 0.0
Tasp_WA = 0.0
Tni = 0.0
Tni_A = 0.0
Tni_W = 0.0
Tni_WA = 0.0
W = 2.89e-06
WA = 6.78e-07
Y = 9.9e-06
Yp = 7e-09
Z = 2e-05


#assignment rules
!F parameter_2 = species_1 / (species_1 + parameter_3)
!F Bias = (M + MYp) / (M + MYp + MYpYp + MYpYpYp + MYpYpYpYp)