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fixed formatting errors that were ignored previously

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ralf 2024-09-02 15:03:33 +03:00
parent 5b630571b3
commit 4864ed8349
1 changed files with 34 additions and 25 deletions
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59
Model.py
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@ -33,46 +33,52 @@ class Model:
self.km_Ca: float = (
1380 # uM, Ca2+ half-saturation constant for Na+/Ca2+ exchange
)
self.k_Na_Ca: float = 292.8 # pA/pF, Scaling factor of Na2+/Ca2+ exchange
self.k_Na_Ca: float = 292.8
# pA/pF, Scaling factor of Na2+/Ca2+ exchange
self.I_max_pCa: float = 1.0 # pA/pF, Maximum Ca2+ pump current
# self.Cai = 0.1 # uM, Cytoplasmic Ca2+ concentration fixed at this point
# self.Cai = 0.1 # uM, Cytoplasmic Ca2+ concentration fixed at point
self.LTRPN_tot: float = (
70.0 # uM, Total myoplasmic troponin low-affinity site concentration
70.0 # uM, Total myoplasmic troponin low-affinity site concentr.
)
self.HTRPN_tot: float = (
140.0 # uM, Total myoplasmic troponin high-affinity site concentration
140.0 # uM, Total myoplasmic troponin high-affinity site concentr.
)
# self.LTRPNCa = 11.2684 # uM, Concentration Ca2+ bound low-affinity troponin-binding sites
# self.HTRPNCa = 125.290 # uM, Concentration Ca2+ bound high-affinity troponin-binding sites
"""
self.LTRPNCa = 11.2684 # uM, Concentration Ca2+ bound
low-affinity troponin-binding sites
self.HTRPNCa = 125.290 # uM, Concentration Ca2+ bound
high-affinity troponin-binding sites
"""
self.k_htrpn_positive: float = (
0.00237 # uM^(-1)/ms, Ca2+ on rate const. for troponin high-affinity sites
0.00237
# uM^(-1)/ms, Ca2+ on rate const. for troponin high-affin sites
)
self.k_htrpn_negative = (
3.2e-5 # ms, Ca2+ off rate const. for troponin high-affinity sites
)
self.k_ltrpn_positive = (
0.0327 # uM^(-1)/ms, Ca2+ on rate const. for troponin low-affinity sites
0.0327
# uM^(-1)/ms, Ca2+ on rate const. for troponin low-affin sites
)
self.k_ltrpn_negative: float = (
0.0196 # ms, Ca2+ off rate const. for troponin low-affinity sites
)
self.CMDN_tot: float = 50 # uM, Total myoplasmic calmodulin concentration
self.Km_CMDN: float = 0.238 # uM, Ca2 half-saturation constant for calmodulin
self.CMDN_tot: float = 50 # uM, Total myoplasmic calmodulin concentr.
self.Km_CMDN: float = 0.238 # uM, Ca2 half-sat const for calmodulin
self.nu_1: float = (
4.5 # 1/ms, Maximum RyR channel Ca2+ permeability Ca2+ leak rate constant from the NSR
4.5 # 1/ms, Max RyR chan Ca2+ perm. Ca2+ leak rate const from NSR
)
self.nu_2: float = 1.74e-5 # ms^(-1), Ca2+ leak rate const. from the NSR
self.nu_2: float = 1.74e-5 # ms^(-1), Ca2+ leak rate const. from NSR
self.nu_3: float = 0.45 # uM/ms, SR Ca2+ -ATPase maximum pupmp rate
self.Km_up: float = 0.5 # uM, Half-saturation constant for SR Ca2+ -ATPase pump
self.Km_up: float = 0.5 # uM, Half-sat const for SR Ca2+ -ATPase pump
self.km_p_ca: float = (
0.5 # uM, Ca2+ half-saturation constant for Ca2+ pump current
)
@ -84,7 +90,7 @@ class Model:
)
self.K_pc_max: float = (
0.23324 # 1/ms, Maximum time constant for Ca2+-induced inactivation
0.23324 # 1/ms, Maximum time constant for Ca2+-induced inact.
)
self.K_pc_half: float = (
20.0 # uM, Half-saturation constant for Ca2+-induced inactivation
@ -97,7 +103,7 @@ class Model:
self.Cao: float = 1130.0 # uM, Ca2+ outside the cell
self.gCaL: float = (
0.1729 # mS/uF, Specific maximum conductivity for L-type Ca2+ channel
0.1729 # mS/uF, Specific max conduct. for L-type Ca2+ channel
)
self.ECaL: float = 43.0 # mV, Reversal potential for L-type Ca2
self.V_ss: float = 1.485e-9 # uL, Dyadic aka subspace volume
@ -117,9 +123,9 @@ class Model:
800.0 # uM, Ca2 half-saturation constant for calsequestrin
)
self.k_a_positive: float = 0.006075 # uM^(-4)/ms, RyR Pc1 - Po1 rate constant
self.k_a_positive: float = 0.006075 # uM^(-4)/ms, RyR Pc1-Po1 rate
self.k_a_negative: float = 0.07125 # 1/ms, RyR Po1 - Pc1 rate constant
self.k_b_positive: float = 0.00405 # uM^(-3)/ms, RyR Po1 - Po2 rate constant
self.k_b_positive: float = 0.00405 # uM^(-3)/ms, RyR Po1 - Po2 rate
self.k_b_negative: float = 0.965 # 1/ms, RyR Po2 - Po1 rate constant
self.k_c_positive: float = 0.009 # 1/ms, RyR Po1 - Pc2 rate constant
self.k_c_negative: float = 0.0008 # 1/ms, RyR Pc2 - Po1 rate constant
@ -160,7 +166,7 @@ class Model:
Kpcf = 13.0 * (1 - np.exp(-((V + 14.5) ** 2) / 100))
alpha = ( # dimensionless parameter for L-type Ca2+ channel closed states
alpha = ( # dimensionless param. for L-type Ca2+ channel closed states
0.4
* np.exp((V + 12.0) / 10)
* (
@ -267,8 +273,10 @@ class Model:
P_C1 = 1 - (P_C2 + P_O1 + P_O2)
dP_O1dt = self.k_a_positive * (Cass) ** self.n_ryr * P_C1
-self.k_a_negative * P_O1 - self.k_b_positive * (Cass) ** self.m_ryr * P_O1
+self.k_b_negative * P_O2 - self.k_c_positive * P_O1 + self.k_c_negative * P_C2
-self.k_a_negative * P_O1
-self.k_b_positive * (Cass) ** self.m_ryr * P_O1
+self.k_b_negative * P_O2 - self.k_c_positive * P_O1
+self.k_c_negative * P_C2
dP_O2dt = (
self.k_b_positive * (Cass) ** self.m_ryr * P_O1 - self.k_b_negative * P_O2
@ -289,7 +297,8 @@ class Model:
"""
dCaidt = Bi * (J_leak + J_xfer - J_up - J_trpn
- (I_Cab - 2 * I_NaCa + I_pCa) * ((self.A_cap * self.C_mem)/(2 * self.V_myo * F)))
- (I_Cab - 2 * I_NaCa + I_pCa) * ((self.A_cap * self.C_mem)/
(2 * self.V_myo * F)))
"""
# J_rel_caf = self.nu_1 * (self.Ca_JSR - Cass) #lisatud ette ennetavalt
@ -308,8 +317,6 @@ class Model:
* ((self.A_cap * self.C_mem) / (2 * self.V_myo * F))
)
# Cass, Os, C2, C3, C4, I1, I2, I3, LTRPNCa, HTRPNCa, Ca_NSR, Ca_JSR, P_RyR, P_O1, P_O2, P_C2, Cai, FCa = states
return [
dCassdt,
dOsdt,
@ -444,6 +451,8 @@ if __name__ == "__main__":
initial_values = model.get_initial_values()
times = np.arange(0, 1000, 1.0)
states, V = model.solve(initial_values=initial_values, tspan=[0, 1000], dt=1.0, times=times)
states, V = model.solve(
initial_values=initial_values, tspan=[0, 1000], dt=1.0, times=times
)
model.plot_results(times, states, V)