Applied good practice tips; Fixed typos in expressions in model.py
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ralf
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139
Model.py
139
Model.py
@ -11,41 +11,45 @@ RT = R * T
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class Model:
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def __init__(self):
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self.A_cap = 1.534e-4 # cm^2, Capacitive membrane area
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self.C_mem = 1.0 # uF/cm2 Specific membrane capacitance
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self.V_myo = 25.84e-6 # uL, Myoplasmic volume
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self.current2flux = self.A_cap * self.C_mem / 2 / F #
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self.A_cap: float = 1.534e-4 # cm^2, Capacitive membrane area
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self.C_mem: float = 1.0 # uF/cm2 Specific membrane capacitance
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self.V_myo: float = 25.84e-6 # uL, Myoplasmic volume
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self.current2flux: float = self.A_cap * self.C_mem / 2 / F #
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self.period = 1000 # ms, pulse period
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self.V_mem_rest = -80.0 # mV, resting membrane potential
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self.period: float = 1000 # ms, pulse period
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self.V_mem_rest: float = -80.0 # mV, resting membrane potential
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self.Nai = 11000 # uM, Myoplasmic Na+ concentration
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self.Nao = 150000 # uM, Extracellular Na+ concentration
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self.Nai: float = 11000 # uM, Myoplasmic Na+ concentration
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self.Nao: float = 150000 # uM, Extracellular Na+ concentration
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self.eta = 0.35 # Controls voltage dependance of Na/Ca2+ exchange
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self.eta: float = 0.35 # Controls voltage dependance of Na/Ca2+ exchange
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self.km_Na = 87500 # uM, Na+ half-saturation constant for Na+/Ca2+ exchange
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self.k_sat = (
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self.km_Na: float = (
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87500 # uM, Na+ half-saturation constant for Na+/Ca2+ exchange
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)
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self.k_sat: float = (
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0.1 # Na+/Ca2+ exchange saturation factor at very negative potentials
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)
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self.km_Ca = (1380,) # uM, Ca2+ half-saturation constant for Na+/Ca2+ exchange
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self.k_Na_Ca = 292.8 # pA/pF, Scaling factor of Na2+/Ca2+ exchange
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self.km_Ca: float = (
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1380 # uM, Ca2+ half-saturation constant for Na+/Ca2+ exchange
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)
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self.k_Na_Ca: float = 292.8 # pA/pF, Scaling factor of Na2+/Ca2+ exchange
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self.I_max_pCa = 1.0 # pA/pF, Maximum Ca2+ pump current
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self.I_max_pCa: float = 1.0 # pA/pF, Maximum Ca2+ pump current
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# self.Cai = 0.1 # uM, Cytoplasmic Ca2+ concentration fixed at this point
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self.LTRPN_tot = (
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self.LTRPN_tot: float = (
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70.0 # uM, Total myoplasmic troponin low-affinity site concentration
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)
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self.HTRPN_tot = (
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self.HTRPN_tot: float = (
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140.0 # uM, Total myoplasmic troponin high-affinity site concentration
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)
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# self.LTRPNCa = 11.2684 # uM, Concentration Ca2+ bound low-affinity troponin-binding sites
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# self.HTRPNCa = 125.290 # uM, Concentration Ca2+ bound high-affinity troponin-binding sites
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self.k_htrpn_positive = (
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self.k_htrpn_positive: float = (
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0.00237 # uM^(-1)/ms, Ca2+ on rate const. for troponin high-affinity sites
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)
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self.k_htrpn_negative = (
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@ -55,65 +59,78 @@ class Model:
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self.k_ltrpn_positive = (
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0.0327 # uM^(-1)/ms, Ca2+ on rate const. for troponin low-affinity sites
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)
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self.k_ltrpn_negative = (
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self.k_ltrpn_negative: float = (
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0.0196 # ms, Ca2+ off rate const. for troponin low-affinity sites
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)
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self.CMDN_tot = 50 # uM, Total myoplasmic calmodulin concentration
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self.Km_CMDN = 0.238 # uM, Ca2 half-saturation constant for calmodulin
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self.CMDN_tot: float = 50 # uM, Total myoplasmic calmodulin concentration
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self.Km_CMDN: float = 0.238 # uM, Ca2 half-saturation constant for calmodulin
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self.nu_1 = 4.5 # 1/ms, Maximum RyR channel Ca2+ permeability Ca2+ leak rate constant from the NSR
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self.nu_2 = 1.74e-5 # ms^(-1), Ca2+ leak rate const. from the NSR
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self.nu_3 = 0.45 # uM/ms, SR Ca2+ -ATPase maximum pupmp rate
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self.nu_1: float = (
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4.5 # 1/ms, Maximum RyR channel Ca2+ permeability Ca2+ leak rate constant from the NSR
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)
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self.nu_2: float = 1.74e-5 # ms^(-1), Ca2+ leak rate const. from the NSR
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self.nu_3: float = 0.45 # uM/ms, SR Ca2+ -ATPase maximum pupmp rate
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self.Km_up = 0.5 # uM, Half-saturation constant for SR Ca2+ -ATPase pump
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self.km_p_ca = 0.5 # uM, Ca2+ half-saturation constant for Ca2+ pump current
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self.Km_up: float = 0.5 # uM, Half-saturation constant for SR Ca2+ -ATPase pump
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self.km_p_ca: float = (
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0.5 # uM, Ca2+ half-saturation constant for Ca2+ pump current
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)
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# self.Ca_NSR = 1299.50 # uM,NSR Ca2+ concentration
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self.tau_xfer = 8.0 # ms, Time constant for transfer from subspace to myoplasm
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self.tau_xfer: float = (
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8.0 # ms, Time constant for transfer from subspace to myoplasm
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)
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self.K_pc_max = (
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self.K_pc_max: float = (
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0.23324 # 1/ms, Maximum time constant for Ca2+-induced inactivation
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)
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self.K_pc_half = (
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self.K_pc_half: float = (
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20.0 # uM, Half-saturation constant for Ca2+-induced inactivation
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)
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self.Kpcb = 0.0005 # 1/ms, Voltage-insensitive rate constant for inactivation
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self.km_Ca = 1380 # uM, Ca2+ half-saturation constant for Na+/Ca2+ exchange
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self.Kpcb: float = (
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0.0005 # 1/ms, Voltage-insensitive rate constant for inactivation
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)
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self.Gcab = 0.000367 # mS/uF
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self.Gcab: float = 0.000367 # mS/uF
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self.Cao = 1130.0 # uM, Ca2+ outside the cell
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self.gCaL = (
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self.Cao: float = 1130.0 # uM, Ca2+ outside the cell
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self.gCaL: float = (
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0.1729 # mS/uF, Specific maximum conductivity for L-type Ca2+ channel
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)
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self.ECaL = 43.0 # mV, Reversal potential for L-type Ca2
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self.V_ss = 1.485e-9 # uL, Dyadic aka subspace volume
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self.ECaL: float = 43.0 # mV, Reversal potential for L-type Ca2
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self.V_ss: float = 1.485e-9 # uL, Dyadic aka subspace volume
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# self.Ca_JSR = 1299.50 # uM, JSR Ca2+ concentration
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self.F_tot = 25 # uM, total concentration of Fluo-4
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self.k_on = 0.1 # 1/uM * 1/ms, Fluo-4 reaction rate constant
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self.k_off = 0.11 # 1/ms, Fluo-4 reaction rate constant 2
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self.F_tot: float = 25 # uM, total concentration of Fluo-4
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self.k_on: float = 0.1 # 1/uM * 1/ms, Fluo-4 reaction rate constant
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self.k_off: float = 0.11 # 1/ms, Fluo-4 reaction rate constant 2
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self.V_NSR = 2.098e-6 # ul, Network SR volume
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self.tau_tr = 20 # ms, Time const for transfer from NSR to JSR
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self.V_NSR: float = 2.098e-6 # ul, Network SR volume
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self.tau_tr: float = 20 # ms, Time const for transfer from NSR to JSR
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self.CSQN_tot = 15000.0 # uM, total junctional SR calsequestrin concentration
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self.Km_CSQN = 800.0 # uM, Ca2 half-saturation constant for calsequestrin
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self.CSQN_tot: float = (
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15000.0 # uM, total junctional SR calsequestrin concentration
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)
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self.Km_CSQN: float = (
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800.0 # uM, Ca2 half-saturation constant for calsequestrin
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)
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self.k_a_positive = 0.006075 # uM^(-4)/ms, RyR Pc1 - Po1 rate constant
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self.k_a_negative = 0.07125 # 1/ms, RyR Po1 - Pc1 rate constant
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self.k_b_positive = 0.00405 # uM^(-3)/ms, RyR Po1 - Po2 rate constant
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self.k_b_negative = 0.965 # 1/ms, RyR Po2 - Po1 rate constant
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self.k_c_positive = 0.009 # 1/ms, RyR Po1 - Pc2 rate constant
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self.k_c_negative = 0.0008 # 1/ms, RyR Pc2 - Po1 rate constant
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self.k_a_positive: float = 0.006075 # uM^(-4)/ms, RyR Pc1 - Po1 rate constant
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self.k_a_negative: float = 0.07125 # 1/ms, RyR Po1 - Pc1 rate constant
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self.k_b_positive: float = 0.00405 # uM^(-3)/ms, RyR Po1 - Po2 rate constant
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self.k_b_negative: float = 0.965 # 1/ms, RyR Po2 - Po1 rate constant
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self.k_c_positive: float = 0.009 # 1/ms, RyR Po1 - Pc2 rate constant
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self.k_c_negative: float = 0.0008 # 1/ms, RyR Pc2 - Po1 rate constant
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self.n_ryr = 4 # RyR Ca2+ cooperativity parameter Pc1 - Po1
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self.m_ryr = 3 # RyR Ca2+ cooperativity parameter Po1 - Po2
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self.n_ryr: int = 4 # RyR Ca2+ cooperativity parameter Pc1 - Po1
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self.m_ryr: int = 3 # RyR Ca2+ cooperativity parameter Po1 - Po2
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self.I_CaL_max = 7.0 # pA/pF, normalization constant for L-type Ca2+ current
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self.V_JSR = 0.12e-6 # ul, Junctional SR volume
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self.I_CaL_max: float = (
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7.0 # pA/pF, normalization constant for L-type Ca2+ current
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)
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self.V_JSR: float = 0.12e-6 # ul, Junctional SR volume
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def ode_system(self, t, states):
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@ -194,9 +211,6 @@ class Model:
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- 4 * beta * self.Kpcb * I3
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)
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# Bi = (1 + (self.CMDN_tot * self.Km_CMDN)/(self.Km_CMDN+(Cai))**2)**(-1)
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# Bss = 1 / ((self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cass) ** 2)
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Bi = 1 / (1 + (self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cai) ** 2)
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Bss = 1 / (1 + (self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cass) ** 2)
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@ -253,7 +267,7 @@ class Model:
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P_C1 = 1 - (P_C2 + P_O1 + P_O2)
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dP_O1dt = self.k_a_positive * (Cass) ** self.n_ryr * P_C1
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-self.k_a_negative * P_O1 - self.k_a_positive * (Cass) ** self.m_ryr * P_O1
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-self.k_a_negative * P_O1 - self.k_b_positive * (Cass) ** self.m_ryr * P_O1
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+self.k_b_negative * P_O2 - self.k_c_positive * P_O1 + self.k_c_negative * P_C2
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dP_O2dt = (
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@ -269,7 +283,7 @@ class Model:
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dOsdt = alpha * C4 - 4 * beta * Os + self.Kpcb * I1
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-gamma * Os + 0.001 * (alpha * I2 - Kpcf * Os)
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ECaN = (R * T) / F * np.log(self.Cao / Cai)
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ECaN = (R * T) / (2 * F) * np.log(self.Cao / Cai)
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I_Cab = self.Gcab * (V - ECaN)
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@ -326,8 +340,10 @@ class Model:
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return np.where((t0 + n <= t) & (t < t1 + n), v1, self.V_mem_rest)
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def get_initial_values(self):
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Cai_0 = 0.11712 # Cai
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FCa_0 = (self.k_on * self.F_tot * Cai_0) / (self.k_on * Cai_0 + self.k_off)
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Cai_0: float = 0.11712 # Cai
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FCa_0: float = (self.k_on * self.F_tot * Cai_0) / (
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self.k_on * Cai_0 + self.k_off
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)
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return [
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Cai_0, # Cass
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0.930308e-18, # Os,
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@ -362,9 +378,6 @@ class Model:
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)
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r.set_initial_value(initial_values, times[0])
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#states = np.array([[0.0] * times.size] * len(initial_values))
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#states[:, 0] = initial_values
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states = np.zeros((len(initial_values), times.size))
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states[:, 0] = initial_values
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@ -427,7 +440,7 @@ if __name__ == "__main__":
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Cai_0 = 0.11712 # Cai
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FCa_0 = (model.k_on * model.F_tot * Cai_0) / (model.k_on * Cai_0 + model.k_off)
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print(FCa_0)
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# print(FCa_0)
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# 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
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initial_values = [
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Binary file not shown.
@ -23,13 +23,13 @@ class Fitter:
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self.fit_results = {}
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self.tspan = [0, 1000]
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self.dt = 1 # 1.0
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self.dt: float = 1 # 1.0
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self.time_points = np.arange(*self.tspan, self.dt)
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model = Model()
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self.initial_values = model.get_initial_values()
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self.iteration = 0 # least squares iteration counter
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self.iteration: int = 0 # least squares iteration counter
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t0, t1 = self.current_fit_range = current_fit_range
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self.current_time_indecies = (t0 <= self.time_points) & (self.time_points <= t1)
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@ -104,8 +104,8 @@ class Fitter:
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m = self.model()
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K_pc_half = m.K_pc_half
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tau_xfer = m.tau_xfer
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tau_RC = 1.5
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offset = 0
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tau_RC: float = 1.5
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offset: float = 0
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d = self.data
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init_parameters = np.array(
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