ralf/Calcium_Model
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minor adjustments after trial and error

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ralf 2024-07-16 15:06:50 +03:00
parent d76122ee7b
commit 48bd4ffaf2
2 changed files with 13 additions and 16 deletions
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16
Model.py
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@ -197,13 +197,9 @@ class Model:
# Bi = (1 + (self.CMDN_tot * self.Km_CMDN)/(self.Km_CMDN+(Cai))**2)**(-1) # Bi = (1 + (self.CMDN_tot * self.Km_CMDN)/(self.Km_CMDN+(Cai))**2)**(-1)
# Bss = 1 / ((self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cass) ** 2) # Bss = 1 / ((self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cass) ** 2)
Bi = 1 / ( Bi = 1 / (1 + (self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cai) ** 2)
1 + (self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cai) ** 2
)
Bss = 1 / ( Bss = 1 / (1 + (self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cass) ** 2)
1 + (self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cass) ** 2
)
J_xfer = (Cass - Cai) / self.tau_xfer J_xfer = (Cass - Cai) / self.tau_xfer
@ -216,9 +212,7 @@ class Model:
J_trpn = ( J_trpn = (
self.k_htrpn_positive * Cai * (self.HTRPN_tot - HTRPNCa) self.k_htrpn_positive * Cai * (self.HTRPN_tot - HTRPNCa)
- self.k_htrpn_negative * HTRPNCa - self.k_htrpn_negative * HTRPNCa
+ self.k_ltrpn_positive + self.k_ltrpn_positive * Cai * (self.LTRPN_tot - LTRPNCa)
* Cai
* (self.LTRPN_tot - LTRPNCa)
- self.k_ltrpn_negative * LTRPNCa - self.k_ltrpn_negative * LTRPNCa
) )
@ -258,9 +252,7 @@ class Model:
P_C1 = 1 - (P_C2 + P_O1 + P_O2) P_C1 = 1 - (P_C2 + P_O1 + P_O2)
dP_O1dt = ( dP_O1dt = self.k_a_positive * (Cass) ** self.n_ryr * P_C1
self.k_a_positive * (Cass) ** self.n_ryr * P_C1
)
-self.k_a_negative * P_O1 - self.k_a_positive * (Cass) ** self.m_ryr * P_O1 -self.k_a_negative * P_O1 - self.k_a_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_b_negative * P_O2 - self.k_c_positive * P_O1 + self.k_c_negative * P_C2

11
fitter.py
View File

@ -26,7 +26,7 @@ class Fitter:
self.dt = 1 # 1.0 self.dt = 1 # 1.0
self.time_points = np.arange(*self.tspan, self.dt) self.time_points = np.arange(*self.tspan, self.dt)
model=Model() model = Model()
self.initial_values = model.get_initial_values() self.initial_values = model.get_initial_values()
self.iteration = 0 # least squares iteration counter self.iteration = 0 # least squares iteration counter
@ -61,7 +61,12 @@ class Fitter:
model.K_pc_half = K_pc_half model.K_pc_half = K_pc_half
model.tau_xfer = tau_xfer model.tau_xfer = tau_xfer
model.solve(times=self.time_points, tspan=self.tspan, dt=self.dt, initial_values=self.initial_values) model.solve(
times=self.time_points,
tspan=self.tspan,
dt=self.dt,
initial_values=self.initial_values,
)
_calc_curr = model.calculated_current() _calc_curr = model.calculated_current()
calculated_current = ( calculated_current = (
@ -207,7 +212,7 @@ if __name__ == "__main__":
eid_cleaned = re.sub( eid_cleaned = re.sub(
r"[^\w.-]", "", eid r"[^\w.-]", "", eid
) # Eemalda kõik eritähed ja jääb alles alphanumbrilised tähed, sidekriipsud ja punktid ) # Eemaldab eritahed
fig.savefig(f"plot_{eid_cleaned}.png") fig.savefig(f"plot_{eid_cleaned}.png")
fig.savefig(f"plot_{eid_cleaned}.pdf") fig.savefig(f"plot_{eid_cleaned}.pdf")