def solve_and_plot(self, SL, Ca_amplitude, tau1, tau2, kn_p, kp_n, f_app,
g_app, h_f, h_b, gxb):
t = np.linspace(0, 1000, 101)
p = rice.init_parameter_values(SLmin=2.5,
Ca_amplitude=Ca_amplitude,
tau1=tau1,
tau2=tau2,
kn_p=kn_p,
kp_n=kp_n,
fapp=f_app,
gapp=g_app,
hf=h_f,
hb=h_b,
gxb=gxb)
force_ind = rice.monitor_indices("active")
ca_ind = rice.monitor_indices("Cai")
init = rice.init_state_values(SL=SL)
s = odeint(rice.rhs, init, t, (p, ))
force = []
cai = []
for tn, sn in zip(t, s):
m = rice.monitor(sn, tn, p)
force.append(m[force_ind])
cai.append(m[ca_ind])
plt.figure(1)
plt.plot(t, cai)
plt.figure(2)
plt.plot(t, force)
plt.show()
def solve_and_plot(self, SL, Fmax, Ca50, n):
"""
Solve the model to steady state for Ca values in [0,10], for a
given value of SL, and plot the resulting F-Ca curve.
"""
t = np.linspace(0, 100, 101)
Cai = np.linspace(0, 10, 101)
force_index = rice.monitor_indices("active")
init = rice.init_state_values(SL=SL)
Fss = np.empty_like(Cai)
for i in range(len(Cai)):
p = (rice.init_parameter_values(start_time=1000,
Ca_diastolic=Cai[i],
SLmin=2.5), )
s = odeint(rice.rhs, init, t, p)
m = rice.monitor(s[-1], t[-1], p[0])
Fss[i] = m[force_index]
plt.semilogx(Cai, Fss)
plt.ylabel('Normalized force at steady state')
plt.xlabel('Ca concentration')
#plot one dynamic Hill curve
Fh = Fmax * np.power(Cai, n) / (math.pow(Ca50, n) + np.power(Cai, n))
plt.plot(Cai, Fh, ':')
#plot two Hill curves for the extreme SL values
Fmax = 0.17
Ca50 = 3.0
n = 7.6
Fh = Fmax * np.power(Cai, n) / (math.pow(Ca50, n) + np.power(Cai, n))
plt.plot(Cai, Fh, '--')
Fmax = 0.92
Ca50 = 0.87
Fh = Fmax * np.power(Cai, n) / (math.pow(Ca50, n) + np.power(Cai, n))
plt.plot(Cai, Fh, '--')
plt.show()
def solve_and_plot(self, SL, Fmax, Ca50, n):
"""
Solve the model to steady state for Ca values in [0,10], for a
given value of SL, and plot the resulting F-Ca curve.
"""
t = np.linspace(0,100,101)
Cai = np.linspace(0,10,101)
force_index = rice.monitor_indices("active")
init = rice.init_state_values(SL=SL)
Fss = np.empty_like(Cai)
for i in range(len(Cai)):
p = (rice.init_parameter_values(start_time=1000,Ca_diastolic=Cai[i],SLmin=2.5),)
s = odeint(rice.rhs,init,t,p)
m = rice.monitor(s[-1],t[-1],p[0])
Fss[i] = m[force_index]
plt.semilogx(Cai,Fss)
plt.ylabel('Normalized force at steady state')
plt.xlabel('Ca concentration')
#plot one dynamic Hill curve
Fh = Fmax*np.power(Cai,n)/(math.pow(Ca50,n)+np.power(Cai,n))
plt.plot(Cai,Fh,':')
#plot two Hill curves for the extreme SL values
Fmax = 0.17
Ca50 = 3.0
n = 7.6
Fh = Fmax*np.power(Cai,n)/(math.pow(Ca50,n)+np.power(Cai,n))
plt.plot(Cai,Fh,'--')
Fmax =0.92
Ca50= 0.87
Fh = Fmax*np.power(Cai,n)/(math.pow(Ca50,n)+np.power(Cai,n))
plt.plot(Cai,Fh,'--')
plt.show()
def solve_and_plot(self,SL,Ca_amplitude,tau1,tau2,kn_p,kp_n,f_app,g_app,h_f,h_b,gxb):
t = np.linspace(0,1000,101)
p = rice.init_parameter_values(SLmin=2.5, Ca_amplitude=Ca_amplitude, tau1=tau1, tau2=tau2,
kn_p=kn_p, kp_n=kp_n, fapp=f_app, gapp=g_app,
hf=h_f,hb=h_b,gxb=gxb)
force_ind = rice.monitor_indices("active")
ca_ind = rice.monitor_indices("Cai")
init = rice.init_state_values(SL=SL)
s = odeint(rice.rhs,init,t,(p,))
force = []
cai = []
for tn,sn in zip(t,s):
m = rice.monitor(sn,tn,p)
force.append(m[force_ind])
cai.append(m[ca_ind])
plt.figure(1)
plt.plot(t,cai)
plt.figure(2)
plt.plot(t,force)
plt.show()
hbT_index = rice.monitor_indices("hbT")
fappT_index = rice.monitor_indices("fappT")
active_index = rice.monitor_indices("active")
lambda_solution = []
l_list = []
Ta_list = []
t_list = []
for i, t in enumerate(global_time[:-1]):
# Set initial values
t_local = np.linspace(t, global_time[i + 1], step + 1)
print t
if i == 0:
p = (rice.init_parameter_values(SLmin=2.5), )
init = rice.init_state_values()
else:
p = (rice.init_parameter_values(SLmin=2.5),
) #SL=lambda_prev*SL0, dExtensionRatiodt=dldt),)
init = rice.init_state_values(SL=lambda_prev * SL0,
intf=intf_prev,
TRPNCaH=TRPNCaH_prev,
TRPNCaL=TRPNCaL_prev,
N=N_prev,
N_NoXB=N_NoXB_prev,
P_NoXB=P_NoXB_prev,
XBpostr=XBpostr_prev,
XBprer=XBprer_prev,
xXBpostr=xXBpostr_prev,
xXBprer=xXBprer_prev)
import rice_model_2008 as rice
from scipy.integrate import odeint
import numpy as np
import pylab
t = np.linspace(0,650,101)
init = rice.init_state_values()
SL_ind = rice.state_indices("SL")
Cai = np.linspace(0,10,101)
sl_ss = []
for ca in Cai:
p = (rice.init_parameter_values(start_time=1000,Ca_diastolic=ca,SEon=0.0),)
s = odeint(rice.rhs,init,t,p)
sl_ss.append(s[-1,SL_ind])
pylab.ylim([1.4,2.0])
pylab.ylabel("SL (micrometers)")
pylab.xlabel("[Ca] (microM)")
pylab.semilogx(Cai,sl_ss)
pylab.show()
"""pylab.ylim([1.4,2.0])
pylab.ylabel("SL (micrometers)")
pylab.xlim([550,1000])
pylab.xlabel("time (ms)")
pylab.legend()
#compute fitted Hill velocity:
f_hill = linspace(0,0.8,101)
a_hill = 0.16
b_hill = 2.4
import rice_model_2008 as rice
from scipy.integrate import odeint
import numpy as np
import pylab
#isometric for t<650:
t1 = np.linspace(0, 650, 101)
init = rice.init_state_values(SL=2.2)
SL_ind = rice.state_indices("SL")
p = (rice.init_parameter_values(start_time=1000, Ca_diastolic=10, SLmin=2.5), )
s1 = odeint(rice.rhs, init, t1, p)
pylab.plot(t1, s1[:, SL_ind])
#release against different afterload values:
al = np.linspace(0, 0.8, 9)
v = []
intf_ind = rice.state_indices('intf')
init = s1[-1, :]
init[intf_ind] = 0.0
t2 = np.linspace(650, 1000, 351)
for load in al:
p = (rice.init_parameter_values(start_time=1000,
Ca_diastolic=10,
SEon=0,
fixed_afterload=load), )
s2 = odeint(rice.rhs, init, t2, p)
v.append(-1000 * (s2[50, SL_ind] - init[SL_ind]) / 50)
pylab.plot(t2, s2[:, SL_ind], label=str(load))
#set correct axes for figure 1:
pylab.ylim([1.4, 2.3])