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Copy pathModel_Figure_S8A_S8B.py
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Model_Figure_S8A_S8B.py
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# Marianne Catanho, UCSD mcatanho@ucsd.edu
# March 20, 2017
from pysb.integrate import odesolve
import numpy
import matplotlib.pyplot as plt
from model_pcb_production import model
def fig1(t,numofint):
# DECREASING BINDING HO-1/PCYA/FD showing species (k3,k9)
k1 = 1.228e-01
k2 = 1e-12
k3 = 5.68750000e-01
k4 = 1e-12
k5 = 2.22857143e-01
k6 = 4.75000000e-01
k7 = 1.82500000e-01
k8 = 1e-12
k9 = 2.5000000e-01
k10 = 1e-12
k11 = 0.122
k12 = 0.2667
k13 = 0.225
kdegpcb = 0.1567
# Initial Conditions
Heme_0 = 100
HO1_0 = 10
Fd_0 = 5
Fde_0 = Fd_0
PcyA_0 = 10
# param = numpy.array([k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, kdegpcb, Heme_0, HO1_0, Fd_0, PcyA_0, 1])
k3 = numpy.linspace(k3, 1e-3, numofint)
k9 = numpy.linspace(k9, 1e-3, numofint)
fig = plt.figure(figsize=(25,15))
ax = fig.add_subplot(1, 1, 1)
plt.rc('font', family='arial')
param = []
for i0 in range(0, numofint):
temp = numpy.array([k1, k2, k3[i0], k4, k5, k6, k7, k8, k9[i0], k10, k11, k12, k13, kdegpcb, Heme_0, HO1_0, Fd_0, PcyA_0, 1])
param.append(temp)
param = numpy.asarray(param)
print param.shape
for i in param:
x = odesolve(model, t, i)
ax.plot(t, x['__s13'], color='red', marker='o', ls='solid', fillstyle='full', markersize=15,
markerfacecolor='red',
markevery=5, markeredgewidth=2, linewidth=2.0, label='Reduced & Oxidized')
x = odesolve(model, t, param[0])
# ax.plot(t, x['__s13'], color='blue', marker='^', ls='solid', fillstyle='full', markersize=15,
# markerfacecolor='blue',
# markevery=5, markeredgewidth=2, linewidth=2.0, label='Reduced & Oxidized')
ax.set_xlabel('Time (h)', fontsize=28, fontweight='bold', labelpad=5)
ax.set_ylabel('PCB concentration (RU)', fontsize=28, fontweight='bold', labelpad=5)
ax.tick_params(axis='both', labelsize=20, pad=5)
ax.tick_params(width=3, length=20)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.yaxis.set_ticks_position('left')
ax.xaxis.set_ticks_position('bottom')
for axis in ['bottom', 'left']:
ax.spines[axis].set_linewidth(8)
plt.yticks(numpy.arange(0, 3, 1.), fontweight='bold')
plt.xticks(numpy.arange(0, 80.5, 20), fontweight='bold')
plt.show()
plt.show()
def fig2(t):
k1 = 1.228e-01
k2 = 1e-12
k3 = 5.68750000e-01
k4 = 1e-12
k5 = 2.22857143e-01
k6 = 4.75000000e-01
k7 = 1.82500000e-01
k8 = 1e-12
k9 = 2.5000000e-01
k10 = 1e-12
k11 = 0.122
k12 = 0.2667
k13 = 0.225
kdegpcb = 0.1567
# Initial Conditions
Heme_0 = 100
HO1_0 = 10
Fd_0 = 5
Fde_0 = Fd_0
PcyA_0 = 10
# param = numpy.array([k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, kdegpcb, Heme_0, HO1_0, Fd_0, PcyA_0, 1])
fig = plt.figure(figsize=(25,15))
ax = fig.add_subplot(1, 1, 1)
plt.rc('font', family='arial')
param = numpy.array([k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, k12, k13, kdegpcb, Heme_0, HO1_0, Fd_0, PcyA_0, 1])
x=odesolve(model,t,param)
ax.plot(t, x['__s13'], color='red', marker='o', ls='solid', fillstyle='full', markersize=15, markerfacecolor='red',
markevery=5, markeredgewidth=2, linewidth=2.0, label='')
ax.set_xlabel('Time (h)', fontsize=28, fontweight='bold', labelpad=5)
ax.set_ylabel('PCB concentration (RU)', fontsize=28, fontweight='bold', labelpad=5)
ax.tick_params(axis='both', labelsize=20, pad=5)
ax.tick_params(width=3, length=20)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.yaxis.set_ticks_position('left')
ax.xaxis.set_ticks_position('bottom')
for axis in ['bottom', 'left']:
ax.spines[axis].set_linewidth(8)
plt.yticks(numpy.arange(0.9, 3, 1.), fontweight='bold')
plt.xticks(numpy.arange(0, 80.5, 20), fontweight='bold')
plt.show()
def fig3(t,numofint):
# DECREASING RENEWAL FD:FNR RATE (k13)
k1 = 1.228e-01
k2 = 1e-12
k3 = 5.68750000e-01
k4 = 1e-12
k5 = 2.22857143e-01
k6 = 4.75000000e-01
k7 = 1.82500000e-01
k8 = 1e-12
k9 = 2.5000000e-01
k10 = 1e-12
k11 = 0.122
k12 = 0.2667
k13 = 0.225
kdegpcb = 0.1567
kdegpcb = 1.87e-1
# Initial Conditions
Heme_0 = 100
HO1_0 = 10
Fd_0 = 5
Fde_0 = Fd_0
PcyA_0 = 10
param = []
k13 = numpy.linspace(k13, 1e-3, numofint)
for i0 in range(0,numofint):
temp = numpy.array([k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, k12, k13[i0], kdegpcb, Heme_0, HO1_0, Fd_0, PcyA_0, 1])
param.append(temp)
param = numpy.asarray(param)
plt.rc('font', family='arial')
fig = plt.figure(figsize=(25,15))
ax = fig.add_subplot(1, 1, 1)
for i in param:
x=odesolve(model,t,i)
ax.plot(t, x['__s13'], color='red', marker='o', ls='solid', fillstyle='full', markersize=15, markerfacecolor='red',
markevery=5, markeredgewidth=2, linewidth=2.0, label='')
ax.set_xlabel('Time (h)', fontsize=28, fontweight='bold',labelpad=5)
ax.set_ylabel('PCB concentration (RU)', fontsize=28, fontweight='bold',labelpad=5)
ax.tick_params(axis='both', labelsize=28, pad=5)
ax.tick_params(width=3,length=20)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.yaxis.set_ticks_position('left')
ax.xaxis.set_ticks_position('bottom')
for axis in ['bottom','left']:
ax.spines[axis].set_linewidth(8)
plt.yticks(numpy.arange(0,3.1,1.0), fontweight='bold')
plt.xticks(numpy.arange(0,80.5,20),fontweight='bold')
plt.show()
def fig4(t):
k1 = 1.228e-01
k2 = 1e-12
k3 = 5.68750000e-01
k4 = 1e-12
k5 = 2.22857143e-01
k6 = 4.75000000e-01
k7 = 1.82500000e-01
k8 = 1e-12
k9 = 2.5000000e-01
k10 = 1e-12
k11 = 0.122
k12 = 0.2667
k13 = 0.225
kdegpcb = 0.1567
# Initial Conditions
Heme_0 = 100
HO1_0 = 10
Fd_0 = 5
Fde_0 = Fd_0
PcyA_0 = 10
param4E = numpy.array([k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, k12, k13, kdegpcb, Heme_0, HO1_0, Fd_0, PcyA_0, 1])
plt.rc('font', family='arial')
fig = plt.figure(figsize=(25,15))
ax = fig.add_subplot(1, 1, 1)
#plt.rc('font', family='arial')
x4E=odesolve(model,t,param4E)
ax.plot(t, x4E['__s13'], color='red', marker='o', ls='solid', fillstyle='full', markersize=15, markerfacecolor='red',
markevery=5, markeredgewidth=2, linewidth=2.0, label='4E')
# 2E
param2E = numpy.array([k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, k12, k13, kdegpcb, Heme_0, HO1_0, 0, PcyA_0, 1])
x=odesolve(model,t,param2E)
ax.plot(t, x['__s13'], color='blue', marker='v', ls='solid', fillstyle='full', markersize=15, markerfacecolor='blue',
markevery=5, markeredgewidth=2, linewidth=2.0, label='2E')
ax.set_xlabel('Time (h)', fontsize=28, fontweight='bold',labelpad=5)
ax.set_ylabel('PCB concentration (RU)', fontsize=28, fontweight='bold',labelpad=5)
ax.tick_params(axis='both', labelsize=28, pad=5)
plt.legend(fontsize=28, loc=5)
ax.tick_params(width=3,length=20)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.yaxis.set_ticks_position('left')
ax.xaxis.set_ticks_position('bottom')
for axis in ['bottom','left']:
ax.spines[axis].set_linewidth(8)
plt.yticks(numpy.arange(0.,3.1,1.0), fontweight='bold')
plt.xticks(numpy.arange(0,80.5,20),fontweight='bold')
plt.show()
def main():
t = numpy.linspace(0,100,100)
# SPECIES SPECIFICITY
fig1(t,40)
#
# # NORMAL MODEL
# fig2(t)
# DECREASING RENEWAL FD:FNR RATE
fig3(t,40)
# # 2E vs 4E
# fig4(t)
main()