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boundaryBath.py
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boundaryBath.py
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from values import *
import numpy as np
from defs import *
def female_conc(cell, i):
# Concentrations of K, Cl are lower in female rat.
cell.conc[1,5]=cell.conc[1,5]-1
cell.conc[2,5]=cell.conc[2,5]-1
if cell.segment == 'PT':
if cell.preg == 'mid':
# conc of Na, K, Cl, HCO3 different in MP rat plasma
cell.conc[0,0] = cell.conc[0,0]*0.95
cell.conc[1,0] = cell.conc[1,0]*1.0 #no change in K in MP
cell.conc[2,0] = cell.conc[2,0]*0.95
cell.conc[3,0] = cell.conc[3,0]*0.95
# also change in starting for bath
cell.conc[0,5] = cell.conc[0,0]
cell.conc[1,5] = cell.conc[1,0]
cell.conc[2,5] = cell.conc[2,0]
cell.conc[3,5] = cell.conc[3,0]
elif cell.preg == 'late':
# conc of Na, K, Cl, HCO3 different in LP rat plasma
cell.conc[0,0] = cell.conc[0,0]*0.95
cell.conc[1,0] = cell.conc[1,0]*1.15 # upregulated K in LP
cell.conc[2,0] = cell.conc[2,0]*0.95
cell.conc[3,0] = cell.conc[3,0]*0.9645
# also change in starting for bath
cell.conc[0,5] = cell.conc[0,0]
cell.conc[1,5] = cell.conc[1,0]
cell.conc[2,5] = cell.conc[2,0]
cell.conc[3,5] = cell.conc[3,0]
def boundaryBath(cell,i):
if cell.species == 'rat':
if cell.inhib == 'NHE3-50':
cell.oi[0] = TotSodOI_noinhib
cell.oi[1] = TotPotOI_noinhib
cell.oi[2] = TotCloOI_noinhib
cell.oi[8] = TotureaOI_50inhib
cell.pap[0] = TotSodPap_50inhib
cell.pap[1] = TotPotPap_noinhib
cell.pap[2] = TotCloPap_50inhib
cell.pap[8] = TotureaPap_50inhib
elif cell.inhib == 'NHE3-80':
cell.oi[0] = TotSodOI_noinhib
cell.oi[1] = TotPotOI_noinhib
cell.oi[2] = TotCloOI_noinhib
cell.oi[8] = TotureaOI_80inhib
cell.pap[0] = TotSodPap_80inhib
cell.pap[1] = TotPotPap_80inhib
cell.pap[2] = TotCloPap_80inhib
cell.pap[8] = TotureaPap_80inhib
elif cell.inhib == 'NKCC2-70':
if cell.preg == 'non':
cell.oi[0] = TotSodOI_70NKCCinhib
cell.oi[1] = TotPotOI_70NKCCinhib
cell.oi[2] = TotCloOI_70NKCCinhib
cell.oi[8] = TotureaOI_70NKCCinhib
cell.pap[0] = TotSodPap_70NKCCinhib
cell.pap[1] = TotPotPap_70NKCCinhib
cell.pap[2] = TotCloPap_70NKCCinhib
cell.pap[8] = TotureaPap_70NKCCinhib
elif cell.preg == 'mid':
cell.oi[0] = TotSodOI_MP_70NKCCinhib
cell.oi[1] = TotPotOI_MP_70NKCCinhib
cell.oi[2] = TotCloOI_MP_70NKCCinhib
cell.oi[8] = TotureaOI_70NKCCinhib
cell.pap[0] = TotSodPap_MP_70NKCCinhib
cell.pap[1] = TotPotPap_MP_70NKCCinhib
cell.pap[2] = TotCloPap_MP_70NKCCinhib
cell.pap[8] = TotureaPap_70NKCCinhib
elif cell.preg == 'late':
cell.oi[0] = TotSodOI_LP_70NKCCinhib
cell.oi[1] = TotPotOI_LP_70NKCCinhib
cell.oi[2] = TotCloOI_LP_70NKCCinhib
cell.oi[8] = TotureaOI_70NKCCinhib
cell.pap[0] = TotSodPap_LP_70NKCCinhib
cell.pap[1] = TotPotPap_LP_70NKCCinhib
cell.pap[2] = TotCloPap_LP_70NKCCinhib
cell.pap[8] = TotureaPap_70NKCCinhib
elif cell.inhib == 'NKCC2-100':
if cell.preg == 'non':
cell.oi[0] = TotSodOI_100NKCCinhib
cell.oi[1] = TotPotOI_100NKCCinhib
cell.oi[2] = TotCloOI_100NKCCinhib
cell.oi[8] = TotureaOI_100NKCCinhib
cell.pap[0] = TotSodPap_100NKCCinhib
cell.pap[1] = TotPotPap_100NKCCinhib
cell.pap[2] = TotCloPap_100NKCCinhib
cell.pap[8] = TotureaPap_100NKCCinhib
elif cell.preg == 'mid':
cell.oi[0] = TotSodOI_MP_100NKCCinhib
cell.oi[1] = TotPotOI_MP_100NKCCinhib
cell.oi[2] = TotCloOI_MP_100NKCCinhib
cell.oi[8] = TotureaOI_100NKCCinhib
cell.pap[0] = TotSodPap_MP_100NKCCinhib
cell.pap[1] = TotPotPap_MP_100NKCCinhib
cell.pap[2] = TotCloPap_MP_100NKCCinhib
cell.pap[8] = TotureaPap_100NKCCinhib
elif cell.preg == 'late':
cell.oi[0] = TotSodOI_LP_100NKCCinhib
cell.oi[1] = TotPotOI_LP_100NKCCinhib
cell.oi[2] = TotCloOI_LP_100NKCCinhib
cell.oi[8] = TotureaOI_100NKCCinhib
cell.pap[0] = TotSodPap_LP_100NKCCinhib
cell.pap[1] = TotPotPap_LP_100NKCCinhib
cell.pap[2] = TotCloPap_LP_100NKCCinhib
cell.pap[8] = TotureaPap_100NKCCinhib
elif cell.inhib == 'SNB-70':
cell.oi[0] = TotSodOI_70NKCCinhib
cell.oi[1] = TotPotOI_70NKCCinhib
cell.oi[2] = TotCloOI_70NKCCinhib
cell.oi[8] = TotureaOI_70NKCCinhib
cell.pap[0] = TotSodPap_70NKCCinhib
cell.pap[1] = TotPotPap_70NKCCinhib
cell.pap[2] = TotCloPap_70NKCCinhib
cell.pap[8] = TotureaPap_70NKCCinhib
elif cell.inhib == 'SNB-100':
cell.oi[0] = TotSodOI_100NKCCinhib
cell.oi[1] = TotPotOI_100NKCCinhib
cell.oi[2] = TotCloOI_100NKCCinhib
cell.oi[8] = TotureaOI_100NKCCinhib
cell.pap[0] = TotSodPap_100NKCCinhib
cell.pap[1] = TotPotPap_100NKCCinhib
cell.pap[2] = TotCloPap_100NKCCinhib
cell.pap[8] = TotureaPap_100NKCCinhib
elif cell.preg == 'mid':
cell.oi[0] = TotSodOI_MP
cell.oi[1] = TotPotOI_MP
cell.oi[2] = TotCloOI_MP
cell.oi[3] = TotHCO3OI_MP
cell.pap[0] = TotSodPap_MP
cell.pap[1] = TotPotPap_MP
cell.pap[2] = TotCloPap_MP
cell.pap[3] = TotHCO3Pap_MP
elif cell.preg == 'late':
cell.oi[0] = TotSodOI_LP
cell.oi[1] = TotPotOI_LP
cell.oi[2] = TotCloOI_LP
cell.oi[3] = TotHCO3OI_LP
cell.pap[0] = TotSodPap_LP
cell.pap[1] = TotPotPap_LP
cell.pap[2] = TotCloPap_LP
cell.pap[3] = TotHCO3Pap_LP
if cell.segment=='cTAL' or cell.segment == 'MD' or cell.segment=='DCT' or cell.segment=='PT' or cell.segment == 'CNT' or cell.segment == 'CCD':
if cell.species == 'rat':
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'mou':
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'hum':
pHplasma = 7.4
phpap = 7.3
else:
print('cell.species: ' + str(cell.species))
raise Exception('what is species?')
if cell.unx == 'Y':
pHplasma = 7.4-0.1
phpap = 7.3-0.1
cell.pH[5] = pHplasma
facbic = np.exp(np.log(10)*(cell.pH[5]-pKHCO3))
facpho = np.exp(np.log(10)*(cell.pH[5]-pKHPO4))
facamm = np.exp(np.log(10)*(cell.pH[5]-pKNH3))
fachco2 = np.exp(np.log(10)*(cell.pH[5]-pKHCO2))
cell.conc[0,5] = cell.cm[0]
cell.conc[1,5] = cell.cm[1]
cell.conc[2,5] = cell.cm[2]
cell.conc[3,5] = cell.cm[3]
cell.conc[4,5] = cell.cm[4]
cell.conc[5,5] = cell.cm[5]
cell.conc[4,5] = cell.conc[5,5]/342.07
cell.conc[3,5] = cell.conc[4,5]*10**(cell.pH[5]-pKHCO3)
cell.conc[6,5] = cell.cm[6]*facpho/(1+facpho)
cell.conc[7,5] = cell.cm[6]/(1+facpho)
cell.conc[8,5] = cell.cm[8]
if cell.segment=='cTAL':
TotAmmCT = 1.0
TotAmmCM = 1.5
pos = (1*(cell.total-i))/(1*cell.total)
elif cell.segment=='MD':
TotAmmCT = 1.0
TotAmmCM = 1.5
pos = 1/200
elif cell.segment=='DCT':
TotAmmCT = 0.1
if cell.type !='sup':
TotAmmCM = 2.9
else:
TotAmmCM = 1.0
pos = (1.0*(cell.total-i))/(1.0*cell.total)
elif cell.segment =='PT':
TotAmmCT = 0.1
TotAmmCM = 1.5
if cell.species == 'hum':
total = cell.total*0.9
elif cell.species == 'rat':
total = cell.total*0.88
elif cell.species == 'mou':
total = cell.total*0.88
else:
print('cell.species: ' + str(cell.species))
raise Exception('what is species?')
pos = i/total
elif cell.segment == 'CNT':
TotAmmCT = 0.1
TotAmmCM = 1.5
pos = (1*(cell.total-i))/(1*cell.total)
elif cell.segment == 'CCD':
TotAmmCT = 0.1
TotAmmCM = 1.5
pos = (1*i)/(1*cell.total)
if cell.segment == 'CNT':
Ammtotz = TotAmmCT
else:
Ammtotz = TotAmmCT+(TotAmmCM-TotAmmCT)*pos
cell.conc[9,5] = Ammtotz*facamm/(1+facamm)
cell.conc[10,5] = Ammtotz/(1+facamm)
cell.conc[2,5] = cell.cm[2]+(Ammtotz/(1+facamm))
cell.conc[11,5] = np.exp(-np.log(10)*cell.pH[5])*1000.0
cell.conc[12,5] = cell.cm[12]*fachco2/(1+fachco2)
cell.conc[13,5] = cell.cm[12]/(1+fachco2)
cell.conc[14,5] = cell.cm[14]
elecS = 0
for j in range(NS):
elecS = elecS+zval[j]*cell.conc[j,5]
cell.conc[2,5] = cell.conc[2,5]+elecS
if cell.sex=='female' and cell.species == 'rat':
female_conc(cell, i)
elif cell.segment=='mTAL' or cell.segment=='SDL' or cell.segment=='OMCD':
if cell.segment == 'mTAL':
pos = (1*(cell.total-i))/(1*cell.total)
elif cell.segment == 'SDL':
pos = 0.3+0.7*i/(1*cell.total)
elif cell.segment == 'OMCD':
pos = (1*i)/(1*cell.total)
if cell.species == 'rat':
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'mou':
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'hum':
pHplasma = 7.4
phpap = 7.3
else:
print('cell.species: ' + str(cell.species))
raise Exception('what is species?')
if cell.unx == 'Y':
pHplasma = 7.4-0.1
phpap = 7.3-0.1
cell.pH[5] = pHplasma-(pHplasma-phpap)*2.0/7.0*pos
facbic = np.exp(np.log(10)*(cell.pH[5]-pKHCO3))
facpho = np.exp(np.log(10)*(cell.pH[5]-pKHPO4))
facamm = np.exp(np.log(10)*(cell.pH[5]-pKNH3))
fachco2 = np.exp(np.log(10)*(cell.pH[5]-pKHCO2))
cell.conc[0,5] = cell.cm[0]+(cell.oi[0]-cell.cm[0])*pos
cell.conc[1,5] = cell.cm[1]+(cell.oi[1]-cell.cm[1])*pos
cell.conc[2,5] = cell.cm[2]+(cell.oi[2]-cell.cm[2])*pos
cell.conc[3,5] = cell.cm[3]+(cell.oi[3]-cell.cm[3])*pos
cell.conc[4,5] = cell.cm[4]+(cell.oi[4]-cell.cm[4])*pos
cell.conc[5,5] = cell.cm[5]+(cell.oi[5]-cell.cm[5])*pos
cell.conc[4,5] = cell.conc[5,5]/342.07
cell.conc[3,5] = cell.conc[4,5]*10**(cell.pH[5]-pKHCO3)
cell.conc[5,5] = cell.conc[4,5]*342.07
Phototz = (cell.cm[6]+(cell.oi[6]-cell.cm[6])*pos)
cell.conc[6,5] = Phototz*facpho/(1+facpho)
cell.conc[7,5] = Phototz/(1+facpho)
cell.conc[8,5] = cell.cm[8]+(cell.oi[8]-cell.cm[8])*pos
TotAmmCM = 1.5
Ammtotz = TotAmmCM+(cell.oi[9]-TotAmmCM)*pos
cell.conc[9,5] = Ammtotz*facamm/(1+facamm)
cell.conc[10,5] = Ammtotz/(1+facamm)
cell.conc[11,5] = np.exp(-np.log(10)*cell.pH[5])*1000
Hco2totz = cell.cm[12]+(cell.oi[12]-cell.cm[12])*pos
cell.conc[12,5] = Hco2totz*fachco2/(1+fachco2)
cell.conc[13,5] = Hco2totz/(1+fachco2)
cell.conc[14,5] = cell.cm[14]+(cell.oi[14]-cell.cm[14])*pos
elecS = 0.0
for j in range(NS):
elecS = elecS+zval[j]*cell.conc[j,5]
cell.conc[2,5] = cell.conc[2,5]+elecS
# Concentrations of K, Cl are lower in female rat.
if cell.sex=='female' and cell.species=='rat':
female_conc(cell, i)
elif cell.segment=='S3':
if i == 1:
if cell.species == 'rat':
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'mou':
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'hum':
pHplasma = 7.4
phpap = 7.3
else:
print('cell.species: ' + str(cell.species))
raise Exception('what is species?')
if cell.unx == 'Y':
pHplasma = 7.4-0.1
phpap = 7.3-0.1
cell.pH[5] = pHplasma
facbic = np.exp(np.log(10)*(cell.pH[5]-pKHCO3))
facpho = np.exp(np.log(10)*(cell.pH[5]-pKHPO4))
facamm = np.exp(np.log(10)*(cell.pH[5]-pKNH3))
fachco2 = np.exp(np.log(10)*(cell.pH[5]-pKHCO2))
cell.conc[0,5] = cell.cm[0]
cell.conc[1,5] = cell.cm[1]
cell.conc[2,5] = cell.cm[2]
cell.conc[3,5] = cell.cm[3]
cell.conc[4,5] = cell.cm[4]
cell.conc[5,5] = cell.cm[5]
cell.conc[4,5] = cell.conc[5,5]/342.07
cell.conc[3,5] = cell.conc[4,5]*10**(cell.pH[5]-pKHCO3)
cell.conc[6,5] = cell.cm[6]*facpho/(1+facpho)
cell.conc[7,5] = cell.cm[6]/(1+facpho)
cell.conc[8,5] = cell.cm[8]
TotAmmCT = 0.1
TotAmmCM = 1.5
pos = 1
Ammtotz = TotAmmCT+(TotAmmCM-TotAmmCT)*pos
cell.conc[9,5] = Ammtotz*facamm/(1+facamm)
cell.conc[10,5] = Ammtotz/(1+facamm)
cell.conc[2,5] = cell.cm[2]+(Ammtotz/(1+facamm))
cell.conc[11,5] = np.exp(-np.log(10)*cell.pH[5])*1000
cell.conc[12,5] = cell.cm[12]*fachco2/(1+fachco2)
cell.conc[13,5] = cell.cm[12]/(1+fachco2)
cell.conc[14,5] = cell.cm[14]
elecS = 0
for j in range(NS):
elecS = elecS+zval[j]*cell.conc[j,5]
cell.conc[2,5] = cell.conc[2,5]+elecS
else:
if cell.species == 'hum':
NPT=0.9*cell.total
pHplasma = 7.4
phpap = 7.3
elif cell.species == 'rat':
NPT=0.88*cell.total
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'mou':
NPT=0.88*cell.total
pHplasma = 7.323
phpap = 7.0
else:
print('cell.species: ' + str(cell.species))
raise Exception('what is species?')
if cell.unx == 'Y':
pHplasma = 7.4-0.1
phpap = 7.3-0.1
pos = (0.3*(i))/(1*cell.total-NPT)
cell.pH[5] = pHplasma-(pHplasma-phpap)*2/7*pos
facbic = np.exp(np.log(10)*(cell.pH[5]-pKHCO3))
facpho = np.exp(np.log(10)*(cell.pH[5]-pKHPO4))
facamm = np.exp(np.log(10)*(cell.pH[5]-pKNH3))
fachco2 = np.exp(np.log(10)*(cell.pH[5]-pKHCO2))
cell.conc[0,5] = cell.cm[0]+(cell.oi[0]-cell.cm[0])*pos
cell.conc[1,5] = cell.cm[1]+(cell.oi[1]-cell.cm[1])*pos
cell.conc[2,5] = cell.cm[2]+(cell.oi[2]-cell.cm[2])*pos
cell.conc[3,5] = cell.cm[3]+(cell.oi[3]-cell.cm[3])*pos
cell.conc[4,5] = cell.cm[4]+(cell.oi[4]-cell.cm[4])*pos
cell.conc[5,5] = cell.cm[5]+(cell.oi[5]-cell.cm[5])*pos
cell.conc[4,5] = cell.conc[5,5]/342.07
cell.conc[3,5] = cell.conc[4,5]*10**(cell.pH[5]-pKHCO3)
cell.conc[5,5] = cell.conc[4,5]*342.07
Phototz = cell.cm[6]+(cell.oi[6]-cell.cm[6])*pos
cell.conc[6,5] = Phototz*facpho/(1+facpho)
cell.conc[7,5] = Phototz/(1+facpho)
cell.conc[8,5] = cell.cm[8]+(cell.oi[8]-cell.cm[8])*pos
TotAmmCM = 1.5
Ammtotz = TotAmmCM+(cell.oi[9]-TotAmmCM)*pos
cell.conc[9,5] = Ammtotz*facamm/(1+facamm)
cell.conc[10,5] = Ammtotz/(1+facamm)
cell.conc[11,5] = np.exp(-np.log(10)*cell.pH[5])*1000
Hco2totz = cell.cm[12]+(cell.oi[12]-cell.cm[12])*pos
cell.conc[12,5] = Hco2totz*fachco2/(1+fachco2)
cell.conc[13,5] = Hco2totz/(1+fachco2)
cell.conc[14,5] = cell.cm[14]+(cell.oi[14]-cell.cm[14])*pos
elecS = 0.0
for j in range(NS):
elecS = elecS+zval[j]*cell.conc[j,5]
cell.conc[2,5] = cell.conc[2,5]+elecS
# Concentrations of K, Cl are lower in female rat.
if cell.sex=='female' and cell.species=='rat':
female_conc(cell, i)
elif cell.segment == 'IMCD' or cell.segment == 'LDL' or cell.segment == 'LAL':
if cell.type == 'jux1':
looplen = 0.2
elif cell.type == 'jux2':
looplen = 0.4
elif cell.type == 'jux3':
looplen = 0.6
elif cell.type == 'jux4':
looplen = 0.8
elif cell.type == 'jux5':
looplen = 1.0
if cell.segment == 'IMCD':
pos = i/cell.total
elif cell.segment == 'LDL':
pos = looplen*i/cell.total #looplen = 0.2 for jux1, 0.4 for jux2, 0.6 for jux3, 0.8 for jux4, 1.0 for jux5
elif cell.segment == 'LAL':
pos = looplen*(cell.total-i)/cell.total
if cell.species == 'rat':
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'mou':
pHplasma = 7.323
phpap = 7.0
elif cell.species == 'hum':
pHplasma = 7.4
phpap = 7.3
else:
print('cell.species: ' + str(cell.species))
raise Exception('what is species?')
if cell.unx == 'Y':
pHplasma = 7.4-0.1
phpap = 7.3-0.1
cell.ep[5]=-0.001e-3/EPref
cell.pH[5] = pHplasma-(pHplasma-phpap)*((2/7)+(5/7)*pos)
facbic = np.exp(np.log(10)*(cell.pH[5]-pKHCO3))
facpho = np.exp(np.log(10)*(cell.pH[5]-pKHPO4))
facamm = np.exp(np.log(10)*(cell.pH[5]-pKNH3))
fachco2 = np.exp(np.log(10)*(cell.pH[5]-pKHCO2))
cell.conc[0,5] = cell.oi[0]+(cell.pap[0]-cell.oi[0])*pos
cell.conc[1,5] = cell.oi[1]+(cell.pap[1]-cell.oi[1])*pos
cell.conc[2,5] = cell.oi[2]+(cell.pap[2]-cell.oi[2])*pos
cell.conc[3,5] = cell.oi[3]+(cell.pap[3]-cell.oi[3])*pos
cell.conc[4,5] = cell.oi[4]+(cell.pap[4]-cell.oi[4])*pos
cell.conc[5,5] = cell.oi[5]+(cell.pap[5]-cell.oi[5])*pos
cell.conc[4,5] = cell.conc[5,5]/342.07
cell.conc[3,5] = cell.conc[4,5]*10.0**(cell.pH[5]-pKHCO3)
cell.conc[5,5] = cell.conc[4,5]*342.07
Phototz = cell.oi[6]+(cell.pap[6]-cell.oi[6])*pos
cell.conc[6,5] = Phototz*facpho/(1+facpho)
cell.conc[7,5] = Phototz/(1+facpho)
cell.conc[8,5] = cell.oi[8]+(cell.pap[8]-cell.oi[8])*pos
Ammtotz = cell.oi[9]+(cell.pap[9]-cell.oi[9])*pos
cell.conc[9,5] = Ammtotz*facamm/(1+facamm)
cell.conc[10,5] = Ammtotz/(1+facamm)
cell.conc[11,5] = np.exp(-np.log(10)*cell.pH[5])*1000
Hco2totz = cell.oi[12]+(cell.pap[12]-cell.oi[12])*pos
cell.conc[12,5] = Hco2totz*fachco2/(1+fachco2)
cell.conc[13,5] = Hco2totz/(1+fachco2)
cell.conc[14,5] = cell.oi[14]+(cell.pap[14]-cell.oi[14])*pos
elecS = 0.0
for j in range(NS):
elecS = elecS+zval[j]*cell.conc[j,5]
cell.conc[2,5] = cell.conc[2,5]+elecS
# Concentrations of K, Cl are lower in female rat.
if cell.sex=='female' and cell.species=='rat':
female_conc(cell, i)
else:
cell.conc[:,5] = cell.conc[:,5]