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Some fixes to Ca-dependent channel prototypes in rdesigneur. #314

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merged 2 commits into from
Oct 2, 2018
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Some fixes to Ca-dependent channel prototypes in rdesigneur. #314

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Some fixes to Ca-dependent channel prototypes in rdesigneur.
upibhalla Oct 2, 2018
b57a6d0
Merge branch 'master' into master
dilawar Oct 2, 2018
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22 changes: 14 additions & 8 deletions python/rdesigneur/rdesigneurProtos.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,8 @@
per_ms = 1e3
PI = 3.14159265359
FaradayConst = 96485.3365 # Coulomb/mol
CA_SCALE = 25000 # Ratio of Traub units to mM. 250::0.01
#CA_SCALE = 25000 # Ratio of Traub units to mM. 250::0.01
CA_SCALE = 1.0 # I have now set sensible ranges in the KCA and KAHP



Expand Down Expand Up @@ -312,13 +313,17 @@ def make_Ca_conc( name ):
# this was specified here in make_Ca_conc.

#========================================================================
# Tabulated Ca-dependent K AHP Channel
# Tabulated Ca-dependent K AHP Channel: Traub 1991
#========================================================================

# This is a tabchannel which gets the calcium concentration from Ca_conc
# in order to calculate the activation of its Z gate. It is set up much
# like the Ca channel, except that the A and B tables have values which are
# functions of concentration, instead of voltage.
# Traub's original equation is min(0.2e-4 Xi, 0.01) which suggests a max
# of 500 for the Xi (calcium) in his system. For dendritic calcium say 10uM
# or 0.01 mM. Elsewhere we estimate that the ratio of Traub units to mM is
# 250:0.01. Using this ratio, we should have xmax = 0.02.

def make_K_AHP( name ):
if moose.exists( '/library/' + name ):
Expand All @@ -332,7 +337,7 @@ def make_K_AHP( name ):
K_AHP.Zpower = 1

zgate = moose.element( K_AHP.path + '/gateZ' )
xmax = 500.0
xmax = 0.02 # 20 micromolar.
zgate.min = 0
zgate.max = xmax
zgate.divs = 3000
Expand All @@ -341,7 +346,7 @@ def make_K_AHP( name ):
dx = (zgate.max - zgate.min)/zgate.divs
x = zgate.min
for i in range( zgate.divs + 1 ):
zA[i] = min( 0.02 * CA_SCALE * x, 10 )
zA[i] = min( 250.00 * CA_SCALE * x, 10 )
zB[i] = 1.0
x = x + dx

Expand Down Expand Up @@ -405,13 +410,14 @@ def make_K_C( name ):
xgate.tableB = xB

# Create a table for the function of concentration, allowing a
# concentration range of 0 to 200, with 3000 divisions. This is done
# concentration range of 0 to 100 uM, with 3000 divisions. This is done
# using the Z gate, which can receive a CONCEN message. By using
# the "instant" flag, the A and B tables are evaluated as lookup tables,
# rather than being used in a differential equation.
zgate = moose.element( K_C.path + '/gateZ' )
zgate.min = 0.0
xmax = 150.0
xmax = 0.02 # Max Ca conc is likely to be 100 uM even in spine, but
# based on estimates above let's keep it at 20uM.
zgate.max = xmax
zgate.divs = 3000
zA = np.zeros( (zgate.divs + 1), dtype=float)
Expand All @@ -420,8 +426,8 @@ def make_K_C( name ):
x = zgate.min
#CaScale = 100000.0 / 250.0e-3
for i in range( zgate.divs + 1 ):
zA[i] = min( 1000.0, x * CA_SCALE / (250 * xmax ) )
zB[i] = 1000.0
zA[i] = min( 1.0, x * CA_SCALE / xmax)
zB[i] = 1.0
x += dx
zgate.tableA = zA
zgate.tableB = zB
Expand Down