'Fluo5F': 100e-3,
'FixedBuffer': 1
},
}
#Buffer density specification -- this is used with difshells - refers to which set above is used
BufferDensity = {everything: BufferTotals[which_dye]}
#Pump Vmax, NCX distribution from Lorincz et al. 2007 PNAS
PumpVmaxDensities = NamedDict('PumpVmaxDensities')
PumpVmaxDensities.MMPump = {soma: 85e-8, dend: 8.e-8, spines: 1.e-8}
PumpVmaxDensities.NCX = {soma: 0, dend: 0, spines: 8.e-8}
##########################################################
tree_shape = ShapeParams(OutershellThickness=CaThick,
ThicknessIncreaseFactor=2,
ThicknessIncreaseMode=GEOMETRIC,
MinThickness=.11e-6)
spines_shape = ShapeParams(OutershellThickness=.01e-6,
ThicknessIncreaseFactor=2,
ThicknessIncreaseMode=LINEAR,
MinThickness=.03e-6)
ShapeConfig = {everything: tree_shape, spines: spines_shape}
#################### Plasticity ##########################
#These thresholds are applied to calcium concentration
##Note that these must be much larger if there are spines
PlasParams = NamedList(
'PlasParams', '''
Name
highThreshold
# Pump Vmax, NCX distribution from Lorincz et al. 2007 PNAS
PumpVmaxDensities = NamedDict('PumpVmaxDensities')
PumpVmaxDensities.MMPump = {soma: 85e-8, dend: 8.e-8, spines: 1.e-8}
PumpVmaxDensities.NCX = {soma: 0, dend: 0, spines: 8.e-8}
##########################################################
# Buffer density specification -- this is used with difshells
BufferDensity = {everything: BufferTotals[which_dye]}
# Buffer capacity specification -- this is used with CaConc (single time constant of Ca decay)
BufferCapacityDensity = {soma: 20, dend: 20}
# Taus = {soma:0.032185, dend: 0.1107359, spines: 0.1107359}
tauScale = None # 'SurfaceArea'
# Specificy the size of the smaller calcium compartments
# When subdividing dendrite or spine, can have the PSD or submembrane shell thinner than inner shells with a thickness increase.
tree_shape = ShapeParams(OutershellThickness=.1e-6,
ThicknessIncreaseFactor=2,
ThicknessIncreaseMode=GEOMETRIC,
MinThickness=.11e-6)
head_shape = ShapeParams(OutershellThickness=.07e-6,
ThicknessIncreaseFactor=2.,
ThicknessIncreaseMode=LINEAR,
MinThickness=.06e-6)
neck_shape = ShapeParams(OutershellThickness=.1667e-6,
ThicknessIncreaseFactor=1.,
ThicknessIncreaseMode=LINEAR,
MinThickness=.13e-6)
ShapeConfig = {everything: tree_shape, heads: head_shape, necks: neck_shape}
#################### Plasticity ##########################
# These thresholds are applied to calcium concentration
##Note that these must be much larger if there are spines