def create_head(self, neck, head_vol, big_spine):
"""Create the head of the spine and populate it with the right channels"""
name_sec = self.id + "_head"
h("create " + name_sec)
head = getattr(h, name_sec)
if big_spine:
head.L = 1
head.diam = 1.175
r = head.diam/2.
self.head_vol = math.pi * r * r * head.L
else:
head.L = 0.5
head.diam = math.sqrt(head_vol / (head.L * math.pi) ) * 2
self.Ra = 150.0
head.nseg = 1
head.connect(neck)
#head.insert("pas")
head.insert("kir")
head.insert("can")
head.insert("caq")
head.insert("car")
head.insert("skkca")
h.factors_caltrack()
head.insert("caltrack")
h.factors_catrack()
head.insert("catrack")
return head
def create_neck(self):
""" Create the neck with the Grunditz value"""
name_sec = self.id + "_neck"
h("create " + name_sec)
neck = getattr(h, name_sec)
neck.nseg = 3
neck.L = 1.5 # um
neck.diam = 0.1
#neck.Ra = 150.0 # Used by Grunditz et al 2008 (see supplemental material)
neck.Ra = 100.0 #
#neck.insert("pas")
neck.insert("kir")
h.factors_catrack() # Called on the NMOD catrack
neck.insert("catrack")
h.factors_caltrack() # Called on the NMOD caltrack
neck.insert("caltrack")
return neck
def create_psd(self, head):
"""Create the Post Synaptic Density of the spine to model the different \
location of the different channel"""
name_sec = self.id + "_psd"
h("create " + name_sec)
psd = getattr(h, name_sec)
psd.L = 0.05 # um, Holmes & Levy 1990
psd.diam = 0.5 # Wilson 1998 (Shepherd book)
psd.Ra =100
psd.nseg = 1
psd.connect(head)
psd.insert("caL13")
psd.insert("caL")
psd.insert("rubin")
h.factors_catrack()
psd.insert("catrack")
h.factors_caltrack()
psd.insert("caltrack")
return psd