Modeling Calcium Accumulation and Diffusion
Posted: Thu Sep 15, 2011 11:33 am
I'm trying to model preBötzinger neurons and one of the key features is a calcium-activated nonspecific current. As the model is written, internal calcium increases after synaptic events (with some delay to account for the 2nd messenger pathways), which are coded in with a state variable s. My main issue is that I want the calcium to accumulate only in specific spots and then diffuse along the dendrites. This should lead to a traveling wave of calcium and also a wave of depolarization. However, the neuron seems to depolarize and change internal calcium uniformly across the whole cell.
Here is my Neuron block
Parameter and state blocks
Assigned and Initial blocks
Breakpoint and derivative blocks
I also define the procedure rates to calculate inf_s as a function of voltage: inf_s = 1/(1+exp((v-theta_s)/sig_s)).
My question is how does neuron handle ions? Is diffusion between compartments already handled (ie. if I make k_ip=gsyn=0 at all places besides the synapses will calcium only accumulate in those compartments and then diffuse with neuron's built-in mechanisms)? or do I need to code for that in an nmodl file?
Here is my Neuron block
Code: Select all
NEURON {
SUFFIX jjn
USEION ca READ cai WRITE cai
NONSPECIFIC_CURRENT i
RANGE gcan, gsyn, Ens, Ca, k_ip
}
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PARAMETER {
gsyn = 0.0000555555556 (mho/cm2) <0,1e9>
gcan = 0.0000888888889 (mho/cm2) <0,1e9>
Ens = 0 (mV)
sig_can = -0.05 (uM)
sig_s = -3 (mV)
theta_s = 15 (mV)
Ca = 0.05 (uM)
k_can = 0.9 (uM)
k_ca = 22.5 (/ms)
k_ip = 1200 (uM/ms) <0,1e9>
k_s = 1
eps_ca = 0.0007
tau_s = 15 (ms)
}
STATE {
s cai
}
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ASSIGNED {
v (mV)
i (mA/cm2)
inf_s
}
INITIAL {
rates(v)
s = inf_s
cai = Ca
}
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BREAKPOINT {
i = gcan*(v-Ens)/(1 + exp((cai-k_can)/sig_can)) + gsyn*s*(v-Ens)
}
DERIVATIVE states {
rates(v)
cai' = eps_ca*(k_ip*s - k_ca*(cai-Ca))
s' = ((1-s)*inf_s - k_s*s)/tau_s
}
My question is how does neuron handle ions? Is diffusion between compartments already handled (ie. if I make k_ip=gsyn=0 at all places besides the synapses will calcium only accumulate in those compartments and then diffuse with neuron's built-in mechanisms)? or do I need to code for that in an nmodl file?