neuron APCount ExpSyn NetStim AlphaSynapse IClamp SEClamp Exp2Syn IntegrateFire VClamp
pointprocesses
stimobj = new IClamp(x)del -- msdur -- msamp -- nAi -- nASingle pulse current clamp point process. This is an electrode current so positive amp depolarizes the cell. i is set to amp when t is within the closed interval del to del+dur. Time varying current stimuli can be simulated by setting del=0, amp=1e9 and playing a vector into amp with the play Vector method.
pointprocesses
syn = new AlphaSynapse(x)syn.onset --- mssyn.tau --- mssyn.gmax --- umhosyn.e --- mVsyn.i --- nA
synaptic current with alpha function conductance defined by
i = g * (v - e) i(nanoamps), g(micromhos);
where
g = 0 for t < onset and
g = gmax * (t - onset)/tau * exp(-(t - onset - tau)/tau)
for t > onset
this has the property that the maximum value is gmax and occurs at
t = delay + tau.
pointprocesses
obj = new VClamp(x)dur[3]amp[3]gain, rstim, tau1, tau2iSee $NEURONHOME/src/nrnoc/vclmp.mod . The comment in this file reads:
Voltage clamp with three levels. Clamp is on at time 0, and off at time dur[0]+dur[1]+dur[2]. When clamp is off the injected current is 0. Do not insert several instances of this model at the same location in order to make level changes. That is equivalent to independent clamps and they will have incompatible internal state values.
The control amplifier has the indicated gain and time constant. The input amplifier is ideal.
tau2 gain +-|\____rstim____>to cell -amp --'\/`-------|/ | |----||--- |___ __|-----/|___from cell `'`' \| tau1
The clamp has a three states which are the voltage input of the gain amplifier, the voltage output of the gain amplfier, and the voltage output of the measuring amplifier. A good initial condition for these voltages are 0, 0, and v respectively.
This model is quite stiff. For this reason the current is updated within the solve block before updating the state of the clamp. This gives the correct value of the current on exit from fadvance(). If we didn't do this and instead used the values computed in the breakpoint block, it would look like the clamp current is much larger than it actually is since it doesn't take into account the change in voltage within the timestep, ie equivalent to an almost infinite capacitance. Also, because of stiffness, do not use this model except with secondorder=0. This model makes use of implementation details of how models are interfaced to neuron. At some point I will make the translation such that these kinds of models can be handled straightforwardly. Note that since this is an electrode current model v refers to the internal potential which is equivalent to the membrane potential v when there is no extracellular membrane mechanism present but is v+vext when one is present. Also since i is an electrode current, positive values of i depolarize the cell. (Normally, positive membrane currents are outward and thus hyperpolarize the cell)
pointprocesses
clampobj = new SEClamp(.5)dur1 dur2 dur3 -- msamp1 amp2 amp3 -- mVrs -- MOhmvc -- mVi -- nASee $NEURONHOME/src/nrnoc/svclmp.mod. The comment in this file reads:
Single electrode Voltage clamp with three levels. Clamp is on at time 0, and off at time dur1+dur2+dur3. When clamp is off the injected current is 0. The clamp levels are amp1, amp2, amp3. i is the injected current, vc measures the control voltage) Do not insert several instances of this model at the same location in order to make level changes. That is equivalent to independent clamps and they will have incompatible internal state values. The electrical circuit for the clamp is exceedingly simple:
vc ---'\/\/`--- cell
rs
This model is careful to ensure the clamp current is properly computed relative to the membrane voltage on exit from fadvance and can therefore be used with time varying control potentials. Like VClamp it is suitable for play ing a Vector into the control potential.
The following example compares the current that results from
clamping an action potential originally elicited by a current pulse.
execute following example
// setup for three simulations
create s1, s2, s3 // will be stimulated by IClamp, SEClamp, and VClamp
forall {insert hh diam=3 L=3 }
objref c1, c2, c3, ap, apc
s1 c1 = new IClamp(.5)
s2 c2 = new SEClamp(.5)
s3 c3 = new VClamp(.5)
{c1.dur=.1 c1.amp=.3}
{c2.dur1 = 1 c2.rs=.01 }
{c3.dur[0] = 1}
// record an action potential
ap = new Vector()
ap.record(&s1.v(.5))
finitialize(-65)
while(t<1) { fadvance() }
// do the three cases while playing the recorded ap
apc = ap.c // unfortunately can't play into two variables so clone it.
ap.play_remove()
ap.play(&c2.amp1)
apc.play(&c3.amp[0])
finitialize(-65)
while(t<.4) {
fadvance()
print s1.v, s2.v, s3.v, c1.i, c2.i, c3.i
}
pointprocesses
apc = new APCount(x)apc.thresh --- mVapc.napc.time --- msapc.record(vector)If a Vector is attached to the apc, then it is resized to 0 when the INITIAL block is called and the times of threshold crossing are appended to the Vector. apc.record() will stop recording into the vector. The apc is not notified if the vector is freed but this can be fixed if it is convenient to add this feature.
See $NEURONHOME/src/nrnoc/apcount.mod
pointprocesses
syn = new ExpSyn(x)syn.tau --- ms rise timesyn.e -- mV reversal potentialsyn.i -- nA synaptic currentThe factor is defined so that the normalized peak is 1. If tau2 is close to tau1 this has the property that the maximum value is weight and occurs at t = delay + tau.i = G * (v - e) i(nanoamps), g(micromhos); G = weight * exp(-t/tau)
This synapse summates.
See $NEURONHOME/src/nrnoc/expsyn.mod
pointprocesses
syn = new Exp2Syn(x)syn.tau1 --- ms rise timesyn.tau2 --- ms decay timesyn.e -- mV reversal potentialsyn.i -- nA synaptic currentThe kinetic scheme
produces a synaptic current with alpha function like conductance (if tau1/tau2 is appoximately 1) defined byA -> G -> bath 1/tau1 1/tau2
The factor is defined so that the normalized peak is 1. If tau2 is close to tau1 this has the property that the maximum value is weight and occurs at t = delay + tau.i = G * (v - e) i(nanoamps), g(micromhos); G = weight * factor * (exp(-t/tau2) - exp(-t/tau1))
Because the solution is a sum of exponentials, the coupled equations for the kinetic scheme can be solved as a pair of independent equations by the more efficient cnexp method.
This synapse summates.
See $NEURONHOME/src/nrnoc/exp2syn.mod
pointprocesses
c = new IntegrateFire(x)c.tau --- ms time constantc.spikedur --- ms width of spikec.refrac --- ms refactory period. Minimum time between events is spikedur+refracc.y --- state variableAn output spike event is sent to all the NetCon instances which have this pointprocess instance as their source when y >= 1 If y(t0) = y0 and an input event occurs at t1 then the value of y an infinitesimal time before the t1 event is exp(-(t1 - t0)/tau). After the input event y(t1) = y(t1) + weight where weight is the weight of the NetCon event. Input events are ignored for spikedur+refrac time after the spike output event.
During the spike, y = 2. During the refractory period, y = -1. At the end of the refactory period, y = 0.
See $NEURONHOME/src/nrnoc/intfire.mod
pointprocesses
s = new NetStim(x)s.fast_invl ms (mean) time between spikes within a burst.s.slow_invl ms (mean) time between end and beginngin of next burst.s.nfast (average) number of spikes in a bursts.nburst (average) number of burstss.start ms (mean)start time of first spike in first bursts.noise ---- range 0 to 1. Fractional randomness. 0 deterministic, 1 intervals have negexp distribution.See $NEURONHOME/src/nrnoc/netstim.mod
neuron extracellular fastpas hh pas
mechanisms
insert hhHodgkin-Huxley sodium, postassium, and leakage channels. Range variables specific to this model are:
gnabar_hh .120 mho/cm2 Maximum specific sodium channel conductance gkbar_hh .036 mho/cm2 Maximum potassium channel conductance gl_hh .0003 mho/cm2 Leakage conductance el_hh -54.3 mV Leakage reversal potential m_hh sodium activation state variable h_hh sodium inactivation state variable n_hh potassium activation state variable ina_hh mA/cm2 sodium current through the hh channels ik_hh mA/cm2 potassium current through the hh channelsThis model used the na and k ions to read ena, ek and write ina, ik.rates_hh(v) computes the global variables [mhn]inf_hh and [mhn]tau_hh from the rate functions. usetable_hh defaults to 1.
mechanisms
insert pasg_pas -- mho/cm2 conductancee_pas -- mV reversal potentiali -- mA/cm2 non-specific currentPassive membrane channel.
mechanismsSee $NEURONHOME/src/nrnoc/passive0.c
Passive membrane channel. Same as the pas mechanism but hand coded to be a bit faster (avoids the wasteful numerical derivative computation of the conductance and does not save the current). Generally not worth using since passive channel computations are not usually the rate limiting step of a simulation.
mechanisms
insert extracellularvext -- mVi_membrane -- mA/cm2xraxial -- MOhms/cmxg -- mho/cm2xc -- uF/cm2e_extracellular -- mVThis mechanism is useful for simulating the stimulation with extracellular electrodes, response in the presence of an extracellular potential boundary condition computed by some external program, leaky patch clamps, incomplete seals in the myelin sheath along with current flow in the space between the myelin and the axon.
i_membrane correctly does not include contributions from ELECTRODE_CURRENT point processes.
The figure illustrates the form the electrical equivalent circuit when this mechanism is present.
Extracellular potentials do a great deal of violence to one's intuition and it is important that the user carefully consider the results of simulations that use them. It is best to start out believing that there are bugs in the method and attempt to prove their existence.Ra o/`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\o vext + v | | | | --- --- --- --- | | | | | | | | --- --- --- --- | | | | | | | | i_membrane | xraxial | | | /`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\ vext | | | | --- --- --- --- xc and xg | | | | | | | | in parallel --- --- --- --- | | | | --- --- --- --- - - - - e_extracellular | | | | -------------------------------------------- ground
See $NEURONHOME/src/nrnoc/extcell.c and $NEURONHOME/examples/nrnoc/extcab*.hoc.
NEURON can be compiled with any number of extracellular layers. See below.
vext(0) and vext(1) are the voltages at the centers of the first and last segments instead of the zero area nodes.
From extcell.c the comment is:
i_membrane = sav_g * ndlist[i]->v + sav_rhs;
#if 1
/* i_membrane is a current density (mA/cm2). However
it contains contributions from Non-ELECTRODE_CURRENT
point processes. i_membrane(0) and i_membrane(1) will
return the membrane current density at the points
.5/nseg and 1-.5/nseg respectively. This can cause
confusion if non-ELECTRODE_CURRENT point processes
are located at these 0-area nodes since 1) not only
is the true current density infinite, but 2) the
correct absolute current is being computed here
at the x=1 point but is not available, and 3) the
correct absolute current at x=0 is not computed
if the parent is a rootnode or there is no
extracellular mechanism for the parent of this
section. Thus, if non-ELECTRODE_CURRENT point processes
eg synapses, are being used it is not a good idea to
insert them at the points x=0 or x=1
*/
#else
i_membrane *= ndlist[i]->area;
/* i_membrane is nA for every segment. This is different
from all other continuous mechanism currents and
same as PointProcess currents since it contains
non-ELECTRODE_CURRENT point processes and may
be non-zero for the zero area nodes.
*/
#endif
Extracellular layers will not be connected across sections unless the parent section of the connection contains the extracellular mechanism. This is because the 0 area node of the connection is "owned" by the parent section. In particular, root nodes never contain extracellular mechanisms and thus multiple sections connected to the root node always appear to be extracellularly disconnected.
nrn/src/nrnoc/options.h#define EXTRACELLULAR 2 /* number of extracellular layers */insert extracellularvext[i] -- mVi_membrane -- mA/cm2xraxial[i] -- MOhms/cmxg[i] -- mho/cm2xc[i] -- uF/cm2e_extracellular -- mVNote that vext is a synonym in hoc for vext[1]. Since the default value for xg[i] = 1e9 all layers start out tightly connected to ground so previous single layer extracellular simulations should produce the same results.
e_extracellular is connected between ground and the last extracellular layer. With two layers the equivalent circuit looks like:
Ra o/`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\o vext + v | | | | --- --- --- --- | | | | | | | | --- --- --- --- | | | | | | | | i_membrane | xraxial | | | /`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\ vext | | | | --- --- --- --- xc and xg | | | | | | | | in parallel --- --- --- --- | | | | | | | | |xraxial[1]| | | /`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\ vext[1] | | | | --- --- --- --- xc[1] and xg[1] | | | | | | | | in parallel --- --- --- --- | | | | --- --- --- --- - - - - e_extracellular | | | | -------------------------------------------- ground