.. currentmodule:: brian2

.. Fig3AB:

Example: Fig3AB
===============


        .. only:: html

            .. |launchbinder| image:: file:///usr/share/doc/python-brian-doc/docs/badge.svg
            .. _launchbinder: https://mybinder.org/v2/gh/brian-team/brian2-binder/master?filepath=examples/frompapers/Brette_2012/Fig3AB.ipynb

            .. note::
               You can launch an interactive, editable version of this
               example without installing any local files
               using the Binder service (although note that at some times this
               may be slow or fail to open): |launchbinder|_

        

Brette R (2013). Sharpness of spike initiation in neurons explained by compartmentalization.
PLoS Comp Biol, doi: 10.1371/journal.pcbi.1003338.

Fig. 3. A, B. Kink with only Nav1.6 channels

::

    from brian2 import *
    from params import *
    
    codegen.target='numpy'
    
    defaultclock.dt = 0.025*ms
    
    # Morphology
    morpho = Soma(50*um)  # chosen for a target Rm
    morpho.axon = Cylinder(diameter=1*um, length=300*um, n=300)
    
    location = 40*um  # where Na channels are placed
    
    # Channels
    eqs='''
    Im = gL*(EL - v) + gNa*m*(ENa - v) : amp/meter**2
    dm/dt = (minf - m) / taum : 1 # simplified Na channel
    minf = 1 / (1 + exp((va - v) / ka)) : 1
    gNa : siemens/meter**2
    Iin : amp (point current)
    '''
    
    neuron = SpatialNeuron(morphology=morpho, model=eqs, Cm=Cm, Ri=Ri,
                           method="exponential_euler")
    
    compartment = morpho.axon[location]
    neuron.v = EL
    neuron.gNa[compartment] = gNa_0/neuron.area[compartment]
    M = StateMonitor(neuron, ['v', 'm'], record=True)
    
    run(20*ms, report='text')
    neuron.Iin[0] = gL * 20*mV * neuron.area[0]
    run(80*ms, report='text')
    
    subplot(121)
    plot(M.t/ms, M[0].v/mV, 'r')
    plot(M.t/ms, M[compartment].v/mV, 'k')
    plot(M.t/ms, M[compartment].m*(80+60)-80, 'k--')  # open channels
    ylim(-80, 60)
    xlabel('Time (ms)')
    ylabel('V (mV)')
    title('Voltage traces')
    
    subplot(122)
    dm = diff(M[0].v) / defaultclock.dt
    dm40 = diff(M[compartment].v) / defaultclock.dt
    plot((M[0].v/mV)[1:], dm/(volt/second), 'r')
    plot((M[compartment].v/mV)[1:], dm40/(volt/second), 'k')
    xlim(-80, 40)
    xlabel('V (mV)')
    ylabel('dV/dt (V/s)')
    title('Phase plot')
    tight_layout()
    show()
    

