Dynamics in Neural Mass Model Networks

The goal of this project is to study the brain dynamics obtained at meso-
scopic scale by considering Neural Mass Model Networks representing small
pieces of brain tissue.

1 Description
The neurons which form the brain are organized in functional units called
cortical columns (see Figure 1). The average activity of these columns results
from the synchronization of the neurons which form them and is responsi-
ble of the activity measured, for instance, by Electroencephalogram (EEG)
recordings. The Neural mass models describe this average activity at the
mesoscopic level reducing the complexity of the dynamics of these thousands
of neurons to a few parameters which describe the average dynamics of the
column. First we will consider the different type of dynamics shown by a
single column when it is driven by a periodic signal. In these conditions
different responses of the driven isolated node are obtained (periodic, quasi-
periodic or chaotic). Once we have studied the dynamics of a single column
we will connect several of them forming a complex network. Then, we will
study the dynamics of the neural mass model nodes in this type of network.

Figure 1: Neurons in the cortex are organized forming cortical columns.

2 Outline and Background

First of all we are going to solve numerically the equations of the Jansen
and Rit’s model which describe the average activity of a “cortical column”.
Jansen and Rit’s model divides the neurons found in a “cortical column”
in three different groups or populations (pyramidal, excitatory inter-neurons

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and inhibitory inter-neurons). The average dynamics of these three popula-
tions is defined through two basic transformations. First, the average action
P
potential density stimulating a population, i pi (t), is transformed, in the
synapses, into an average excitatory post-synaptic potential (EPSP), xe (t),
or an average inhibitory post-synaptic potential (IPSP), xi (t). This trans-
formation is introduced mathematically into the model by the equation:
d2 xe (t) dxe (t)
La [xe (t)] ≡ 2
+ 2a + a2 xe (t)
dtX dt
= Aa pi (t), (1)
i

for the excitatory inputs and, similarly, Lb [xi (t)], for the inhibitory inputs.
The second transformation corresponds to the conversion, in the somas,
of the net average PSP, m(t) = xe (t) − xi (t), into an average action potential
density, S(m(t)). This is represented mathematically in the model by:
2e0
S(m(t)) = (2)
1+ e 0 −m(t))
r(ν

and, depending of the population considered, defines the different terms pi (t)
entering into the first transformation.
The Jansen and Rit’s model used here is defined by the following equa-
tions (the superscript i represents the node number in the network) :

La [y0i (t)] = Aa{S(y1i (t) − y2i (t)}, (3)

La [y1i (t)] = Aa{p̄ + C2 S(C1 y0i (t)) + δsin(2πf t + φ)}, (4)
Lb [y2i (t)] = Bb{C4 S(C3 y0i (t))}. (5)

We drive the column using a periodic signal characterized by an ampli-

tude, δ, and a frequency, f . By varying the amplitude and the frequency of
the driving we will obtain different type of responses (periodic, quasi-periodic
and chaotic) that we will have to characterize. The degree of regularity of
the activity defined by y = y1 − y2 can be calculated by taking the second ab-
solute maxima of the autocorrelation function. When this second maximum
is high the signal is periodic when it is low it is chaotic.
Once we have studied the dynamics of a single cortical column we will
build networks of coupled “cortical columns” using the python package Net-
workx. We will observe that the time average activity, < y2k (t) − y1k (t) >,
of each node, k, in the network will be either positive (excitatory activity)

2
or negative (inhibitory activity). When a network of nodes has at the same
time nodes which have excitatory and inhibitory activity we will say that the
network is segregated. We want to study when network segregates. Besides,
we may also (this is optional) consider the regularity of the activity of the
nodes in the networks.
In order to couple the different nodes which form the network we will add
the term
K
1
i
S(y1j (t) − y2j (t))
X
pα (t) = α q (6)
j=1 Ni Nj
to Equation (4) and the term
K
1
piβ (t) = β S(C3 y0j (t))
X
q (7)
j=1 Ni Nj

to Equation (5). Here, Ni corresponds to the in-degree (number of connec-

tions entering the node) of the receiver node, Nj is the out-degree (number of
connections leaving the node) of the emitter nodes and K is node’s i number
of neighbors. Coupling is bidirectional.

3 The project and Report

1. Implement numerically the Equations (3-5) using Heun’s method. Use
a time step of 1 milisecond and remove a few seconds in all your simu-
lations. Then compute a few tens of seconds. Use the following model
parameters: A=3.25 mV, B= 22 mV, a=100 Hz, b=50 Hz, C=133.5,
C1 =C, C2 =0.8 C, C3 =0.25 C, C4 =0.25 C, e0 =2.5 Hz, r=0.56 mV −1 ,
v0 =6.0 mV, p̄=155.0 Hz, δ=65.0 Hz, f=8.5 Hz. Print the code and add
comment lines to make it understable. Plot y2i (t) − y1i (t) and its Power
Spectrum.

2. Run different simulations changing the driving properties δ and f . δ/C

should change from 0.3 to 0.9 and f from 7 to 11 Hz. Among these sim-
ulations you should observe three types of dynamics (periodic, quasi-
periodic and chaotic). Plot y2i (t) − y1i (t) and its Power Spectrum for, at
least two of these dynamics. Search the literature to find other systems
which also show chaos when they are driven periodically.

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3. Analyze the previous set of simulations by considering the degree of
regularity of the activity defined by y = y1i − y2i . By taking the heigh
of the second absolute maxima of the autocorrelation function we will
create a colormap plot. Show the heigh of the second maximum as a
funtion of f and δ/C. You will see that for some combinations of these
two parameters we obtain choatic dynamics and for others we don’t.

4. Build a scale-free network using the python package Networkx. The

network should have around 50 nodes but if your computer is not pow-
erful enough reduce the number of nodes acordingly. Add the coupling
terms (Eqs. (6) and (7)) to the dynamics of each node. If you have
to use a simpler numerical algorithm (a simple Euler) to solve this dy-
namics you may use it. Print the code you have used and add comment
lines to make it understable.

5. Using the previous code, find examples of networks where segregation

is produced and examples where segregation is not produced. Useful
combinations of coupling parameters are the following: α/C = 0.790
and β/C = 0.190 or α/C = 0.075 and β/C = 0.037. Show histograms
representing the number of nodes in terms of < y2k (t) − y1k (t) >. Op-
tional: Using the same techniques you have used for a single column
(the autocorrelation), analyze the regularity of the nodes in these net-
works.