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Modelling biological oscillations
Modelling biological oscillations
Shan He
School for Computational ScienceUniversity of Birmingham
Module 06-23836: Computational Modelling with MATLAB
Modelling biological oscillations
Outline
Outline of Topics
Limit circle oscillation: Van der Pol equationVan der Pol equationVan der Pol equation and Hopf bifurcationClassification of oscillationsThe forced Van der Pol oscillator and chaos
Oscillations in biologyCircadian clocks and Van der Pol equation
Modelling neural oscillation
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
Van der Pol equation
Van der Pol equation
I Discovered by Dutch electrical engineer Balthasar Van der Polin 1927.
I The first experimental report about chaos.
I The Van der Pol equation has been widely used in thephysical and biological sciences.
I The equation:
d2x
dt2− µ(1 − x2)
dx
dt+ x = 0
where x is the position coordinate, which is a dynamicalvariable, and µ is a scalar parameter which controls thenonlinearity and the strength of the damping.
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
Van der Pol equation
Van der Pol equation: two dimensional form
I We can transform the above second order ODE as a firstorder system: {
dxdt = ydydt = µ(1 − x2)y − x .
I By Lienard transform, the equation can be also written as:{dxdt = µ(x − 1
3x3 − y)
dydt = 1
µx .
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
Van der Pol equation
MATLAB implementation
18 function dy=vandePolfun(t,y)19 mu = 1;20 dy = [mu*(y(1) - 1/3*y(1)ˆ3 - y(2));21 1/mu*y(1)]22 end23
24 function dy=vandePolfun2(t,y)25 mu = 1;26 dy = [y(2); mu*(1-y(1)ˆ2)*y(2)-y(1)]27 end28
29 end
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
Van der Pol equation
MATLAB implementation
1 function VanderPol2 clear all; % clear all variables3 tspan = [0, 20];4 y0 = [20; 0];5
6 [t,Y] = ode45(@vandePolfun,tspan,y0);
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
Van der Pol equation and Hopf bifurcation
Bifurcation in the Van der Pol oscillator
I By change the scalar parameter µ, we can observe bifurcation.
I The bifurcation is Hopf bifurcation: a spiral point of adynamical system switch from stable to unstable, or viceverse, and a periodic solution, e.g., limit circle appears.
I Without any external force, the Van der Pol oscillator will runinto limit cycle.
I The limit cycle frequency depends on constant µ
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
Classification of oscillations
Limit cycle oscillation vs harmonic oscillation
I Harmonic oscillator: a system that executes a periodicbehaviour, the amplitude of the oscillations depends on theinitial conditions.
I The examples of harmonic oscillators: swinging pendulum andthe Lotka-Volterra model
I This contrasts with limit cycle oscillators, where the amplitudeis not determined by the initial conditions.
I Instead, limit cycle oscillators will automatically come back toa limit cycle after perturbation. In other words, they have acharacteristic amplitude
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
Classification of oscillations
Limit cycle oscillators
I Limit cycle has an isolated closed trajectory, e.g., itsneighbouring trajectories are not closed but spiral eithertowards or away from the limit cycle.
I Stable limit cycle: it attracts all neighbouring trajectories.
I A system with a stable limit cycle exhibits self-sustainedoscillation.
I self-sustained oscillations can be seen in many biologicalsystems, e.g., electroencephalogram (EEG), mammaliancircadian clocks, stem cell differentiation, etc.
I Essentially involves a dissipative mechanism to damposcillators that grow too large and a source of energy to pumpup those that become too small.
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
The forced Van der Pol oscillator and chaos
The forced Van der Pol oscillator
I By adding a driving function A sin(ωt), the new equation is:
d2x
dt2− µ(1 − x2)
dx
dt+ x = A sin(ωt)
where A is the amplitude (displacement) of the wave functionand ω is its angular frequency.
I There are two frequencies in the oscillator:I The frequency of self-oscillation determined by µ;I The frequency of the periodic forcing ω.
I We can transform the above second order ODE as a firstorder system:{
dxdt = ydydt = µ(1 − x2)y − x − A sin(ωt).
Modelling biological oscillations
Limit circle oscillation: Van der Pol equation
The forced Van der Pol oscillator and chaos
Chaotic behaviour of the forced Van der Pol oscillator
I By setting the parameters to µ = 8.53, amplitude A = 1.2 andangular frequency ω = 2π
10 we can observe chaotic behaviour
I Source code for the forced Van der Pol oscillator
Modelling biological oscillations
Oscillations in biology
Oscillations in biology
I We have seen oscillation in predator-prey interaction system,e.g., Lotka-Volterra equations.
I Oscillations are prevalent, e.g., swinging pendulum, Businesscycle, AC power, etc.
I Oscillations play an important role in many cellular dynamicprocess such as cell cycle
Modelling biological oscillations
Oscillations in biology
Oscillations in cell biology
Novak, Tyson (2008) Design principles of biochemical oscillators.Nature review 9:981-991.
Modelling biological oscillations
Oscillations in biology
Circadian clocks and Van der Pol equation
Circadian clockI Circadian clock: or circadian rhythm, is an endogenously
driven, roughly 24-hour cycle in biochemical, physiological, orbehavioural processes.
Source: wikipedia
Modelling biological oscillations
Oscillations in biology
Circadian clocks and Van der Pol equation
Circadian clock
I Circadian clock had been widely observed in bacteria, fungi,plants and animals.
I Biological mechanism partially understood, used mathematicalmodels to piece together diverse experimental data and guidefuture research.
I Applications: jet lag countermeasures, schedules of shiftworkers, treat circadian disorders.
I Circadian clock acts as a limit cycle oscillator.
Modelling biological oscillations
Oscillations in biology
Circadian clocks and Van der Pol equation
Circadian clock and Van der Pol oscillator
I Only has one nonlinear term, Van der Pol oscillator is thesimplest possible two-dimensional limit cycle oscillator.
I Many studies of circadian clock used Van der Pol oscillator forsimulation
Modelling biological oscillations
Oscillations in biology
Circadian clocks and Van der Pol equation
Circadian clock of Drosophila
I Van der Pol oscillator cannot accurately describe the internalmechanism of the circadian clock
I Goldbeter model of circadian clock of Drosophila:
Goldbeter (1995), A model for circadian oscillations in theDrosophila period protein (PER), Proc. Roy. Soc. London B, 261
Modelling biological oscillations
Modelling neural oscillation
FitzHugh–Nagumo oscillatorsI Proposed by Richard FitzHugh in 1961 and implemented by
Nagumo using electronic circuit in 1962.I Used to describes how action potentials in neurons are
initiated and propagated.I FitzHugh–Nagumo model is a simplified version of the famous
Hodgkin–Huxley model, which won a Nobel Prize.I FitzHugh–Nagumo model equation:
dv
dt= v − v3
3− w + Iext
dw
dt= ε(v − a− bw)
where v is the membrane potential, w is a recovery variable,Iext is the magnitude of stimulus current, and a, b and ε areconstants.
Modelling biological oscillations
Modelling neural oscillation
Assignment
I Search literature for the parameters a, b and ε.
I Implement the model in MATLAB.
I Try different value of Iext and observe output v of the neuron.
I If you have more time, try to find the chaotic behaviour andbifurcation of the model.