Part 2: Cellular Automata
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Emergent Patterns
During Aggregation
• a-c. As aggregate,
wave lengths shorten
Lecture 6
• d. Population divides
into disjoint domains
• e-f. Domains contract
into “fingers”
(streaming stage)
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Belousov-Zhabotinski Reaction
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fig. from Solé & Goodwin
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Hodgepodge Machine
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Universal Properties
Demonstration of
Hodgepodge Machine
• What leads to these expanding rings and
spirals in very different systems?
• Under what conditions do these structures
form?
• What causes the rotation?
• These are all examples of excitable media
Run NetLogo B-Z Reaction Simulator
or
Run Hidgepodge simulator at CBN
Online Experimentation Center
<mitpress.mit.edu/books/FLAOH/cbnhtml/java.html>
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Part 2: Cellular Automata
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Reading
Excitable Media
Read Flake, ch. 16
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Characteristics of
Excitable Media
Examples of Excitable Media
•
•
•
•
•
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Slime mold amoebas
Cardiac tissue (& other muscle tissue)
Cortical tissue
Certain chemical systems (e.g., BZ reaction)
Hodgepodge machine
• Local spread of excitation
– for signal propagation
• Refractory period
– for unidirectional propagation
• Decay of signal
– avoid saturation of medium
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Behavior of Excitable Media
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Stimulation
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Part 2: Cellular Automata
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Relay (Spreading Excitation)
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Continued Spreading
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Recovery
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Restimulation
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Typical Equations for
Excitable Medium
(ignoring diffusion)
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Nullclines
• Excitation variable:
u˙ = f (u,v)
• Recovery variable:
v˙ = g(u,v)
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Part 2: Cellular Automata
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Rest State
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Stability
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Super-threshold Excitation
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Phase 1: Increasing Excitation
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Phase 2: Start of Extinction
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Phase 3: End of Extinction
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Part 2: Cellular Automata
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Elevated Thresholds During
Recovery
Phase 4: Recovery
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Equations
Modified Martiel & Goldbeter
Model for Dicty Signalling
Variables (functions of x, y, t):
= intracellular concentration of cAMP
= extracellular concentration of cAMP
= fraction of receptors in active state
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Negative Feedback Loop
Positive Feedback Loop
• Extracellular cAMP increases
( increases)
• cAMP receptors desensitize
• Extracellular cAMP increases
(f 1 increases, f2 decreases, decreases)
( increases)
• Rate of synthesis of intracellular cAMP
decreases
• Rate of synthesis of intracellular cAMP
increases
( decreases)
( increases)
• Intracellular cAMP decreases
• Intracellular cAMP increases
( decreases)
( increases)
• Rate of secretion of cAMP decreases
• Extracellular cAMP decreases
• Rate of secretion of cAMP increases
• ( Extracellular cAMP increases)
( decreases)
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See Equations
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See Equations
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Part 2: Cellular Automata
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Circular & Spiral Waves
Observed in:
Dynamics of Model
• Unperturbed
cAMP concentration reaches steady state
• Small perturbation in extracellular cAMP
returns to steady state
• Perturbation > threshold
large transient in cAMP,
then return to steady state
• Or oscillation (depending on model
parameters)
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Cause of
Concentric Circular Waves
Slime mold aggregation
Chemical systems (e.g., BZ reaction)
Neural tissue
Retina of the eye
Heart muscle
Intracellular calcium flows
Mitochondrial activity in oocytes
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Spiral Waves
• Persistence & propagation of spiral waves
explained analytically (Tyson & Murray,
1989)
• Rotate around a small core of of nonexcitable cells
• Propagate at higher frequency than circular
• Therefore they dominate circular in
collisions
• But how do the spirals form initially?
• Excitability is not enough
• But at certain developmental stages, cells
can operate as pacemakers
• When stimulated by cAMP, they begin
emitting regular pulses of cAMP
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•
•
•
•
•
•
•
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Some Explanations
of Spiral Formation
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Step 0: Passing Wave Front
• “the origin of spiral waves remains obscure”
(1997)
• Traveling wave meets obstacle and is
broken
• Desynchronization of cells in their
developmental path
• Random pulse behind advancing wave front
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Part 2: Cellular Automata
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Step 1: Random Excitation
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Step 2: Beginning of Spiral
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Step 3
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Step 4
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Step 5
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Step 6: Rejoining & Reinitiation
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Part 2: Cellular Automata
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Step 7: Beginning of New Spiral
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Step 8
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NetLogo Simulation
Of Spiral Formation
Formation of Double Spiral
• Amoebas are immobile at timescale of wave
movement
• A fraction of patches are inert (grey)
• A fraction of patches has initial
concentration of cAMP
• At each time step:
– chemical diffuses
– each patch responds to local concentration
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from Pálsson & Cox (1996)
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Response of Patch
if patch is not refractory (brown) then
if local chemical > threshold then
set refractory period
produce pulse of chemical (red)
else
decrement refractory period
degrade chemical in local area
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Demonstration of NetLogo
Simulation of Spiral Formation
Run SlimeSpiral.nlogo
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Part 2: Cellular Automata
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NetLogo Simulation of
Streaming Aggregation
Observations
• Excitable media can support circular and spiral
waves
• Spiral formation can be triggered in a variety of
ways
• All seem to involve inhomogeneities (broken
symmetries):
1.
2.
3.
4.
– in space
– in time
– in activity
1.
if chemical > movement threshold then
2.
else if chemical > relay threshold then
take step up chemical gradient
produce more chemical (red)
become refractory
• Amplification of random fluctuations
• Circles & spirals are to be expected
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chemical diffuses
if cell is refractory (yellow)
then chemical degrades
else (it’s excitable, colored white)
3.
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else wait
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Demonstration of NetLogo
Simulation of Streaming
Run SlimeStream.nlogo
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