Biology Reference
In-Depth Information
d
.
growth cone expressing both DCC and Robo 1 receptors initially moves toward
the midline, then away.
Before you proceed with building a model on axon development, let us recap some
of the assumptions we have made:
e
agents
in the ABM mimic the behavior of the developing axons, see exercise
4.25
;
the diffusion of Netrin and Slit is modeled via the
diffuse
command in NetLogo,
see exercise
4.25
;
the response to the chemicals is dependent on the type of axon, see exercise
4.26
.
There are some important aspects of the biology that we have not yet worked out
how to code in NetLogo, for example:
1.
tracking the path of the axon (the
agent
): we need to visualize the path of the
developing growth cone (the
agent
) because it needs to represent whole neuron
(cell body, axon and growth cone, see Figure
4.4
);
2.
contact-mediated chemo-attraction/repulsion (this requires there to be “enough"
chemical in the environment before the axon will respond to gradients);
3.
in some cases, the axonal response changes once the axon crosses the midline
(see axon a in Figure
4.5
);
4.
how can the simulation be stopped? (We do not want the simulation to carry on
indefinitely.)
Exercise 4.27.
Tracking the path of the axons:
a.
Which command traces the path of an agent? (Hint: search for
pen
in the Netlogo
dictionary.)
b.
Use the command from (a) in
Diffusion2.nlogo
to display the paths of the
agents
.
(You should probably restrict the number of
agents
to 5.)
Exercise 4.28.
Contact-mediated movement:
Adapt your program so that the agent only responds to chemical gradients when
there are at least 10 particles the agents patch. (This mimics contact-mediated chemo-
taxis.)
Exercise 4.29.
a.
Adapt your program so that a single
agent
starting at (30,0) is attracted up gra-
dients of the “chemical." However, when the
agent
crosses
x
=
0 the response
changes and the chemical acts as a chemorepulsant.
b.
Alter the code so that you can change how fast the
agent
moves.
Exercise 4.30.
Stopping the code:
Look up the
stop
command and use it to stop the simulation after 500 ticks.
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