Global Dynamics Emerging from Local Interactions: Agent-Based Modeling for the Life Sciences - Mathematical Concepts and Methods in Modern Biology - page 114

FIGURE 4.5
Diagram of the growth cones modeled. Netrin and Slit are produced at the midline and
then diffuse into the rest of the environment. There are four growth cones that will be
modeled, three of which have known responses: a - attracted over the midline (by Netrin)
and then repelled away from the midline (by Slit); b - repelled from the midline (by Netrin
and Slit); c - repelled from the midline (by Netrin, when concentration is large enough);
d - unknown. (Adapted from: Evans and Bashaw [ 75 ])
b. Fill in all the sections requiring comments.
c. Use the find-gradients command to make the agents move up positive gradi-
ents of particles (chemotaxis).
d. Use the find-gradients command to make the agents move down negative
gradients of particles (chemorepulsion).
4.2.3 Breaking Down the Problem
An essential part of research is being able to take complex phenomena and break them
down into theirmost important attributes. ABMs require the hard coding of how agents
interact with each other and their environment, which forces the developer to restrict
the information to its most important features.
In the following exercise you will develop the assumptions that will help build
the agent-based model to study the unknown response of a neuron to given guidance
cues. The guidance cues diffuse out from the midline of the brain, therefore the rate
of diffusion of these cues is an essential parameter of the system.