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NW
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NE
W
C
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Fig. 2. The Moore neighbourhood where C = central cell, N = north, NE = northeast,
E = east, SE = southeast, S = south, SW = southwest, W = west and NW = northwest
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Fig. 3. An example of the stages involved in the diffusion rule in the chemical space
by random numbers. The chemokine gradient produced by these rules can be
seen visually in Fig. 4, where the value of chemical is represented by a greyscale
value with black being the lowest, and white the highest. Here, a lighter band
can be seen in the centre of the space representing the paracortex region.
4.3
Agent Space
Cells in the agent space layer of the model can be either empty or contain
one of the following agents types: antigen, APC or T H cell. Upon initialisation,
agents are placed at random positions in the agent space. When updating, all
agents within the space move according to rules defined by their agent type.
This is followed by all agents interacting with other agents present in their
Moore neighbourhood, again according to the rules of their agent type. The
functionality of the three agent types, based on the biological details presented
in section 3, are described below in turn.
The antigen agents have associated with them a bit string that represents their
molecular shape. The movement of the antigen agents mimics the movement of
real antigen in the lymph node which drain through the node, entering at the
top through afferent lymph vessels and exiting at the bottom via the efferent
lymph vessel. The antigen agents, therefore, can only move down or sideways in
the agent space, i.e. movements to the east, west, south, southeast and southwest
neighbours. At each iteration, a random number determines which of the neigh-
bours the agent moves to. Once an antigen leaves the bottom of the agent space
it is automatically reinserted to a cell at the top of the agent space to mimic a
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