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Fig. 4.
A snapshot of the simulator user interface with a visual representation of the
agent space on top of the chemical space in the left panel
constant flow of antigen through the node. The antigen agents do not themselves
initiate any interactions with other agents, although APCs do interact with them
which is described below.
The APC agents can be in one of two states that dictate their behaviour: not
presenting antigen (naive) or presenting antigen (activated). All APC agents
start off in the naive state and move to the activated state upon ingestion of an
antigen agent. In the naive state, real dendritic cells (APCs) lack the receptor
for the chemokine produced in the paracortex, thus naive APCs in this model
move to a Moore neighbour determined by a random number at each iteration.
Once activated, real dendritic cells produce the chemokine receptor and move
towards the paracortex region. This is mimicked in the model by activated APC
agents consulting the chemical space level of the model, and moving to the
unoccupied Moore neighbour with the highest level of chemokine, thus following
the chemokine gradient. APC agents in both the naive and activated states
initiate interactions with antigen agents in their Moore neighbourhood. If the
APC is naive it ingests the antigen agent, thus removing it from the agent space.
Upon ingesting, the APC becomes activated, and an antigen concentration count
for that APC is set to 1. A peptide bit string is generated from the bit string
of the antigen that represents the peptide presented by real APCs via MHC
for recognition by T
H
cells. This peptide bit string is the same length as the
T
H
cell agent receptors in the model, and is generated as a sub-string of the
