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antigen bit string that was ingested. If the APC agent is activated, it can ingest
further antigen agents it interacts with, depending on a model parameter that
determines how many antigen agents each APC is allowed to ingest. APC agents
also interact with naive T H cell agents, but this interaction is initiated by the
T H cell agent, and is described below.
All T H cell agents in the model have associated with them a unique bit string
that represents its antigen receptor. Like the APC agents, the T H cell agents can
be in one of two states that affect their behaviour: naive or activated. Again,
all T H cell agents start off in the naive state and move to the activated state
upon interaction with a suitable APC agent. Like activated dendritic cells, real
naive T H cells have the receptor for the chemokine produced in the paracortex,
thus the movement of naive T H cell agents in the model is the same as activated
APC agents. When real T H cells become activated, they lose this chemokine
receptor and so in the model activated T H cell agents move to random Moore
neighbours. T H cell agents have associated with them an anity measure type
and activation threshold that is used when they interact with APC agents. Only
naive T H cell agents interact with APC agents, and these APC agents must be
in the activated state, and thus, presenting a peptide bit string. When such an
APC agent is in the Moore neighbourhood of a naive T H cell agent, the avidity
between the two is calculated. The anity between the peptide being presented
by the APC and the receptor of the T H cell is calculated. As the antigen and T H
cell receptor are implemented as bit strings, two anity measures are defined
in the model which are the Hamming distance and R-contiguous bits measure.
The Hamming distance returns as the anity the result of applying the XOR
operator to the strings, while the R-contiguous bits measure returns the size of
the longest run of complementary bits between the strings. This anity measure
is then multiplied by the antigen concentration level of the APC to provide the
avidity. This avidity is then compared to the user-defined activation threshold
to determine whether the T H cell becomes activated or not.
4.4 The Simulator
To run useful experiments, a simulator written in the Java programming lan-
guage is used to execute the model just described. This can be run either in-
teractively via a graphical user interface (see Fig. 4) or on the command line
allowing for batch simulation runs. The results of a simulation run, such as the
T T cells that have become activated, can be saved to a log file for future analy-
sis. The simulator has the following user defined parameters which are set via a
configuration file:
- Width, w: The width of the cellular space in number of cells. Typically in
the range 50 to 200.
- Height, h: The height of the cellular space in number of cells. Typically the
same as the width.
- Number of Pre-Iterations, pre itns: The number of simulation iterations be-
fore the agents are inserted. During this time only the chemical space settings
up date thus allowing it time to settle down from a random initialisation.
 
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