Information Technology Reference
In-Depth Information
-
Number of Iterations,
itns:
The number of simulation iterations once the
agents have been inserted.
-
Chemokine Producer Percentage,
chem prod:
The percentage of the total
chemical space set to be the chemokine producing area.
-
Maximum Chemokine Level,
chem max:
The maximum allowed chemokine
value of a chemical space cell upon initialisation of the simulator.
-
Maximum Antigen Ingestion,
ag max:
The maximum number of antigen
agents a single APC is allowed to ingest.
-
Number of APCs,
apc num:
The number of APC agents.
-
Number of Antigens,
ag num:
The number of antigen agents.
-
Number of T
H
Cells,
th num:
The number of T
H
cell agents.
-
Recognition Threshold,
recog:
A user defined avidity threshold to determine
whether a T
H
cell becomes activated upon interaction with an APC.
-
A
nity Measure,
aff:
Thetypeofmetricusedtocalculatethea
nitybe-
tween an APC peptipe string and a T
H
cell receptor.
-
Antigen String,
ag:
The bit string that represents the antigen shape. This is
the same for all antigen agents in the simulation.
-
T
H
Cell Receptors,
ths:
The list of bit strings that represent the unique
receptors for each T
H
cell in the simulation. The size of the list equals the
number of T
H
cells parameter.
5
Initial Results and Observations
In this section we first describe the behaviour of the simulator, and then show
the type of results it generates. During a typical run of the simulator, a number
of emergent behaviours can be seen that result from the rules of the model
described above. Firstly, during the pre-iterations stage when only the chemical
space updates, a visually stable chemokine gradient emerges that flows from a
high concentration in the central paracortex region to a low concentration at the
top and bottom of the chemical space. After the pre-iterations have finished, all
the agents are inserted into the agent space at random positions and start to
move and update as the iterations proceed. As the antigen agents cannot move
upwards in the agent space, they cycle as a population from the top to the bottom
of the agent space, being ingested as they encounter APC agents. As a results,
the number of free antigen agents decreases during a run of the simulator. All
the T
H
cell agents are inserted in the naive state, so they immediately start to
follow the chemokine gradient in the chemical space and soon settle in the centre
of the paracortex area where the chemokine gradient is at its greatest. Once in
the centre, the naive T
H
cell agents continue to move due to the stochasticity
in chemokine values at the local level of the chemical space. Like the T
H
cell
agents, all the APC agents are naive when inserted and thus move randomly
until the ingest antigen and become activated. Once activated, they follow the
same movement behaviour of the naive T
H
cell agents, gravitating to the centre
of the paracortex region. Once in the centre, the activated APC agents are close
enough to the naive T
H
cell agents for them to interact, which results in some
