Immune System

Assignment P3: Create an immune system.

Eden Weizman 6/24/12

Instructions for Use When the simulation launches, the user will be presented with two windows. The toolbox, and the Self Color Window. The toolbox is for all of the initial parameters.

Radius defines the distance from which an antibody may be from an antigen to recognize it. Affinity Recognition Threshold defines the limit that the affinity of the antibody to the antigen must be for it to recognize it. Antibody Density is the minimum density that antibodies will have on the screen. If the density is ever lower than the input, then more antibodies will be added. Lifespan of an Antibody defines how long a non-memory cell antibody will live after creation. Lifespan of a Memory Cell defines how long a memory cell will live after creation. Antigen Creation Rate is the rate at which new antigens will appear on the screen.

Kill density is the density of antibodies that recognize an antigen within the radius around that antigen required for that antigens destruction. Number of Memory Cells Created per Successful Kill is the number of long living antibodies that were highly successful against an antigen that will be created and scattered throughout the screen after that antigens destruction.

The self color window is for adding colors that will be identified as self and will thus not be destroyed by antibodies. Many can be added, but it is discouraged to add more after the simulation has started, as existing antibodies will not have been exposed to these new colors during the negative selection process. Experimentation Control:

Antibodies performed as expected. They had the greatest difficulty destroying colors that were far enough from black to be recognized, but close enough to black that slightly mutated antibodies could not be recognized.

(Close to black)

Antigens similar to those that had already been destroyed and those that appeared in areas that had just experienced an invasion were destroyed much more quickly the second time around. After a while, the frame was filled up with almost entirely memory cells, meaning that if an antigen popped up and was not recognized by an existing memory cell, the memory cells lasted a very long time and no new antibodies were created to fill up the minimum density. Memory Cells probably need a shorter lifespan.

Radius: 20

Trial 1

There was a lower chance for an antibody that would recognize the antigen to be in the radius, so sometimes antigens lived for quite a while the antigens in the area refreshed before they were discovered and promptly destroyed. It was, however, much easier to reach the kill density requirement, so discovered antigens were destroyed much more quickly. Radius 20 was more effective when there was a higher density of antibodies.

Affinity Threshold: 600

Trial 2

Not effective. Antigens were not discovered because the chances for nearby antibodies to recognize them was vastly lowered. However, when they were recognized, the radius was filled with a much more consistent color.

(Antigens not getting noticed)

(Finally one is recognized!)

Raising of affinity threshold was noted to be more effective when radius was increased. Affinity Threshold: 100 Trial 3

Antibodies recognized self-colors too easily and as a result were much rarer, and could not fill up the minimum density.

Because of this, antigens were less likely to be discovered, and remained without large threat. Trial 4 Antibody Density: 5 Antigens found and killed more easily. Especially because the original density is over the kill density, meaning once they were found it took a lot less to kill them.

Trial 5 Antibody Density: 1 Too sparse. Antigens survived longer and it took a while for them to be discovered. Very similar to Trial 3. Trial 6 Antibody Lifespan: 40 It took a lot longer for existing antibodies to refresh and thus if an antigen happened to be unnoticed by antibodies within its radius, it survived until those antibodies died off and were replaced by new ones. It can be noted that a longer lifespan worked out better with a higher density of antibodies. Trial 7 Antibody Lifespan: 3 Antibodies died off too quickly and could not reach the kill density. Antigens survived. Trial 8 Memory Cell Lifespan: 20 Simulation went as before, but without memory cells, as they acted as all other cells. Antigens that had attacked before took as long to kill as they had the first time. Trial 9 Antigen Creation Rate: 900 At first, antigens far outnumbered antibodies, but antibodies were created at a much more rapid pace and became much more dense than they had been before, killing all existing antigens and future ones as well. Everything moved much faster than before. Antibodies were more efficient. Note: Towards the end the space was almost entirely memory cells. This was fine because the density was so great and there was such a variety of them from the initial attack.

Trial 10 Kill Density: 5 It took longer to kill the antigens, as it took longer for enough antibodies to be created to reach the kill density. However, this created a higher density of antibodies, that killed off the antigens to appear immediately after much more quicker. It can be noted that this worked well with a faster antigen creation rate. Trial 11 Kill Density: 1 It was much easier for the antibodies to reach the kill density. Antigens were killed faster. Trial 12 Number of Memory Cells Created: 5 Similar to trial 8, but occasionally a memory cell would attack a similar antigen quickly. Trial 13 Number of Memory Cells Created: 50 This worked out much better than Trial 6. The antibodies lived very long, but they were very effective against incoming antigens.