Invariant parameters for the experiments described in the paper:

A systematic approach to vaccine complexity using an automaton model of the cellular and humoral response

Brynja Kohler, Roberto Puzone, Philip E. Seiden and Franco Celada

Vaccine 19, 862-876 (2000)

Cells:

Upon receiving the necessary signals to divide, B, Th, and Tc cells divide for three time steps so that 8 new cells are produced. For B cells an additional division step provides 8 plasma cells.

Th0 cells stimulated by APCs become Th1 or Th2 cells with equal probability. The progeny of stimulated Th1 or Th2 cells retain their type, there is no Th1/Th2 conversion.

The three-in-a-bed stimulation of APC/Th/Tc does not require simultaneity. Up to 5 time steps are allowed between the APC/Th and APC/Tc contacts.

The initial population of APC, B, Th, and Tc cells is 1000 randomly distributed over the body array. The initial population of epithelial cells is 20,000. The B cells have complete receptor diversity but the Th and Tc cells go through a perfect thymus where all self-reacting cells and completely non-reacting cells are removed.

Plasma cells produce 5 antibodies on each time step.

B-cell anergy is not turned on.

B-cell mutation is not turned on. Since the B-cell diversity is complete mutation would not have an important effect.

It takes one unit of damage to activate an APC with 50% probability. Each necrotic cell death contributes one unit of damage to the site in which the cell death takes place. No contribution by antibody-antigen complexes is considered.

Half-lives:

Entity	Time steps
APC	50
B cell	50
Th cell	50
Tc cell	50
Epithelial cell	100
Plasma cell	10
Active state of an APC	50
Active state of a Th cell	50
Active state of a Tc cell	50
Anergy state	100
Antibody	10
Damage	3

Bound MHC/peptide complexes and antigen half-lives (other than the direct influence of the immune system) are 10,000 (essentially infinite).

Epitopes, peptides and binding :

Antigen epitope	51
Antigen peptide	240
MHC1	9
MHC2	234

These values are the decimal equivalent of the binary bit strings.  

There are no self-epitopes defined. The only self-peptide defined is 255 (but it plays no role in the experiments described in the paper).

All receptors have 8 bits, binding is allowed for 8 bits with a probability of 1 and 7 bits with a probability of 0.05. Matches of 6 bits or less do not bind. This holds for all specific receptor bindings except peptide/MHC binding. In this case the bindings for a 4, 3, 2, 1 bit match are 1, 0.5, 0.25 0.125, respectively. APCs bind antigen with a probability of 0.001. No bystander stimulation is allowed.

Presentation of peptides by B cells endocytosing antigen is on MHC2 only. Presentation by APCs is on MHC1 and MHC2 with equal probability. Presentation of peptides by infecting antigens (virus) is on MHC1 only.

General:

The size of the body array is 16x15 sites

The diffusion rate is chosen so that entities spread uniformly over the site and its six neighbors on one time step. Epithelial cells do not diffuse.

All runs are terminated at 2000 time steps (and called chronic) if they have not previously terminated due to cure or death. Cure results when all antigen is eliminated. Death results when 50% of the epithelial cells are infected or the viral load is greater than 200,000.