Cybercillin - The detailed model

Genes

Each individual micro-organism in the colony has its own set of four genes controlling:

Motility. This is the percentage likelihood of movement at each 0.2 second update. If the gene value is 100, then the micro-organism will move continuously. If the figure is 50, then there is a 50% chance of movement at each update; or put another way, out of 100 updates the micro-organism is likely to move during 50 of them. Direction of movement is chosen randomly in one of 8 directions (N, NE, E, SE, S, SW, W, NW). Travel is always to an immediate neighbour of the starting point, i.e. one 'square' of the bug-world grid.
Lifespan. This gene determines how long a micro-organism will survive (in the absence of antibiotic). The actual lifespan (in seconds) is calculated at random between upper and lower boundaries contained in the gene. A micro-organism's life 'clock' is set at the time of 'birth' following asexual reproduction. It is also reset after conjugation.
Breeder. This gene determines how frequently a micro-organism divides asexually. The time to the next division is calculated at random between upper and lower boundaries contained in the gene. The 'countdown' is set at the time of 'birth' following asexual reproduction, and also after conjugation. Breeder time must be shorter than lifespan, or micro-organisms will die before they have the opportunity to divide.
Antibiotic resistance. This gene determines whether or not the micro-organism emits a 'penicillinase'.

The user must define and name three variations for each gene type, e.g. motility:

'speedy' ........ 100% movement probability 'rambler' ........ 55% movement probability 'snail' ........ 2% movement probability

These represent the gene pool, from which mutated genes are selected.

Reproduction

Asexual division. This is a 3 stage process that is triggered by an individual micro-organism's 'clock'. The time taken for each stage is defined by the user. Stage 1: Cell dividing wall begins to form. Movement still occurs. Stage 2: Dividing wall formed. No movement. During this stage, antibiotic can cause rupture of the cell wall and death. Stage 3: Two cells about to separate. Although effectively two identical new cells, one is considered the parent and the other the child. Mutation of the child may occur.
Mutation. One or more of the child micro-organism's genes may be randomly selected to mutate. The new genes are selected at random from the user-defined gene pool. The overall likelihood of mutation is set by a global percentage probability.
Conjugation. This may occur when two micro-organisms occupy the same position on the bug world grid. Only one pair of micro-organisms may begin conjugation per update cycle, but the process itself may last for many cycles (Conjugation time is a user-defined parameter). The likelihood of conjugation occurring is governed by a global percentage probability. During conjugation there is exchange of genetic material between the two micro-organisms; one or more genes may be affected. The following table considers just one gene and shows the possible outcomes for bug A and bug B, following various exchange strategies:
```
				    Resulting gene
			Bug A                           Bug B
Exchange strategy       -----                           -----
-----------------
Both A                  No change                       A               
Both B                  B                               No change       
Swap                    B                               A       
Keep                    No change                       No change
```
Strategies are selected at random. There are no recessive or dominant genes.

Antibiotic

Micro-organisms can only be killed by antibiotic during stage 2 of asexual division. The concentration of antibiotic to which the colony is exposed is measured in arbitrary units (up to 32,000). Antibiotic concentration dynamically mimics blood plasma levels during a typical oral antibiotic regimen. The peak level, ramp gradient, frequency of dosing and number of doses are defined by the user. The user must also define the antibiotic level which will kill:

All normal micro-organisms
All resistant micro-organisms

When antibiotic level is below this 100% kill level, only a proportion of the micro-organisms will be destroyed. For example:


    100% kill level = 10,000 units
    Actual level    = 5,000 units

    There is a 50% chance that each micro-organism will be killed;
    i.e. 50 out of 100 micro-organisms are likely to be killed.

An antibiotic regimen is started manually by the user during the simulation.

Seed

The colony begins with a single micro-organism. The user must define its position, and its genes before the simulation can begin.

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This page was last updated on 21st April 1998