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view/download model file: makers_moochers_8.nlogo
We have discovered a concern about using Programmed Evolution for theophylline production in E. coli. It has to do with the ability of theophylline to freely cross the membrane of a bacterial cell that made it. The theophylline could then diffuse to a cell that does not make it, and enter that cell. The cell that did not make theo could then gain fitness (unfairly).
There are three agents:
1) Maker Cells - E. coli cells that produce theophylline
2) Moocher Cells - E. coli cells that DO NOT produce theophylline
3) Theophylline
Maker cells and moocher cells have all of the same properties with the exception of:
a) color
b) the ability to produce theophylline
*All agents have a lifespan, and will die when that runs out. Theophylline has a lifespan of about (1/3) of the cells
*The cells gain energy when theophylline is present in the cell. It takes energy to move, so every tick they slowly spend energy (but gain if theophylline is present)
*Cells reproduce when they have reached a certain threshold (user can set). Then a new cell of the same type is formed, and each cell now has half of the energy of the parent.
modifications:
*
*theo-production: controls the amount (likelihood) that a maker cell produces theophylline on any givin tick.
*diffusion-out-rate: countrols the likelihood that a theophylline will leave a cell when it is located at the membrane.
*diffusion-in-rate: controls the likelyihood that a theophylline will leave a cell when it is located at the membrane.
*initial-amount-makers: sets the amount of makers to be created at setup
*initial-amount-moochers: sets the amount of moocher cells to be created at setup
*initial-lifespan: sets the lifespan of the E. coli cells at setup
*initial-energy: sets the energy of E. coli cells at setup
*initial-theophylline: set teh amount ot theophylline to be created at setup
notice graph (plot) over time
does changing permeability of membrane help the makers or moochers?
does starting out with more makers hurt or help the moochers? who is dependent on who?
**give theophylline a faster movement outside of the cell.
uses a “membrane” to determine when the theophylline is about to pass through. Uses the cone radius feature of netlogo.
independent model.
http://modelingcommons.org/browse/one_model/3772
http://gcat.davidson.edu
http://www.bio.davidson.edu
;*********************************************
;Author: Micah Brown
;Model: Maker/Moocher Cells
;*********************************************
breed [ cells cell ]
breed [ theo theophylline-molecule ]
turtles-own [
energy
lifespan
time-since-reproduction
]
to setup
ca
setup-background
setup-turtles ;turtles set up in random location, ensuring no overlaps.
reset-ticks
end
to setup-background
ask patches [
set pcolor white
]
end
;------------------------------
to setup-turtles
set-default-shape cells "circle 2"
set-default-shape theo "lightning"
create-cells (initial-amount-makers + initial-amount-moochers) [
set color black
setxy random-xcor random-ycor
set size 10
ifelse who < initial-amount-makers
[set color red
set time-since-reproduction random maker-reproduction-downtime]
[set color cyan
set time-since-reproduction random moocher-reproduction-downtime]
set energy initial-energy
set lifespan initial-lifespan
]
;overlaps handled by killing overlaping cell :/
ask turtles [
if (count turtles in-radius (size + 1) > 1) [
die
]
]
create-theo initial-theophylline [
set color black
setxy random-xcor random-ycor
set size 3
set lifespan initial-lifespan / ( 2 / 3 )
]
end
;------------------------------
to go
;stops when everyone has died
if (count cells = 0)
[stop]
move-turtles
degredation
reproduce
tick
end
;------------------------------
to move-turtles
ask theo [
let nearest-cell min-one-of other cells [distance myself]
let nearest-cell-distance distance nearest-cell
;test whether theophylline is in "membrane" 4<x<6 distance from center of cell
if ( nearest-cell-distance <= 6 ) and ( nearest-cell-distance) >= 4 [
ifelse count cells in-cone 6.0 180 < 1
[if random-float 1 > probability-diffusion-out ;if facing (and moving) away from cell
[ face nearest-cell
fd 2
]
]
[if random-float 1 > probability-diffusion-in ;else must be facing (and moving) towards a cell
[ face nearest-cell
set heading heading + 180
fd 1.5
]
]
]
random-movement-theo
set lifespan lifespan - 1
]
ask cells [
random-movement-cell
if count cells in-radius 10.1 > 1 [ ;ensures cells don't "overlap"
rt 180
fd 1
]
if color = red [ ;only makers produce theophylline
if random-float 1 <= theo-production / 2 [
hatch-theo 1 [
set size 3
set color black
set lifespan initial-lifespan / ( 2 / 3) ;we give theophylline a lifespan equal to (1.5) of a cell's.
setxy ( xcor + (random-float (4 * sqrt 2) ) - (2 * sqrt 2) ) (ycor + (random-float (4 * sqrt 2) ) - (2 * sqrt 2) )
]
]
]
if count theo in-radius 6 > 0
[ set energy energy + log ( count theo in-radius 6 ) 2 + 1 ] ;energy gained from having theophylline is scaled logarithmically
if energy >= 100 [ ;maximum energy is 100
set energy 100
]
set energy energy - .5
set lifespan lifespan - 1
set time-since-reproduction time-since-reproduction + 1
]
end
;--------------------------------------
to degredation
ask cells [
if energy <= 0 [
if random 10 = 1 [die] ;randomness gives more variation
]
]
ask turtles [
if lifespan <= 0 [
if random 10 = 1 [die]
]
]
end
;-----------------------------
to random-movement-cell
with-local-randomness [
ifelse random 2 = 1
[right random 30 forward .5]
[right random -30 forward .5]
]
ask other theo in-radius 6 [ ; moves its theophylline contained in cell in the same direction that it just moved
ifelse random 2 = 1
[right random 30 forward .5]
[right random -30 forward .5]]
end
;------------------------------
to random-movement-theo
ifelse random 2 = 1
[right random 30 forward 1 ]
[right random -30 forward 1 ]
end
;--------------------------------
to reproduce
;this is an approximate for how many cells will fit into the space given the coordinates that the user sets.
let carrying-capacity (max-pxcor * max-pxcor) / 50
if (count cells > carrying-capacity) [
stop
]
ask cells [
if ( (color = red) and (energy >= maker-reproduction-energy-threshold) and time-since-reproduction >= maker-reproduction-downtime ) or
( (color = cyan) and (energy >= moocher-reproduction-energy-threshold) and (time-since-reproduction >= moocher-reproduction-downtime ) ) [
set time-since-reproduction 0
let child-color color
let half-energy energy / 2
set energy half-energy
let num-theo count theo in-radius 6
;kills half of the theophylline in the cell (but "adds" them to the new cell, later)
repeat num-theo * 0.5 [
ask one-of theo in-radius 6 [die]
]
hatch-cells 1 [
set color child-color
set lifespan initial-lifespan
set energy half-energy
set time-since-reproduction 0
while [count cells in-radius (size + 1) > 1] [ ;attempts to set child cell close to parent cell
setxy xcor + ((random count cells) - (count cells) / 2 ) ycor + ((random count cells) - (count cells) / 2 )
]
hatch-theo ( num-theo / 2 ) [
set size 3
set color black
]
]
]
]
end
;-----------------------------------