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Team:Dundee/Project/Netlogo
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powered by NetLogo
view/download model file: SECGATEcoloursprobabilities.nlogo
WHAT IS IT?
This model follows on the Simple Kinetics 2 model. In Simple Kinetics 2, we saw how changes to variables such as temperature, volume, and concentration affected the rate at which a chemical reaction reached an equilibrium state. Here we model the same phenomenon based upon a physical separation.
This model investigates some laboratory methods that chemists use to purify chemicals. Most of these methods are based upon physical properties of molecular separation. The same principles that affect chemical equilibrium affect physical equilibrium as well. By changing the variables of temperature, volume, and concentration, we can affect not only the speed at which a system reaches equilibrium, but also the nature of the distribution ratio. In this model, we watch how these factors affect the physical distribution of red molecules that are considered “dissolved” in a blue solvent.
HOW TO USE IT
Setup the model by pressing either the SETUP-RANDOM or the SETUP-SIDE buttons at the top of the Interface tab. SETUP-RANDOM distributes all the molecules randomly around the world. SETUP-SIDE distributes the blue molecules evenly, while placing the red molecules on the right side of the world.
Press GO to watch the molecules move about the world as they achieve equilibrium. The plot tracks the relative concentrations of each color molecule on each side of the central divider. If the red line dips below 0, there are more red molecules on the left side of the divider than on the right. If it rises above 0, there are more red molecules on the right side of the divider than on the left. The blue line plots the same relationship for blue molecules.
You can add more red molecules to the right side of the world by pressing ADD RED.
Similarly, you can shrink or expand the right side of the box with the buttons SHRINK RIGHT and EXPAND RIGHT, respectively.
Finally, to change the size of the connection window, move the WINDOW slider to your desired size and then press the CHANGE WINDOW button.
THINGS TO NOTICE
Pay attention to the plot and compare it what you see in the world. Is there an equal number of blue and red molecules on each side of the divider according to the plot and according to what you see in the view?
THINGS TO TRY
Run the model with several different states for each variable. Do you observe similar equilibrium effects to those seen in Simple Kinetics 2? Are there significant differences?
Does the temperature affect the system in the same way it affected the chemical reaction in Simple Kinetics 2? Why or why not?
How does changing the concentration affect the rate at which the molecules achieve equilibrium? Does this make sense?
EXTENDING THE MODEL
The system we have established here always comes to an approximately identical equilibrium state, no matter how you change the variables. In the lab, this is not useful to chemists, who want to separate one type of molecule from another. Can you extend the model to separate all of the red molecules from the blue molecules?
Try adding another color of molecule to the system and randomly distributing all the molecules around the world. Can you devise a way to separate the new molecules from the red molecules?
Add a slider that allows you to alter the temperature of the system. Think about what effect cooling and heating the system would have on the molecules. Be sure to include a command in the procedures window that will execute your proposed effect.
RELATED MODELS
Simple Kinetics 1, Simple Kinetics 2
RELATED MODELS
Simple Kinetics 1
Simple Kinetics 2
CREDITS AND REFERENCES
Thanks to Mike Stieff for his work on this model.
HOW TO CITE
If you mention this model in a publication, we ask that you include these citations for the model itself and for the NetLogo software:
- Stieff, M. and Wilensky, U. (2001). NetLogo Simple Kinetics 3 model. http://ccl.northwestern.edu/netlogo/models/SimpleKinetics3. Center for Connected Learning and Computer-Based Modeling, Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL.
- Wilensky, U. (1999). NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL.
COPYRIGHT AND LICENSE
Copyright 2001 Uri Wilensky.
This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.
Commercial licenses are also available. To inquire about commercial licenses, please contact Uri Wilensky at uri@northwestern.edu.
This model was created as part of the projects: PARTICIPATORY SIMULATIONS: NETWORK-BASED DESIGN FOR SYSTEMS LEARNING IN CLASSROOMS and/or INTEGRATED SIMULATION AND MODELING ENVIRONMENT. The project gratefully acknowledges the support of the National Science Foundation (REPP & ROLE programs) – grant numbers REC #9814682 and REC-0126227.
CODE
breed [PP1s PP1] ;; red molecules
breed [degPs degP] ;; degradation proteins
breed [mcs mc] ;; microcystin, assuming so small that kinetic interaction is negligible
breed [complexes complex] ;; PP1 bounded to microcystin
breed [secBs secB]
globals [
shrink ;; how many steps right side has been shrunk
i
seperation
j
current
k
l
g
deg-number
PP1-transported
init-avg-speed init-avg-energy ;; initial averages
avg-speed avg-energy ;; current averages
secBs-dead
]
turtles-own
[
speed mass energy ;; particle info
last-collision
bound
linked?
]
to-report particles
report (turtle-set PP1s degPs mcs complexes)
end
to-report lefties
report (turtle-set degPs mcs complexes)
end
to setup-PP1 ;; particle procedure
set speed 10
set mass 37500
set energy (0.5 * mass * (speed ^ 2))
set last-collision nobody
set color red
set size 1.5
set linked? false
end
to setup-degPs ;; particle procedure
set speed 10
set mass 37500
set energy (0.5 * mass * (speed ^ 2))
set last-collision nobody
set size 2
set color black
end
to setup-mcs ;; particle procedure
set speed 10
set mass 995
set energy (0.5 * mass * (speed ^ 2))
set last-collision nobody
set bound false
set size 1
set color 114
end
to setup-complex ;; particle procedure
set speed 10
set mass 38495
set energy (0.5 * mass * (speed ^ 2))
set last-collision nobody
end
to setup-secB ;; particle procedure
set speed 10
set mass 17278
set energy (0.5 * mass * (speed ^ 2))
set last-collision nobody
set color 55
set size 2
set linked? false
end
to setup [both-sides?]
clear-all
set-default-shape PP1s "circle"
set-default-shape degPs "square"
set-default-shape mcs "turtle"
set-default-shape secBs "key"
set shrink 0
set i 0
set k ( 99 )
set l ( - 99 )
set g 0
set deg-number 0
set PP1-transported 0
set j 0
set current 0
set seperation 0
set init-avg-speed avg-speed
set init-avg-energy avg-energy
set secBs-dead 0
walls
gates
create-PP1s initial-PP1 ;; makes 42 red PP1s
[setup-PP1
randomize-right ]
create-degPs degP-number ;; makes xx degradation proteins
[setup-degPs
randomize-left ]
create-mcs mc-number
[ setup-mcs
randomize-left]
create-secBs initial-secB ;; makes 42 red PP1s
[setup-secB
randomize-right ]
reset-ticks
end
to randomize-left
setxy (- (abs random-xcor))
random-ycor
if any? patches in-radius 1 with [pcolor != 87]
[ randomize-left ] ;; try again until we don't land on or near blue
end
to randomize-right
setxy abs random-xcor
random-ycor
if any? patches in-radius 1 with [pcolor != 19.9]
[ randomize-right ] ;; try again until we don't land on or near blue
end
to go
ask particles [
if collide? [check-for-collision]
if random-walk? [rt random-float 360]
bounce
fd 1
]
ask PP1s [
loss-PP1
degrade
]
if ticks mod 5 = 0 [
create-PP1s PP1-production
[
setxy abs 48
random-ycor
setup-PP1
]
create-mcs mc-production
[
setxy ( - 48 )
random-ycor
setup-mcs
]
]
ask mcs [
loss-mc
bind
]
ask secBs [
stick
if collide? [check-for-collision]
if random-walk? [rt random-float 360]
bounce
if linked? = false [fd 1]
]
create-secBs (initial-secB - (count secBs)) [
setup-secB
setxy 1 (one-of [random-pxcor] of patches with [pcolor = 78])
set secBs-dead 0
]
tick
end
to walls
ask patches with [pxcor > 0 and pxcor < 50][ set pcolor 19.9]
;; ask patches with [pxcor = 17 or pxcor = (- 17) or pycor = 17 or pycor = (- 17) or pxcor = 0] [ set pcolor blue ]
ask patches with [ pxcor = (- 50)] [ set pcolor 3 ]
ask patches with [ pxcor = 0] [ set pcolor 75 ]
ask patches with [ pxcor = 50 ] [ set pcolor 8 ]
if k != -16 [
periplasm
set k ( k - 1 )
walls
]
end
to periplasm
if l != 0 [
ask patches with [pxcor = l or pycor = k ] [ set pcolor 87 ]
set l ( l + 1 )
periplasm
]
end
to gates
set seperation ( round ( 99 / ( gate-number * 2 ) ) )
if (gate-number mod 2 ) = 1 [
set seperation ( round ( 99 / ( (gate-number + 1) * 2 ) ) )
if j != ((gate-number + 1) / 2) [
ask patches with [ pxcor = 0 and ( pycor = 0 + (seperation * j * 2) or pycor = 0 - (seperation * j * 2) )] [set pcolor 78
set g 0
gate-width]
set j (j + 1)
gates
]
]
if (gate-number mod 2) = 0 [
if j != (gate-number / 2) [
ask patches with [ pxcor = 0 and ( pycor = ( - seperation) + (seperation * (j + 1) * 2) or pycor = seperation - (seperation * (j + 1) * 2) )] [set pcolor 78
set g 0
gate-width
]
set j (j + 1)
gates
]
]
end
to gate-width
if ( gate-size mod 2) = 1 [
if g !=(( gate-size + 1 ) / 2 ) [
ask patch-at-heading-and-distance 0 g [set pcolor 78]
ask patch-at-heading-and-distance 180 g [set pcolor 78]
set g ( g + 1 )
gate-width
]]
if ( gate-size mod 2) = 0 [
if g !=(( gate-size ) / 2 ) [
ask patch-at-heading-and-distance 0 1 [set pcolor 78]
ask patch-at-heading-and-distance 0 (g + 1) [set pcolor 78]
ask patch-at-heading-and-distance 180 g [set pcolor 78]
set g ( g + 1 )
gate-width
]
]
end
to loss-PP1 ;;loss inside cell
if [pcolor] of patch-ahead 1 = 8 [
if linked? = false [die
; ask secBs in-radius 2 [
; set linked? false
; ask links [untie die]
]
]
end
to loss-mc ;;loss inside cell
if [pcolor] of patch-ahead 1 = 3 [die]
if [pcolor] of patch-ahead 2 = 3 [die]
end
to degrade
ask degPs [ let prey one-of PP1s-here
if prey != nobody [
ask PP1s-here [
if bound = false [
if random 100 <= degprob [
ask prey [die] ]
set deg-number ( deg-number + 1 )
]]
]
]
; ask degPs [ let prey one-of complexes-here
; if prey != nobody [
; ask complexes-here [
; if bound = false [
; ask prey [die] ]
; set deg-number ( deg-number + 1 )
; ]
; ]
; ]
end
to bind
if count PP1s-here = 1 [
if bound = false [
if random 100 <= bindprob [
ask PP1s-here [
set bound true
set breed complexes
;;set turtle-type "complex"
set shape "x"
set color 126
set size 3]
die]
]]
end
to bounce ;; turtle procedure
;; or [pcolor] of patch-ahead 1 = 87
if [pcolor] of patch-ahead 1 = 75 or [pcolor] of patch-ahead 1 = 3 [
set heading (- heading)
]
if [pcolor] of patch-ahead 1 = 78 and [pcolor] of patch-here = 87 [
set heading (- heading)
]
ask lefties [
if [pcolor] of patch-ahead 1 != 87 [set heading (- heading)]
]
ask secBs [
if [pcolor] of patch-ahead 1 = 87 or [pcolor] of patch-ahead 1 = 8 [set heading (- heading)]
]
ask PP1s [
if [pcolor] of patch-ahead 1 = 78 and [pcolor] of patch-here = 19.9 [
if linked? = false [
set heading (- heading)]
if linked? = true [
if gateprob <= (random 100) [
set heading (- heading)
]
]
]
if [pcolor] of patch-ahead 1 = 87 and [pcolor] of patch-here = 78 [
set linked? false
unstick
]
]
end
to check-for-collision ;; PP1 procedure
if count other turtles-here = 1
[
let candidate one-of other turtles-here with
[who < [who] of myself and myself != last-collision]
if (candidate != nobody) and (speed > 0 or [speed] of candidate > 0)
[
collide-with candidate
set last-collision candidate
ask candidate [ set last-collision myself ]
]
]
end
to collide-with [ other-particle ] ;; PP1 colliding with other PP1 proteins
let mass2 [mass] of other-particle
let speed2 [speed] of other-particle
let heading2 [heading] of other-particle
let theta (random-float 360)
let v1t (speed * cos (theta - heading))
let v1l (speed * sin (theta - heading))
let v2t (speed2 * cos (theta - heading2))
let v2l (speed2 * sin (theta - heading2))
let vcm (((mass * v1t) + (mass2 * v2t)) / (mass + mass2) )
set v1t (2 * vcm - v1t)
set v2t (2 * vcm - v2t)
set speed sqrt ((v1t ^ 2) + (v1l ^ 2))
set energy (0.5 * mass * speed ^ 2)
if v1l != 0 or v1t != 0
[ set heading (theta - (atan v1l v1t)) ]
ask other-particle [
set speed sqrt ((v2t ^ 2) + (v2l ^ 2))
set energy (0.5 * mass * (speed ^ 2))
if v2l != 0 or v2t != 0
[ set heading (theta - (atan v2l v2t)) ]
]
end
to stick
if random 100 <= secBprob [
if (count other PP1s-here = 1 ) and (linked? = false)
[
let candidate one-of other PP1s-here ; with [stick-count = 1]
if (candidate != nobody); and (speed > 0 or [speed] of candidate > 0)
[
ask candidate [
if linked? = false [
create-link-to myself[
tie
hide-link
] ask one-of other secBs-here [set linked? true]
set linked? true
]
]
]
]
]
end
to unstick
ask out-link-neighbors [
; set heading (- heading)
; set linked? false
; fd 1
die
]
; set linked? false
end
