globals [
  soak-hour
  soak-done
  speed
]

breed [sugars sugar]
breed [etohs etoh]
breed [esters ester]
breed [prvts prvt] ;pyruvate
breed [sugar-trps sugar-trp] ;sugar transporters
breed [glycolyses glycolysis] ;glycolysis enzyme complex
breed [aats aat] ;alcohol acetyltransferase
breed [adhs adh] ;alcohol dehydrogenase

to reset
  clear-all
  reset-ticks
  clear-all-plots

  ask patches [set pcolor black]
end

to cold-soak
  tick
  ask patch 16 16 [
    if (pcolor = 123) or (pcolor = 44) [set soak-done 1]
  ]

  if (soak-done = 1) [stop]
end

to setup
  reset-ticks
  clear-turtles
  clear-all-plots

  ask patches [
    if (16 - pycor >= 5) [set pcolor [220 220 220] ]
  ]

  set-default-shape sugars "dot"
  create-sugars 50 ; ideal start sugar for red : 2lb / gallon (22 Brix, ~120g/L)
  ask sugars [
    set color [255 255 0] ;yellow
    setxy random-xcor (15 - (random-float 3.5))
    set size 0.8
  ]

  set-default-shape etohs "dot"

  set-default-shape esters "dot"

  set-default-shape prvts "dot"

  set-default-shape sugar-trps "square"
  create-sugar-trps 10
  ask sugar-trps [
    set color [255 215 0]
    setxy random-xcor 11.5
  ]

  set-default-shape aats "dot"
  if overexpress-aats = true [create-aats 10]
  create-aats 1
  ask aats [
    set color [0 191 255]
    setxy random-xcor ((random 25) - 16)
    set size 3
  ]

  set-default-shape adhs "dot"
  create-adhs 10
  ask adhs [
    set color [255 165 0]
    setxy random-xcor ((random 25) - 16)
    set size 3
  ]

  set-default-shape glycolyses "dot"
  create-glycolyses 12
  ask glycolyses [
    set color [34 139 34]
    setxy random-xcor ((random 25) - 16)
    set size 3
  ]
end

to go

  if (ferment-temp < 18) [set speed 1]
  if (ferment-temp >= 18) and (ferment-temp < 25) [set speed 1.5]
  if (ferment-temp >= 25) and (ferment-temp <= 30) [set speed 2]
  if (ferment-temp > 30) and (ferment-temp <= 40) [set speed 3]

  if (reaction-monitor = true) [

    ask sugars [ ; random movement
      check-sugar-membrane-collision
      fd speed
      lt random 360
      check-g-collision-m
    ]
    ask esters [
      export
      fd speed
      lt random 360
    ]
    ask etohs [
      export
      fd speed
      lt random 360
    ]
    ask prvts [
      keep-in
      fd speed
      lt random 360
      check-aat-collision-m
      check-adh-collision-m
    ]
    ask aats [
      keep-in
      fd speed
      lt random 360
    ]
    ask adhs [
      keep-in
      fd speed
      lt random 360
    ]
    ask glycolyses [
      keep-in
      fd speed
      lt random 360
    ]
  ]

  if (reaction-monitor = false) [
    ask sugars [ ; random movement
      check-sugar-membrane-collision
      fd speed
      lt random 360
      check-g-collision
    ]
    ask esters [
      export
      fd speed
      lt random 360
    ]
    ask etohs [
      export
      fd speed
      lt random 360
    ]
    ask prvts [
      keep-in
      fd speed
      lt random 360
      check-aat-collision
      check-adh-collision
    ]
    ask aats [
      keep-in
      fd speed
      lt random 360
    ]
    ask adhs [
      keep-in
      fd speed
      lt random 360
    ]
    ask glycolyses [
      keep-in
      fd speed
      lt random 360
    ]
  ]

  tick
end

to check-sugar-membrane-collision
    if (count sugar-trps-here = 1) [
      set heading 180
      fd 3
    ]
    if (ycor < 12) and (ycor > 11.5) [
      set heading 0
      fd 3
    ]
end

to check-g-collision
    if (count glycolyses-here = 1) [hatch-prvts 2 die]
    ask prvts [
      set size 0.8
      set color [34 139 34]
    ]
end

to check-g-collision-m
  if (count glycolyses-here = 1) and (color != [160 82 45]) [hatch-prvts 2 set color [160 82 45]]
  ask prvts [
    set size 0.8
    set color [34 139 34]
  ]
end

to check-aat-collision
  if (count aats-here = 1) and (random 10 = 1) [hatch-esters 1 die]
  ask esters [
    set size 0.8
    set color [0 191 255]
  ]
end

to check-aat-collision-m
  if (count aats-here = 1) and (color = [34 139 34]) [hatch-esters 1 set color [0 0 205]]
  ask esters [
    set size 0.8
    set color [0 191 255]
  ]
end

to check-adh-collision
  if (count adhs-here = 1) [hatch-etohs 1 die]
  ask etohs [
    set size 0.8
    set color [255 165 0] ;orange
  ]
end

to check-adh-collision-m
  if (count adhs-here = 1) and (color = [34 139 34]) [hatch-etohs 1 set color [218 114 124]]
  ask etohs [
    set size 0.8
    set color [255 165 0] ;orange
  ]
end

to export
  if (ycor > 11) and (ycor <= 12) [
    set heading 0
    fd 1
  ]
end

to keep-in
  if (ycor >= 9) [
    set heading 180
    fd 1
  ]
end
@#$#@#$#@
GRAPHICS-WINDOW
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ticks
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BUTTON
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Start
reset
NIL
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T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
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Cold Soak!
set soak-hour ticks / 1000\n  \n  if soak-hour mod 5 <= 50 [\n  \n    if (cold-soak-temp >= 0) and (cold-soak-temp <= 10) [\n      set pcolor scale-color magenta soak-hour 10 0\n    ]\n  \n    if (cold-soak-temp > 10) and (cold-soak-temp <= 15) [\n      set pcolor scale-color 46 soak-hour 10 0\n    ]\n    \n    if (cold-soak-temp > 15) [\n      set pcolor white\n    ]\n  ]\n  \n  if soak-hour mod 5 > 20 [\n    \n    if (cold-soak-temp >= 0) and (cold-soak-temp <= 10) [\n      set pcolor 123\n    ]\n  \n    if (cold-soak-temp > 10) and (cold-soak-temp <= 15) [\n      set pcolor 46\n    ]\n    \n    if (cold-soak-temp > 15) [\n     set pcolor white\n    ]\n  ]\n  \n  if (pcolor = 123) or (pcolor = 44) or (pcolor = 9.9) [stop]
T
1
T
PATCH
NIL
NIL
NIL
NIL
1

BUTTON
212
49
346
83
Cold Soak Timer
cold-soak\n
T
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

SLIDER
18
11
258
44
cold-soak-temp
cold-soak-temp
0
40
6
1
1
degree Celsius
HORIZONTAL

BUTTON
19
238
236
271
Set Fermentation Environment
setup
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
242
238
328
271
Ferment!
go
T
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

MONITOR
20
280
131
325
Sugar
count sugars with [color = [255 255 0]]
17
1
11

MONITOR
18
89
129
134
Cold Soak Time/hr
precision (soak-hour * 10) 2
17
1
11

SLIDER
18
158
252
191
ferment-temp
ferment-temp
0
40
5
1
1
degree Celsius
HORIZONTAL

MONITOR
139
280
204
325
Pyruvate
;count prvts with [color = [34 139 34]]\ncount prvts
17
1
11

PLOT
965
25
1256
286
Ester/Ethanol Production Over Time
Time
Molecules
0.0
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0.0
50.0
true
false
"" ""
PENS
"ester" 1.0 0 -13345367 true "" "plotxy ticks count esters"
"ethanol" 1.0 0 -955883 true "" "plotxy ticks count etohs"

TEXTBOX
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334
282
478
LEGEND:\nwhite field: inside a yeast cell\nyellow squares: sugar transporters\nyellow dots: sugar molecules\ngreen circles: glycolysis enzyme complex\ngreen dots: pyruvate molecules\norange circles: pyruvate carboxylase\norange dots: ethanol molecules\nblue circles: alcohol acetyltransferase\nblue dots: ester molecules
11
0.0
1

MONITOR
212
280
279
325
Ethanol
count etohs with [color = [255 165 0]]
17
1
11

MONITOR
286
280
353
325
Esters
count esters
17
1
11

SWITCH
19
198
196
231
Overexpress-AATs
Overexpress-AATs
1
1
-1000

SWITCH
204
198
369
231
Reaction-Monitor
Reaction-Monitor
1
1
-1000

@#$#@#$#@
## WHAT IS IT?

This model demonstrates the wine fermentation process in a cellular level, simulating the molecule-enzyme interactions inside of a yeast cell.

## HOW IT WORKS

The cold soak step of the simulation is majorly controlled by the cold soak temperature. For red wine, the cold soak temperature should be lower than or equal to 10 degree Celsius. If the cold soak temperature is set in this range, the background color will advance into the red wine color. Otherwise the background color will advance into either yellowish white (white wine color), or white (representing transparent solution).

The fermentation model has seven agents: sugar transporters (yellow square), glucose (yellow, smalldot), pyruvate (green, small dot), ethanol (orange, small dot), ester (blue, small dot), glycolysis enzyme complex (green circle), alcohol dehydrogenase (ADH, orange circle), and alcohol acetyltransferase (AAT, blue circle). The glucose diffuse in the environment and collide with the sugar transporters to get in and out of the yeast cell. Upon collision of glucose and glycolysis enzyme complex, the glucose disappear and generate two pyruvate agents. The pyruvate agents then diffuse in the cell and collide with either ADHs or AATs. Each collision with ADHs will kill the pyruvate agent and generate an ethanol agent. Each collision with AATs will kill the pyruvate agent but only generate an ester agent in a 1:10 chance. This is to ensure the enzyme abundance disparity in the real yeast cells, however since showing 1 AAT and 90 ADHs is not visually welcoming, the grow by chance algorithm was introduced.

The biochemical pathway applied in this simulation:

Glucose + 2 NAD+ + 2 ADP + Pi --glycolysis--> 2 Pyruvate + 2 NADH + 2 ATP + 2 H2O + 2 H+

Pyruvate --> Acetylaldehyde --ADH--> Ethanol

Pyruvate --> Acetyl-CoA --AAT--> Esters

## HOW TO USE IT

First set a temperature for the cold soak process. Click Cold Soak! and then click Cold Soak Timer to start cold soaking. The cold soak process will stop when the wine background reaches the optimum color. However, the timer can be stopped at any time you would like just by clicking on the Cold Soak Timer again. If you would like to reset the color of the wine, click on “Start” button.

Then set a temperature for the fermentation process. This will dictate the yeast growth rate as well as the speed of the molecule movement in wine. Then “Set Up Fermentation” to have all the agents in the environment. Then “Ferment!”.

## THINGS TO NOTICE

The legend on the left lower corner shows what agent represents what molecule. The monitors under the buttons shows the current amount of molecules in the environment.

## THINGS TO TRY

As mentioned in the previous descriptions, the cold soak temperature slider controls the final color of the wine; the fermentation temperature slider controls the speed of molecule movements. Users are encouraged to try out different temperatures to discover how temperature influences the wine fermentation process.

If the "Overexpress-AATs" switch is on before setting up the fermentation, the amount of ester producing enzymes (alcohol acetyltransferase, AAT) will be made 10 times more than when the switch is off, giving the pyruvate agents more chances to interact with the AATs and therefore make more ester products.

If the "Reaction-Monitor" switch is on, the sugar molecules will not disappear after colliding with the glycolysis enzyme complex, but turns into dark brown and can no longer interact with other agents in the environment. This is to give the users a clearer demonstration of the biochemical pathway, showing the life path of the sugar molecules, as well as the production of the pyruvate agents.

## RELATED MODELS

This model is developed the same time as the wine view of wine fermentation process, which demonstrates the interactions between chemicals and the yeast cells in a more detailed perspective, where users can see the chemical reactions happen.

## CREDITS AND REFERENCES

Credit to the Major Qualifying Project "Yeast and Wine Aroma", Tete Zhang, Class of 2016, Department of Bioinformatics and Computational Biology, Worcester Polytechnic Institute, 2016.
@#$#@#$#@
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