globals [ sugar-intake-count soak-hour soak-done ferment-hour etoh-collisions ester-collisions speed ] breed [yeasts yeast] breed [sugars sugar] breed [etohs etoh] breed [esters ester] to reset clear-all clear-all-plots reset-ticks ask patches [set pcolor white] end to cold-soak tick ask patches [ if (pcolor = 123) or (pcolor = 44) or (pcolor = white) [set soak-done 1] ] if (soak-done = 1) [stop] end to setup reset-ticks clear-turtles clear-all-plots set sugar-intake-count 0 set etoh-collisions 0 set ester-collisions 0 set-default-shape yeasts "egg" create-yeasts 5 ; initial yeast count: 20 OD units, one agent represents 4 OD units of cells ask yeasts [ set color [245 245 245] ;light grey set size 5 setxy random-xcor ((random 5) - 14) ; scatter the yeast cells in wine ] set-default-shape sugars "dot" create-sugars 167 ; ideal start sugar for red : 2lb / gallon (22 Brix, ~120g/L, 30g in 125 ml reaciton, 30g -> 0.167 mole, one agent per 1mmole glucose) ask sugars [ set color [255 255 0] ;yellow set size 0.8 setxy random-xcor random-ycor ] set-default-shape etohs "dot" set-default-shape esters "dot" end to go if (count yeasts < 500) [ ; the yeast cell cap is 2000 OD (125ml reaction) if (random 10 = 1) [ask one-of yeasts [grow-yeast]] ] 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] ask sugars [ ; random movement fd speed lt random 360 if (count yeasts-here > 1) [ if (random 90 = 1) [hatch-esters 1] ask esters [ set color [0 191 255] ;deep sky blue set size 0.8 setxy random-xcor random-ycor ] if (random 90 != 1) [hatch-etohs 1] ask etohs [ set color [255 69 0] ;orange red set size 0.8 setxy random-xcor random-ycor ] die ] ] ask esters [ ;random movement fd speed lt random 360 ] ask etohs [ ;random movement fd speed lt random 360 ] if (count sugars <= 10) [ ; when the sugar content is higher than 20g/L ; the sugar is consumed at a rate of 1g/L per 10 hour unit time stop ] tick set ferment-hour ticks end to grow-yeast if (ferment-temp >= 30) and (ferment-temp <= 35) [ hatch 4 [ setxy random-xcor ((random 5) - 14) ; scatter the new yeast cells randomly in wine ] ] if (ferment-temp > 35) or ((ferment-temp < 30) and (ferment-temp >= 20)) [ hatch 2 [ setxy random-xcor ((random 5) - 14) ] ] if (ferment-temp < 20) [ hatch 1 [ setxy random-xcor ((random 5) - 14) ] ] end @#$#@#$#@ GRAPHICS-WINDOW 372 10 878 537 16 16 15.030303030303031 1 10 1 1 1 0 1 1 1 -16 16 -16 16 1 1 1 ticks 30.0 BUTTON 5 216 174 249 Set Up Fermentation setup NIL 1 T OBSERVER NIL NIL NIL NIL 1 BUTTON 186 216 272 249 Ferment! go T 1 T OBSERVER NIL NIL NIL NIL 1 SLIDER 7 18 247 51 cold-soak-temp cold-soak-temp 0 40 3 1 1 degree Celsius HORIZONTAL MONITOR 5 259 154 304 Fermentation Time/hr ferment-hour 17 1 11 MONITOR 158 259 252 304 Yeast Total/OD count yeasts 17 1 11 MONITOR 256 259 339 304 Sugar g/L precision ((count sugars) / 1000 * 180 * 4) 2 17 1 11 BUTTON 119 59 215 92 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 6 59 110 92 Start reset NIL 1 T OBSERVER NIL NIL NIL NIL 1 BUTTON 225 59 357 92 Cold Soak Timer cold-soak T 1 T OBSERVER NIL NIL NIL NIL 1 MONITOR 6 100 124 145 Cold Soak Time/hr precision (soak-hour * 10) 2 17 1 11 SLIDER 5 173 247 206 ferment-temp ferment-temp 0 40 21 1 1 degree Celsius HORIZONTAL MONITOR 5 312 129 357 Ethanol Content % precision (count etohs / 1000 * 46 / 0.78924) 2 17 1 11 MONITOR 132 313 248 358 Ester Level mg/L (count esters * 88) 17 1 11 TEXTBOX 9 426 192 496 LEGEND:\negg shaped, white: yeast cells\nyellow dots: sugar\norange dots: ethanol\nblue dots: ester 11 0.0 1 @#$#@#$#@ ## WHAT IS IT? This model demonstrates the molecular interaction in wine fermentation and provides insight on the production level of ethanol and esters in wine. ## 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 four agents: yeast cells (white, big, egg shaped, one agent representing 1 OD unit of yeast cells), glucose (yellow, small, dot, one agent representing 1 mmol of glucose), ethanol (orange, small, dot, one agent representing 1 mmol of ethanol), and ester (blue, small, dot, one agent representing 1 mmol of ester). The glucose diffuse in the environment and collide with the stationary yeast cells at the bottom of the "fermentation container". Upon collision, the glucose disappear and generate two transparent pyruvate agents (since pyruvates only exist inside of the yeast cells but to follow the biochemical pathways the pyruvates are set to be transparent and cannot be seen by the users). The pyruvate agents then diffuse in the wine and collide with yeast cells. Each collision has a 1:90 chance to create an ester agent. Otherwise the collision will create an ethanol agent and delete the pyruvate agent. This chance disparity is to simulate the abundance disparity between the alcohol dehydrogenase (ADH) and the alcohol acetyltranseferase (AAT) in yeast cell. The simulation stops when the level of sugar in the environment reaches 10 mmol. 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 unit that they are commonly measured. ## 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 the yeast growth as well as the speed of molecule movements. Users are encouraged to try out different temperatures to discover how temperature influences the wine fermentation process. ## RELATED MODELS This model is developed at the same time with the yeast view fermentation model, which demonstrates the wine fermentation process within the yeast cell -- interactions between the chemicals and the yeast enzymes. ## 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. @#$#@#$#@ default true 0 Polygon -7500403 true true 150 5 40 250 150 205 260 250 airplane true 0 Polygon -7500403 true true 150 0 135 15 120 60 120 105 15 165 15 195 120 180 135 240 105 270 120 285 150 270 180 285 210 270 165 240 180 180 285 195 285 165 180 105 180 60 165 15 arrow true 0 Polygon -7500403 true true 150 0 0 150 105 150 105 293 195 293 195 150 300 150 box false 0 Polygon -7500403 true true 150 285 285 225 285 75 150 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