Ocean Acidification

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ocean acidificationD 

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WHAT IS IT?

Today's average ocean pH has dropped from 8.2 to about 8.1 as the ocean has taken up a large amount of CO2 from human activities since the industrial revolution. One aspect of ocean acidification that has confused many students is the decrease in carbonate ion concentration in the ocean resulting from the increase in oceanic CO2 uptake. This model provides students with an established oceanic carbon system. Students may uncouple the three reactions involving the changes in three inorganic carbon species as well as explore the long-term system dynamics resulting from the coupled reactions.

HOW IT WORKS

Six particles are presented in the model: Carbon dioxide, Carbonic acid, bicarbonate ion, carbonate ion, hydronium ion, and hydroxide ion. Two visual styles are provided in the model. The icon visual is more user-friendly and the molecule visual provides more authentic molecule properties. The numbers of particles are transformed from the corresponding ion concentrations in the model. Since the H3O+ concentration is much lower than those of carbon species, a different equation is used to increase the number of H3O+ and OH- so that their changes are more visible.

In the model, a total DIC concentration of 0.002 (mol kg-1) is used initially. The values of two equilibrium constants, Ka1 = 10 ^ (-5.903) and Ka2 = 10 ^ (-9.702), obtained from Millero et al. (2006), are used to calculate the concentrations of three species in a closed system where salinity is 3.3758% and temperature is 20 degree Celsius. The concentrations of Carbonic acid (H2CO3), bicarbonate ion (HCO3-), carbonate ion (CO3(2-)) are calculated using the following equations:

1) [H2CO3] = K-co2 * P-co2 (partial pressures of carbon dioxide) 2) [HCO3-][H+]/[H2CO3]=Ka1 3) [CO3--][H+]/[HCO3]=Ka2

The initial ocean pHs and partial pressures of carbon dioxide were obtained from CO2SYS (https://cdiac.ess-dive.lbl.gov/ftp/co2sys/). The resulting pH in the model is calibrated based on CO2SYS and the average pH deviation is 0.5%.

HOW TO USE IT

  1. Choose a visual style, and then click on the set up/restart button the confirm the setting.

  2. Use the Run 3 coupled reactions continuously to run the three reactions in sequence, i.e.,[CO2+H2O<-->H2CO3; H2CO3<-->(HCO3-)+(H+);(HCO3-)<-->(CO3--)+(H+)] repeatedly. While the model is running, you may change the P-CO2 slider, representing the partial pressures of carbon dioxide, to view the corresponding changes in oceanic pH and the concentrations of three carbon species.

  3. The Run 3 coupled reactions 1000 times button and Run 3 coupled reactions once button allow you to run the three reactions in sequence 1000 times or once per click.

  4. To observe the dynamic changes in depth, you may also run the three reactions individually using the buttons 1-(CO2) + (H2O) <--> (H2CO3), 2-(H2CO3) <--> (H+) + (HCO3-), and 3-(HCO3-) <--> (H+) + (CO3(2-))

THINGS TO TRY AND NOTICE

  • Run the system using the Run 3 coupled reactions continuously button. Drag the P-CO2 slider to increase or decrease the partial pressures of carbon dioxide in the air. Observe 1) how the concentrations of three carbon species changes accordingly and 2) how oceanic pH value change accordingly.

  • The changes in HCO3- might not be very visible in plots. Use the numeric monitors to track the changes in ion concentrations.

  • Use switches to show/hide some ions to focus your observation. For example, only show H2CO3 and hide the rest ions.

  • Apply equilibrium constants and reaction quotients to explain the concentration changes in the model.

RELATED MODELS

Find the learning activity worksheets and more chemistry models at https://sites.google.com/view/3d-science-abm/physics-chemistry

CREDITS AND REFERENCES

Dr. Lin Xiang created this module at the University of Kentucky in 2022. If you mention this model in a publication, we ask that you include the citations below.

Xiang, L. (2022). Ocean Acidification. Department of STEM Education, University of Kentucky, Lexington, KY.

CC BY-NC-SA 4.0

This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/.

References: Millero, F. J.; Graham, T. B.; Huang, F.; Bustos-Serrano, H.; Pierrot, D. Dissociation constants of carbonic acid as a function of salinity and temperature. (2006). Marine Chemistry, 100 (1-2), 80-94.

This model is inspired by the KCVS applets from the 2100 C.E. RCP projections. https://applets.kcvs.ca/OceanAcidification/oceanAcid.html?rcp=2.6

Comments and Questions

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;Dr. Lin Xiang created this module at the University of Kentucky in 2022. If you mention this model in a publication, we ask that you include the citations below.
;
;Xiang, L. (2022). Ocean Acidification. Department of STEM Education, University of Kentucky, Lexington, KY.
;
;This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/.
;
;References:
;Millero, F. J.; Graham, T. B.; Huang, F.; Bustos-Serrano, H.; Pierrot, D. Dissociation constants of carbonic acid as a function of salinity and temperature. (2006). Marine Chemistry, 100 (1-2), 80-94.
;
;This model is inspired by the KCVS applets from the 2100 C.E. RCP projections. https://applets.kcvs.ca/OceanAcidification/oceanAcid.html?rcp=2.6
;;------------------------------


breed [factories factory]
breed [CO2s CO2]
breed [H2CO3s H2CO3]
breed [HCO3s HCO3]
breed [CO3s CO3]
breed [H3OS H30]
breed [OHs OH]
breed [legends legend]

turtles-own[ ]
globals [
  Num-H
  Num-OH
  Num-CO2
  Num-H2CO3
  Num-HCO3
  Num-CO3
  current-ph
  current-pOH
  current-conc-H
  current-conc-OH
  current-conc-H2CO3s
  current-conc-HCO3s
  current-conc-CO3s
  M-H2CO3
  M-HCO3
  M-CO3
  M-H
  M-OH
  K-co2
  Ka1
  Ka2
  change-1
  change-2
  reaction-num
  ]

to setup
  ca

  set-bk
  set-legends
  set-shapes
  set-tt
  display-particles
  hiding-ions
  output


  reset-ticks
end 

to set-bk
  ask patches with [pycor > 35 ] [set pcolor 86]
  ask patches with [pycor <= 35 and pycor >= 30] [set pcolor (-0.5 * pycor + 104)]
  ask patches with [pycor < 30 ] [set pcolor 96.5]
  ask patches with [ pycor = max-pycor or pycor < 6] [set pcolor 101]
  ask patches with [ pxcor = min-pxcor or pxcor = max-pxcor] [set pcolor 101]
end 

to set-tt

  set K-co2 3.886647 * 10 ^ (-8)   ;calculater based on T CO2 0.002 and 250 ppm
  set Ka1 10 ^ (-5.903)         ;from Millero et al. (2006)
  set Ka2 10 ^ (-9.702)         ;;from Millero et al. (2006)

  ;set CO2 in air
  set p-co2 250                  ;when initiating model, PCO2 is always 250. This helps fix students' beginning exploration. It could be less convenient during exploration.
  set current-conc-H 6.29624889 * 10 ^ (-9)
  set current-ph (- log current-conc-H 10) ; 8.201          ;set the initital ph based on p-CO2 referenced from CO2sys 2.1
  set num-CO2 round (P-CO2 / 10)
  create-CO2s num-CO2  [set-tt-properties-air]

  ;set initial carbon species
  set current-conc-H2CO3s 0.0000097166175      ; based on Total C 0.002
  set current-conc-HCO3s 0.00192942933173    ; based on Total 0.002
  set current-conc-CO3s 0.00006086210779    ; based on Total 0.002

  ;reach equlibria
  CO2-dissolve
  Ka1-equilibrium
  Ka2-equilibrium

  ;set visual numbers
  set num-H2CO3 round (5000 * 3 ^ (log current-conc-H2CO3s 10))
  set num-HCO3 round (5000 * 3 ^ (log current-conc-HCO3s 10))
  set num-CO3 round (5000 * 3 ^ (log current-conc-CO3s 10))

  create-H2CO3s Num-H2CO3  [set-tt-properties-aq]
  create-HCO3s Num-HCO3  [set-tt-properties-aq]
  create-CO3s Num-CO3  [set-tt-properties-aq]

  set num-H round (500 * 1.3895 ^ (-1 * current-ph))
  set num-OH round (500 * 1.3895 ^ (-1 * (14 - current-ph)))

  create-h3os num-H [set-tt-properties-aq ]
  create-ohs num-OH [set-tt-properties-aq ]

  ;set factory
  create-factories 1
  [setxy 12 32 set color 35 set size 6 ]
end 

to set-tt-properties-aq
  setxy 1 + random-float (max-pxcor - 2) 6 + random-float (max-pycor - 15)
  (ifelse
    choose-a-visual = "Molecule visual" [set size 1.25]
    choose-a-visual = "Symbolic visual" [set size 1.75])
end 

to set-tt-properties-air
  setxy 1 + random-float (max-pxcor - 2) (30 + random-float 7)
   (ifelse
    choose-a-visual = "Molecule visual" [set size 1.25]
    choose-a-visual = "Symbolic visual" [set size 1.75])
end 

to set-legends
 create-legends 12 [set label-color white]

 ask legend 0[setxy 4 3.5]

 ask legend 1
   [set shape "blank" set size 1.5
    set label "Hydroxide(OH-)" setxy 13.3 3.9]

  ask legend 2 [setxy 4 1]

  ask legend 3
  [set shape "blank" set size 1.5
    set label "Hydronium (H3O+)" setxy 14.5 1.3]

  ask legend 4[setxy 20 3.5]

  ask legend 5
  [set shape "blank" set size 1.5
    set label "Carbon dioxide (CO2)" setxy 32.4 3.9]

  ask legend 6 [setxy 39 3.5]

  ask legend 7
  [set shape "blank" set size 1.5
    set label "Carbonic acid (H2CO3)" setxy 52 3.9]

   ask legend 8 [setxy 20 1]

  ask legend 9
  [set shape "blank" set size 1.5
    set label "Bicarbonate (HCO3-)" setxy 32 1.3]

   ask legend 10[setxy 39 1]

  ask legend 11
  [set shape "blank" set size 1.5
    set label "Carbonate (CO3(2-))" setxy 50.5 1.3]
end 

to go

set-shapes-1
aq-move
H2CO3-move
CO2-move
repeat 1000 [
    CO2-dissolve
    Ka1-equilibrium
    Ka2-equilibrium
    set reaction-num reaction-num + 1]
display-particles
hiding-ions
output


tick
end 

to go-1

set-shapes-1
aq-move
H2CO3-move
CO2-move
    CO2-dissolve tick
    Ka1-equilibrium tick
    Ka2-equilibrium
display-particles
hiding-ions
output


tick
end 

to hiding-ions
  if Hide-CO2-&-Carbonic-acid? = true
    [if any? H2CO3s [ask H2CO3s [die]]
     if any? CO2s [ask CO2s [die]]]

  if Hide-Bicarbonate-ions? = true
    [if any? HCO3s [ask HCO3s [die]]]

  if Hide-Carbonate-ions? = true
    [if any? CO3s [ask CO3s [die]]]

  if Hide-H-&-OH-ions? = true
    [if any? H3Os [ask H3Os [die]]
     if any? OHs [ask OHs [die]]]
end 

to display-particles
  set num-CO2 round (P-CO2 / 10)
  set num-H2CO3 round (5000 * 3 ^ (log current-conc-H2CO3s 10))
  set num-HCO3 round (5000 * 3 ^ (log current-conc-HCO3s 10))
  set num-CO3 round (5000 * 3 ^ (log current-conc-CO3s 10))


ifelse hide-CO2-&-Carbonic-acid? = false
  [
   let current-CO2 count CO2s
   let current-H2CO3 count H2CO3s

    (ifelse
    current-CO2 > num-CO2
     [ask up-to-n-of (current-CO2 - num-CO2) CO2s [die]]
    current-CO2 < num-CO2
     [create-CO2s (num-CO2 - current-CO2)
        [ifelse random 2 = 0 [setxy 10 33 set size 1.25 set heading -90 + random 180]
          [set-tt-properties-air]
        ]])

  (ifelse
    current-H2CO3 > num-H2CO3
     [ask up-to-n-of (current-H2CO3 - num-H2CO3) H2CO3s [die]]
    current-H2CO3 < num-H2CO3
     [create-H2CO3s (num-H2CO3 - current-H2CO3) [set-tt-properties-aq]])
    ]

   [if any? H2CO3s [ask H2CO3s [die]]
    if any? CO2s [ask CO2s [die]]]

ifelse Hide-Bicarbonate-ions? = false
    [let current-HCO3 count HCO3s
  (ifelse
    current-HCO3 > num-HCO3
     [ask up-to-n-of (current-HCO3 - num-HCO3) HCO3s [die]]
    current-HCO3 < num-HCO3
     [create-HCO3s (num-HCO3 - current-HCO3) [set-tt-properties-aq]])]
    [if any? HCO3s [ask HCO3s [die]]]

ifelse Hide-Carbonate-ions? = false
    [let current-CO3 count CO3s
  (ifelse
    current-CO3 > num-CO3
     [ask up-to-n-of (current-CO3 - num-CO3) CO3s [die]]
    current-CO3 < num-CO3
     [create-CO3s (num-CO3 - current-CO3) [ set-tt-properties-aq]])]
    [if any? CO3s [ask CO3s [die]]]

ifelse Hide-H-&-OH-ions? = false
    [ H-OH-equilibrium]
    [if any? H3Os [ask H3Os [die]]
     if any? OHs [ask OHs [die]]]
end 

to CO2-dissolve
  set current-conc-H2CO3s (P-CO2 * K-co2)
end 

to Ka1-equilibrium

  set current-conc-H 10 ^ (- current-ph)

  let Q1 current-conc-H * current-conc-HCO3s / current-conc-H2CO3s

  (ifelse
   (Q1 - Ka1) < Ka1 * -0.00001          ; if Q1 < Ka1 , reaction forward
  [set change-1 ((-1 * (current-conc-HCO3s + current-conc-H) + sqrt ((current-conc-HCO3s + current-conc-H) ^ 2 + 4 * (Ka1 * current-conc-H2CO3s - current-conc-HCO3s * current-conc-H))) / 2)
   set current-conc-H current-conc-H + change-1
   set current-conc-HCO3s current-conc-HCO3s + change-1
   set current-conc-H2CO3s current-conc-H2CO3s - change-1
   set current-ph (- log current-conc-H 10)
  ]

   (Q1 - Ka1) > Ka1 * 0.00001          ; if Q1 > Ka1 , reaction reverse
  [set change-1 ((current-conc-HCO3s + current-conc-H + Ka1) - sqrt ((current-conc-HCO3s + current-conc-H + Ka1) ^ 2 + 4 * (Ka1 * current-conc-H2CO3s - current-conc-HCO3s * current-conc-H))) / 2
   set current-conc-H current-conc-H - change-1
   set current-conc-HCO3s current-conc-HCO3s - change-1
   set current-conc-H2CO3s current-conc-H2CO3s + change-1
   set current-ph (- log current-conc-H 10)
  ])
end 

to Ka2-equilibrium

 set current-conc-H 10 ^ (- current-ph)

 let Q2 current-conc-H * current-conc-CO3s / current-conc-HCO3s

 (ifelse
    (Q2 - Ka2) < Ka2 * -0.00001            ;if Q2 < Ka2 , reaction forward
  [set change-2 (-0.5 * ((current-conc-H + current-conc-CO3s + Ka2) - sqrt ((current-conc-H + current-conc-CO3s + Ka2) ^ 2 + 4 * (Ka2 * current-conc-HCO3s - current-conc-H * current-conc-CO3s))))
   set current-conc-H current-conc-H + change-2
   set current-conc-CO3s current-conc-CO3s + change-2
   set current-ph (- log current-conc-H 10)
   set current-conc-HCO3s current-conc-HCO3s - change-2]

     (Q2 - Ka2) > Ka2 * 0.00001            ;if Q2 > Ka2 , reaction reverse
  [set change-2 ((current-conc-H + current-conc-CO3s + Ka2) - sqrt ((current-conc-H + Ka2 + current-conc-CO3s) ^ 2 + 4 * (Ka2 * current-conc-HCO3s - current-conc-H * current-conc-CO3s))) / 2
   set current-conc-H current-conc-H - change-2
   set current-conc-CO3s current-conc-CO3s - change-2
   set current-ph (- log current-conc-H 10)
   set current-conc-HCO3s current-conc-HCO3s + change-2])
end 

to H-OH-equilibrium

  set num-H round (500 * 1.3895 ^ (-1 * current-ph))
  set num-OH round (500 * 1.3895 ^ (-1 * (14 - current-ph)))

  let current-H count H3Os
  let current-OH count OHs

  (ifelse
    num-H > current-H
     [create-h3os abs (num-H - current-H) [set-tt-properties-aq ]]
    num-H < current-H
    [ask n-of abs (num-H - current-H) h3os [die]])

   (ifelse
    num-OH > current-OH
    [create-ohs abs (num-OH - current-OH) [set-tt-properties-aq ]]
    num-OH < current-OH
    [ask n-of abs (num-OH - current-OH) OHs [die]])
end 

to CO2-move
  ask CO2s
  [(ifelse
    [pcolor] of patch-at dx dy = 101 [rt random 360]    ;if it's boundary ahead, rotate
    [pcolor] of patch-at dx dy <= 89 and [pcolor] of patch-at dx dy >= 86  [fd 0.2]; rt random 360] ;if the patch-ahead has the proper color,move forward
    [pcolor] of patch-at dx dy = 96.5                     ;if water ahead,
       [ifelse random 100 < 20 [set heading 180 fd 1 set breed H2CO3s] [rt random 360]])]  ;dissolve at a certain rate, create the animation
end 

to H2CO3-move
   ask H2CO3s
    [if [pcolor] of patch-at dx dy = 89                ;if air aheas,
      [ifelse random 100 < 20
        [set heading 0 fd 1 set breed CO2s]
        [rt random 360]
    ]]
end 

to aq-move
  ask turtles with [breed != CO2s and breed != legends]    ;ask aq turtles
     [(ifelse
        [pcolor] of patch-at dx dy = 101 or [pcolor] of patch-at dx dy = 89  [rt random 360]    ;if it's boundary ahead, rotate
        [pcolor] of patch-at dx dy = 96.5  [fd 0.2 rt random 360 if ycor < 6 [set ycor 6]] ;if the patch-ahead has the proper color, move forward.If ycor is low, put ycor higher
          )]
end 

to set-shapes
  (ifelse
    choose-a-visual = "Molecule visual"
    [set-default-shape ohs "ab-oh-1"
     set-default-shape H3Os "ab-h3o-1"
     set-default-shape CO2s "ab-CO2"
     set-default-shape H2CO3s "ab-H2CO3"
     set-default-shape HCO3s "ab-HCO3"
     set-default-shape CO3s "ab-CO3"
     set-default-shape factories "factory"
      ask legend 0 [set shape "ab-oh-1" set size 1.75]
      ask legend 2 [set shape "ab-h3o-1" set size 1.75]
      ask legend 4 [set shape "ab-CO2" set size 1.75]
      ask legend 6 [set shape "ab-H2CO3" set size 1.75]
      ask legend 8 [set shape "ab-HCO3" set size 1.75]
      ask legend 10 [set shape "ab-CO3" set size 1.75]

    ]

   choose-a-visual = "Symbolic visual"
    [set-default-shape ohs "ab-oh-2"
     set-default-shape H3Os "ab-h3o-2"
     set-default-shape CO2s "ab-CO2-1"
     set-default-shape H2CO3s "ab-H2CO3-1"
     set-default-shape HCO3s "ab-HCO3-1"
     set-default-shape CO3s "ab-CO3-1"
     set-default-shape factories "factory"
      ask legend 0 [set shape "ab-oh-2" set size 1.75]
      ask legend 2 [set shape "ab-h3o-2" set size 1.75]
      ask legend 4 [set shape "ab-CO2-1" set size 1.75]
      ask legend 6 [set shape "ab-H2CO3-1" set size 1.75]
      ask legend 8 [set shape "ab-HCO3-1" set size 1.75]
      ask legend 10 [set shape "ab-CO3-1" set size 1.75]
  ])
end 

to set-shapes-1
  (ifelse
    choose-a-visual = "Molecule visual"
    [set-default-shape ohs "ab-oh-1"
     set-default-shape H3Os "ab-h3o-1"
     set-default-shape CO2s "ab-CO2"
     set-default-shape H2CO3s "ab-H2CO3"
     set-default-shape HCO3s "ab-HCO3"
     set-default-shape CO3s "ab-CO3"
     set-default-shape factories "factory"
     ask ohs [set shape "ab-oh-1" set size 1.25]
     ask H3Os [set shape "ab-h3o-1" set size 1.25]
     ask CO2s [set shape "ab-CO2" set size 1.25]
     ask H2CO3s [set shape "ab-H2CO3" set size 1.25]
     ask HCO3s [set shape "ab-HCO3" set size 1.25]
     ask CO3s [set shape "ab-CO3" set size 1.25]
      ask legend 0 [set shape "ab-oh-1" set size 1.75]
      ask legend 2 [set shape "ab-h3o-1" set size 1.75]
      ask legend 4 [set shape "ab-CO2" set size 1.75]
      ask legend 6 [set shape "ab-H2CO3" set size 1.75]
      ask legend 8 [set shape "ab-HCO3" set size 1.75]
      ask legend 10 [set shape "ab-CO3" set size 1.75]

    ]

   choose-a-visual = "Symbolic visual"
    [set-default-shape ohs "ab-oh-2"
     set-default-shape H3Os "ab-h3o-2"
     set-default-shape CO2s "ab-CO2-1"
     set-default-shape H2CO3s "ab-H2CO3-1"
     set-default-shape HCO3s "ab-HCO3-1"
     set-default-shape CO3s "ab-CO3-1"
     set-default-shape factories "factory"
     ask ohs [set shape "ab-oh-2" set size 1.75]
     ask H3Os [set shape "ab-h3o-2" set size 1.75]
     ask CO2s [set shape "ab-CO2-1" set size 1.75]
     ask H2CO3s [set shape "ab-H2CO3-1" set size 1.75]
     ask HCO3s [set shape "ab-HCO3-1" set size 1.75]
     ask CO3s [set shape "ab-CO3-1" set size 1.75]
      ask legend 0 [set shape "ab-oh-2" set size 1.75]
      ask legend 2 [set shape "ab-h3o-2" set size 1.75]
      ask legend 4 [set shape "ab-CO2-1" set size 1.75]
      ask legend 6 [set shape "ab-H2CO3-1" set size 1.75]
      ask legend 8 [set shape "ab-HCO3-1" set size 1.75]
      ask legend 10 [set shape "ab-CO3-1" set size 1.75]
  ])
end 

to output
  output-type P-CO2
  repeat 3 [output-type " "]
  output-write precision (current-conc-H2CO3s * 1000000) 5
  repeat 3 [output-type " "]
  output-write precision (current-conc-HCO3s * 1000000) 5
  repeat 3 [output-type " "]
  output-type precision (current-conc-CO3s * 1000000) 5
  repeat 3 [output-type " "]
  output-type precision (current-conc-H) 12
  repeat 3 [output-type " "]
  output-type precision current-ph 3
  repeat 3 [output-type " "]
  output-type precision (current-conc-H * current-conc-HCO3s / current-conc-H2CO3s) 9
  repeat 3 [output-type " "]
  output-print precision (current-conc-H * current-conc-CO3s / current-conc-HCO3s) 13
end

There are 14 versions of this model.

Uploaded by When Description Download
lin xiang 8 months ago adjust interface Download this version
lin xiang 8 months ago reset PCO2 Download this version
lin xiang 8 months ago Update the ions show/hide switches Download this version
lin xiang almost 2 years ago Simplify the interface Download this version
lin xiang about 2 years ago H2CO3 concentration change is fixed. Download this version
lin xiang about 2 years ago Add an output to improve student data collection Download this version
lin xiang about 2 years ago minor updates Download this version
lin xiang about 2 years ago Add reaction quotients Download this version
lin xiang about 2 years ago Adjust the units to help identify numeric data patterns Download this version
lin xiang about 2 years ago Refine the parameters to improve use Download this version
lin xiang about 2 years ago Add a button to run coupled reactions 1000 times Download this version
lin xiang about 2 years ago Fix info typos Download this version
lin xiang about 2 years ago Update the interface to fix small window Download this version
lin xiang about 2 years ago Initial upload Download this version

Attached files

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Ocean Acidification.png preview Preview almost 2 years ago, by lin xiang Download

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