AquaEnv: An aquatic acid-base modelling environment in R

Aquatic Geochemistry

Volumn 16, Issue 4, 2010, Pages 507-546

  Hofmann, Andreas F ^a,b   Soetaert, Karline ^a   Middelburg, Jack J ^a,c   Meysman, Filip J R ^b  

^a NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^b VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^c UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Acid base chemistry; CO2 air sea exchange; In silico titration; Marine estuarine and freshwater systems; Ocean acidification; pH modelling; Reactive transport models; TA determination

Indexed keywords

ACID; ACIDIFICATION; AIR-SEA INTERACTION; ALKALINITY; CARBON CYCLE; CARBON DIOXIDE; ESTUARINE CHEMISTRY; MODELING; POREWATER; REACTIVE TRANSPORT; SOFTWARE; WATER CHEMISTRY;

EID: 77954217923     PISSN: 13806165     EISSN: 15731421     Source Type: Journal    
DOI: 10.1007/s10498-009-9084-1     Document Type: Article

References (79)

1. Aloisi G (2008) The calcium carbonate saturation state in cyanobacterial mats throughout Earth's history. Geochim Cosmochim Acta 72: 6037-6060.
2. Anderson LG, Turner DR, Wedborg M, Dyrssen D (1999) Determination of total alkalinity and total dissolved inorganic carbon. In: Grasshoff K, Gremling K, Ehrhardt M (eds) Methods of seawater analysis. Wiley-VCH, New York.
3. Atkins PW (1996) Physikalische Chemie, 2nd edn. VCH, Weinheim.
4. 2 induced acidification in the North Sea. J Mar Syst 64: 229-241.
5. Boudreau BP (1996) Diagenetic models and their implementation. Springer, Berlin.
6. Caldeira K, Wickett ME (2003) Anthropogenic carbon and ocean pH. Nature 425: 365-365.
7. Caldeira K, Wickett ME (2005) Ocean model predictions of chemistry changes from carbon dioxide emissions to the atmosphere and ocean. J Geophys Research-Oceans 110: C09S04.
8. Dickson AG (1981) An exact definition of total alkalinity and a procedure for the estimation of alkalinity and total inorganic carbon from titration data. Deep-Sea Res Part A: Oceanogr Res Pap 28: 609-623.
9. Dickson AG (1984) pH scales and proton-transfer reactions in saline media such as sea-water. Geochim Cosmochim Acta 48: 2299-2308.
10. Dickson AG (1990a) Thermodynamics of the dissociation of boric-acid in synthetic seawater from 273. 15 to 318. 15 K. Deep-Sea Res Part A: Oceanogr Res Pap 37: 755-766.
11. - in synthetic sea-water from 273. 15 to 318. 15 K. J Chem Thermodyn 22: 113-127.
12. Dickson AG, Millero FJ (1987) A comparison of the equilibrium-constants for the dissociation of carbonic-acid in seawater media. Deep-Sea Res Part A: Oceanogr Res Pap 34: 1733-1743.
13. Dickson AG, Riley JP (1979a) Estimation of acid dissociation-constants in seawater media from potentiometric titrations with strong base. 1. Ionic product of water-Kw. Mar Chem 7: 89-99.
14. Dickson AG, Riley JP (1979b) Estimation of acid dissociation-constants in seawater media from potentiometric titrations with strong base. 2. Dissociation of phosphoric-acid. Mar Chem 7: 101-109.
15. 2 measurements. PICES special publications 1-191.
16. DOE (1994) Handbook of methods for the analysis of the various parameters of the carbon dioxide system in sea water, ORNL/CDIAC-74.
17. Doney SC, Mahowald N, Lima I, Feely RA, Mackenzie FT, Lamarque J-F, Rasch PJ (2007) Impact of anthropogenic atmospheric nitrogen and sulfur deposition on ocean acidification and the inorganic carbon system. Proc Natl Acad Sci 104: 14580-14585.
18. 2 problem. Annu Rev Mar Sci 1: 169-192.
19. Durst R (1975) Standard reference materials: standardisation of pH measurements. NBS Special Publications 260-53.
20. Elzhov TV, Mullen KM (2008) minpack. lm: R interface to the Levenberg-Marquardt non-linear least-squares algorithm found in the MINPACK Fortran library, http://cran. r-project. org/package=minpack. lm, R package version 1. 1-1.
21. -1. Deep-Sea Res Part I: Oceanogr Res Pap 55: 1639-1671.
22. Fofonoff NP, Millard RCJ (1983) Algorithms for computation of fundamental properties of seawater. UNESCO technical papers in marine science 44: 55 pp.
23. Follows MJ, Ito T, Dutkiewicz S (2006) On the solution of the carbonate chemistry system in ocean biogeochemistry models. Ocean Model 12: 290-301.
24. 2 system in seawater. J Mar Syst 5: 111-118.
25. 2 on shellfish calcification. Geophys Res Lett 34: L07603.
26. Guinotte JM, Fabry VJ (2008) Ocean acidification and its potential effects on marine ecosystems. Year in Ecology and Conservation Biology 320-342.
27. Harned HS, Davis R (1943) The ionization constant of carbonic acid in water and the solubility of carbon dioxide in water and aqueous salt solutions from 0 to 50°C. J Am Chem Soc 65: 2030-2037.
28. - from 0 to 50°C. J Am Chem Soc 63: 1706-1709.
29. Hofmann AF, Meysman FJR, Soetaert K, Middelburg JJ (2008) A step-by-step procedure for pH model construction in aquatic systems. Biogeosciences 5: 227-251.
30. Hofmann AF, Soetaert K, Middelburg JJ, Meysman FJR (2009a) pH modelling in aquatic systems with time-variable acid-base dissociation constants applied to the turbid, tidal Scheldt estuary. Biogeosciences 6: 1539-1561.
31. Hofmann AF, Middelburg JJ, Soetaert K, Wolf-Gladrow DA, Meysman FJR (2009b) Buffering, stoichiometry and the sensitivity of pH to biogeochemical and physical processes: a proton-based model perspective, in: Quantifying the influences of biogeochemical processes on pH of natural waters, A. F. Hofmann, PhD thesis, 129-151, http://igitur-archive. library. uu. nl/dissertations/2009-0513-200343/UUindex. html.
32. IPCC (2007) Climate Change 2007: Synthesis Report. Contributions of working groups I, II, and III to the fourth assessment report of the intergovernmental panel on climate change [Core Writing team, Pachauri RK, Reisinger A (eds)], IPCC, Geneva, Switzerland.
33. Johansson O, Wedborg M (1982) On the evaluation of potentiometric titrations of sea-water with hydrochloric-acid. Oceanol Acta 5: 209-218.
34. Jourabchi P, van Cappellen P, Regnier P (2005) Quantitative interpretation of pH distributions in aquatic sediments: a reaction-transport modeling approach. Am J Sci 305: 919-956.
35. Khoo KH, Ramette RW, Culberson CH, Bates RG (1977) Determination of hydrogen ion concentrations in seawater from 5 to 40°C: standard potentials at salinities from 20 to 45%. Anal Chem 49: 29-34.
36. Kremling K (1999) Determination of the major constituents, In: Grasshoff K, Gremling K, Ehrhardt M (eds) Methods of seawater analysis. Wiley-VCH, New York.
37. Lavigne H, Proye A, Gattuso J-P, Epitalon J-M, Gentili B, Orr J, Soetaert K (2008) seacarb: calculates parameters of the seawater carbonate system, http://cran. r-project. org/package=seacarb, R package version 2. 1. 4.
38. 2 system calculations, ORNL/CDIAC-105. Carbon dioxide information analysis center, Oak Ridge National Laboratory, U. S. Department of Energy, Oak Ridge.
39. 2 in gas and seawater at equilibrium. Mar Chem 70: 105-119.
40. Luff R, Haeckel M, Wallmann K (2001) Robust and fast FORTRAN and MATLAB® libraries to calculate pH distributions in marine systems. Comput Geosci 27: 157-169.
41. Millero FJ (1979) Thermodynamics of the carbonate system in seawater. Geochim Cosmochim Acta 43: 1651-1661.
42. Millero FJ (1982) The thermodynamics of seawater, Part 1. The PVT properties. Ocean Sci Eng 7: 403-460.
43. Millero FJ (1995) Thermodynamics of the carbon-dioxide system in the oceans. Geochim Cosmochim Acta 59: 661-677.
44. Millero FJ, Pierrot DA (1998) Chemical equilibrium model for natural waters. Aquat Geochem 4: 153-199.
45. Millero FJ, Poisson A (1981) International one-atmosphere equation of state of seawater. Deep-Sea Res Part A: Oceanogr Res Pap 28: 625-629.
46. Millero FJ, Plese T, Fernandez M (1988) The dissociation of hydrogen-sulphide in seawater. Limnol Oceanogr 33: 269-274.
47. Millero FJ, Yao WS, Aicher J (1995) The speciation of Fe(II) and Fe(III) in natural-waters. Mar Chem 50: 21-39.
48. Millero FJ, Graham TB, Huang F, Bustos-Serrano H, Pierrot D (2006) Dissociation constants of carbonic acid in seawater as a function of salinity and temperature. Mar Chem 100: 80-94.
49. Millero FJ, Feistel R, Wright DG, McDougall TJ (2008) The composition of standard seawater and the definition of the reference-composition salinity scale. Deep-Sea Res Part I: Oceanogr Res Pap 55: 50-72.
50. Morel FM, Hering JG (1993) Principles and applications of aquatic chemistry. John Wiley & sons, New York.
51. Morse JW (1983) The kinetics of calcium carbonate dissolution and precipitation. In: Reeder RJ (eds) Carbonates: mineralogy and chemistry, 227-264. Mineral Soc Am.
52. 3 precipitation kinetics in waters from the great bahama bank: implications for the relationship between bank hydrochemistry and whitings. Geochim Cosmochim Acta 67: 2819-2826.
53. Mucci A (1983) The solubility of calcite and aragonite in seawater at various salinities, temperatures, and one atmosphere total pressure. Am J Sci 283: 780-799.
54. Mucci A (1986) Growth-kinetics and composition of magnesian calcite overgrowths precipitated from seawater-quantitative influence of ortho-phosphate ions. Geochim Cosmochim Acta 50: 2255-2265.
55. Murray CN, Riley JP, Wilson TRS (1969) Solubility of gases in distilled water and sea water. I. Nitrogen. Deep-Sea Res 16: 297-310.
56. Perez FF, Fraga F (1987) Association constant of fluoride and hydrogen-ions in seawater. Mar Chem 21: 161-168.
57. 2 system calculations, ORNL/CDIAC-105a. Carbon dioxide information analysis center, Oak Ridge National Laboratory, U. S. Department of Energy, Oak Ridge.
58. R Development Core Team (2005) R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, http://www. r-project. org, ISBN 3-900051-07-0.
59. Riordan E, Minogue N, Healy D, O'Driscoll P, Sodeau JR (2005) Spectroscopic and optimization modeling study of nitrous acid in aqueous solution. J Phys Chem A 109: 779-786.
60. Roy RN, Roy LN, Lawson M, Vogel KM, Moore CP, Davis W, Millero FJ (1993a) Thermodynamics of the dissociation of boric-acid in seawater at S = 35 from 0 to 55°C. Mar Chem 44: 243-248.
61. Roy RN, Roy LN, Vogel KM, PorterMoore C, Pearson T, Good CE, Millero FJ, Campbell DM (1993b) The dissociation constants of carbonic acid in seawater at salinities 5 to 45 and temperatures 0 to 45°C (see also erratum: Mar Chem 52: 183, 1996). Mar Chem 44: 249-267.
62. Royal Society (2005) Ocean acidification due to increasing atmospheric carbon doxide. Policy Document 12/05, The Royal Society, London, UK.
63. Skoog DA, West DM (1982) Fundamentals of analytical chemistry. Holt-Saunders International Editions, Philadelphia.
64. Soetaert K (2008) rootSolve: Non-linear root finding, equilibrium and steady-state analysis of ordinary differential equations, http://cran. r-project. org/package=rootSolve, Rpackage version 1. 2.
65. Soetaert K, Herman PMJ (2009) A practical guide to ecological modelling. Springer, Berlin.
66. Soetaert K, Meysman FJR (2009) ReacTran: reactive-transport modelling in 1D, 2D and 3D, http://cran. r-project. org/package=ReacTran, R package version 1. 1.
67. Soetaert K, Hofmann AF, Middelburg JJ, Meysman FJR, Greenwood J (2007) The effect of biogeochemical processes on pH. Mar Chem 105: 30-51.
68. Soetaert K, Petzold T, Setzer RW (2008) deSolve: general solvers for (ordinary) differential (algebraic) equations, http://cran. r-project. org/package=deSolve, R package version 1. 1.
69. Soetaert K, Petzoldt T, Meysman FJR (2009) marelac: Constants, conversion factors, utilities for the MArine, Riverine, Estuarine, LAcustrine and Coastal sciences, http://cran. r-project. org/package=marelac, R package version 1. 4.
70. Stumm W, Morgan JJ (1996) Aquatic chemistry: chemical equilibria and rates in natural waters. Wiley Interscience, New York.
71. Thomann RV, Mueller JA (1987) Principles of surface water quality modeling and control. Harper & Row, New York.
72. 2 system calculations, ORNL/CDIAC-105b. Carbon dioxide information analysis center, Oak Ridge National Laboratory, U. S. Department of Energy, Oak Ridge.
73. 2 in a river-estuarine-coastal zone system: Application to the Scheldt estuary, marine chemistry special issue: dedicated to the memory of Professor Roland Wollast 106: 92-110.
74. Weiss RF (1970) Solubility of nitrogen, oxygen and argon in water and seawater. Deep-Sea Res 17: 721-735.
75. Weiss RF (1974) Carbon dioxide in water and seawater: the solubility of a non-ideal gas. Mar Chem 2: 203-215.
76. Williams DR (2004) NASA earth fact sheet, http://nssdc. gsfc. nasa. gov/planetary/factsheet/earthfact. html.
77. Wischmeyer AG, Del Amo Y, Brzezinski M, Wolf-Gladrow DA (2003) Theoretical constraints on the uptake of silicic acid species by marine diatoms, Mar Chem 82: 13-29.
78. 2 in seawater: equilibrium, kinetics, isotopes, no. 65 in Elsevier Oceanography Series, 1st edn. Elsevier, Amsterdam.
79. Zeebe RE, Zachos JC, Caldeira K, Tyrrell T (2008) Oceans-Carbon emissions and acidification. Science 321: 51-52.