Sensitivity of a coupled physical-biological model to turbulence: High-frequency simulations in a northern Adriatic station

Chemistry and Ecology

Volumn 23, Issue 2, 2007, Pages 157-175

  Carniel, Sandro ^a   Vichi, Marcello ^b   Sclavo, Mauro ^a  

^a INSTITUTE OF MARINE SCIENCES   (Italy)

^b CENTRO EURO MEDITERRANEO SUI CAMBIAMENTI CLIMATICI   (Italy)

Author keywords

BFM; Coastal zone; Pelagic environment; Physical biogeochemical modelling; Simulation; Turbulent diffusion

Indexed keywords

ADVECTION; BIOGEOCHEMISTRY; BIOLOGICAL SURVEY; BOUNDARY CONDITION; COASTAL ZONE; FREQUENCY ANALYSIS; HYDRODYNAMICS; NUMERICAL MODEL; SENSITIVITY ANALYSIS; TURBULENT DIFFUSION;

ADRIATIC SEA; MEDITERRANEAN SEA;

EID: 34047224746     PISSN: 02757540     EISSN: 10290370     Source Type: Journal    
DOI: 10.1080/02757540701197903     Document Type: Article

References (57)

1. Valiela, I. (1995) Marine Ecological Processes, Springer, New York
2. Wild-Allen, K., Lane, A. and Tett, P. (2002) Phytoplankton, sediment and optical observations in Netherlands coastal water in spring. J. Sea Res., 47, pp. 303-315.
3. Sharples, J., Moore, C., Rippeth, T., Holligan, P., Hydes, D., Fisher, N. and Simpson, J. (2001) Phytoplankton distribution and survival in the thermocline. Limnol. Oceanogr., 46, pp. 486-496.
4. Hofmann, E. and Lascara, C. (1998) Overview of Interdisciplinary Modeling for Marine Ecosystems. The Sea, 10, pp. 507-540. Wiley, New York
5. Simpson, J. (1997) Physical processes in the ROFI regime. J. Mar. Syst., 12, pp. 3-15.
6. Umani, S. Fonda, Sun, C., Feoli, E., Cataletto, B., Cabrini, M. and Milani, L. (1995) Is it possible to identify any plankton succession in the Gulf of Trieste (Northern Adriatic Sea)? In Biology and Ecology of Shallow Coastal Waters. 28th European Marine Biology Symposium
7. Legendre, L. and Rassoulzadegan, F. (1995) Plankton and nutrient dynamics in marine waters. Ophelia, 41, pp. 153-172.
8. Umlauf, L. and Burchard, H. (2005) Second-order turbulence closure models for geophysical boundary layers. A review of recent work. Cont. Shelf Res., 25, pp. 795-827.
9. Chen, F. and Annan, J. (2000) The influence of different turbulence schemes on modelling primary production in a 1D physical-biological model. J. Mar. Syst., 26, pp. 259-288.
10. Kantha, L. (2004) A general ecosystem model for applications to primary productivity and carbon cycle studies in the global oceans. Ocean Modell., 6, pp. 285-335.
11. Allen, J. I., Siddorn, J. R., Blackford, J. C. and Gilbert, F. J. (2004) Turbulence as a control on the microbial loop in a temperate seasonally stratified Mar. Syst. model. J. Sea Res., 52, pp. 1-20.
12. Lacroix, G. and Nival, P. (1998) Influence of meteorological variability on primary production dynamics in the Ligurian Sea (NW Mediterranean Sea) with a 1D hydrodynamic/biological model. J. Mar. Syst., 16, pp. 23-50.
13. Vichi, M., Ruardij, P. and Baretta, J. W. (2004) Link or sink: A model interpretation of the open Baltic biogeochemistry. Biogeosciences, 1, pp. 79-100.
14. Bernardi-Aubry, F., Acri, F., Bastianini, M., Pugnetti, A. and Socal, G. (2006) Phytoplankton contribution to phytoplankton community structure in the Gulf of Venice (NW Adriatic Sea). Int. Rev. Hydrobiol., 91, pp. 51-70.
15. Burchard, H., Bolding, K. and Villarreal, M. R. (1999) Technical Reports EUR 18745 EN, European Commission.
16. Baretta, J., Ebenḧh, W. and Ruardij, P. (1995) The European Regional Seas Ecosystem Model, a complex marine ecosystem model. J. Sea Res., 33, pp. 233-246.
17. Baretta-Bekker, J. and Baretta, J. W. (1997) Ebenhöh. Microbial dynamics in the marine ecosystem model ERSEM II with decoupled carbon assimilation and nutrient uptake. J. Sea Res., 38, pp. 195-212.
18. Allen, J. I., Blackford, J. C., Ashworth, M. I., Proctor, R., Holt, J. T. and Siddorn, J. R. (2001) A highly spatially resolved ecosystem model for the north-west European continental shelf. Sarsia, 86, pp. 423-440.
19. Vichi, M., Oddo, P., Zavatarelli, M., Coluccelli, A., Coppini, G., Celio, M., Umani, S. Fonda and Pinardi, N. (2003) Calibration and validation of a one-dimensional complex marine biogeochemical fluxes model in different areas of the northern Adriatic shelf. Ann. Geophys., 21, pp. 413-436.
20. Vichi, M., Pinardi, N. and Masina, S. (2007) A generalized model of pelagic biogeochemistry for the global ocean ecosystem. Part I: Theory. J. Mar. Syst., 64, pp. 89-109.
21. Vichi, M., Masina, S. and Navarra, A. (2007) A generalized model of pelagic biogeochemistry for the global ocean ecosystem. Part II: numerical simulations. J. Mar. Sys., 64, pp. 110-134.
22. Kantha, L. (2006) Comments on 'Second-order turbulence closure models for geophysical boundary layers. A review of recent work'. Cont. Shelf Res., 26, pp. 819-822.
23. Warner, J. C., Sherwood, C. R., Arango, H. G. and Signell, R. P. (2005) Performance of four turbulence closure models implemented using a generic length scale method. Ocean Modell., 8, pp. 81-113.
24. Rodi, W. (1987) Examples of calculation methods for flow and mixing in stratified fluids. J. Geophys. Res., 92, pp. 5305-5328.
25. Kantha, L. (2004) The length scale equation in turbulence models. Nonlin. Process. Geophys., 7, pp. 1-12.
26. Mellor, G. and Yamada, T. (1982) Development of a turbulence closure model for geophysical fluid problems. Rev. Geophys. Space Phys., 20, pp. 851-875.
27. Galperin, B., Kantha, L., Hassid, S. and Rosati, A. (1988) A quasi-equilibrium turbulent energy model for geophysical flows. J. Atmos. Sci., 45, pp. 55-62.
28. Kantha, L. and Clayson, C. (1994) An improved mixed layer model for geophysical applications. J. Geophys. Res., 99, pp. 25235-25266.
29. Baumert, H. and Peters, H. (2000) Second-moment closures and length scales for weakly stratified turbulent shear flows. J. Geophys. Res., 105, pp. 6453-6468.
30. Xing, J. and Davies, A. (1995) Applications of three dimensional turbulence energy models to the determination of tidal mixing and currents in a shallow sea. Prog. Oceanogr., 35, pp. 135-205.
31. Wilcox, D. (1988) Reassessment of the scale-determining equation for advanced turbulence models. AIAA J., 26, pp. 1299-1310.
32. Umlauf, L., Burchard, H. and Hutter, K. (2003) Extending the k-ω model towards oceanic applications. Oceanogr. Meteorol., 5, pp. 195-218.
33. Hanjalic, K. and Launder, B. (1972) A Reynolds stress model of turbulence and its application to thin shear flows. J. Fluid Mech., 52, pp. 609-638.
34. Wilcox, D. (1998) Turbulence modeling for CFD, DCW Industries, La Cãnada, CA
35. Umlauf, L. and Burchard, H. (2003) A generic length-scale equation for geophysical turbulence. J. Mar. Res., 61, pp. 235-265.
36. Kantha, L. and Carniel, S. (2003) Comments on 'A generic length-scale equation for geophysical turbulence models' by L. Umlauf, H. Burchard. J. Mar. Res., 61, pp. 693-702.
37. Kantha, L. and Clayson, C. (2004) On the effect of surface gravity waves on mixing in the oceanic mixed layer. Ocean Modell., 6, pp. 101-124.
38. Terray, E., Donelan, M., Agarwal, Y., Drennan, W., Kahma, K., Williams III, A. J., Hwang, P. and Kitaigorodskii, S. (1996) Estimates of kinetic energy dissipation under breaking waves. J. Phys. Oceanogr., 26, pp. 972-987.
39. Burchard, H. (2001) Simulating the wave-enhanced layer under breaking surface waves with two-equation turbulence models. J. Phys. Oceanogr., 31, pp. 3133-3145.
40. Large, W., McWilliams, J. and Doney, S. (1994) Oceanic vertical mixing: a review and a model with nonlocal boundary layer parameterisation. Rev. Geophys., 32, pp. 363-403.
41. Craig, P. and Banner, M. (1994) Modelling wave-enhanced turbulence in the ocean surface layer. J. Phys. Oceanogr., 24, pp. 2546-2559.
42. Artegiani, A., Bregant, D., Paschini, E., Pinardi, N., Raicich, F. and Russo, A. (1997) The Adriatic Sea general circulation. Part II: Baroclinic circulation structure. J. Phys. Oceanogr., 27, pp. 97-114.
43. Zavatarelli, M., Bregant, D., Raicich, F., Russo, A. and Artegiani, A. (1998) Climatological biogeochemical characteristic of the Adriatic Sea. J. Mar. Syst., 18, pp. 227-263.
44. Bergamasco, A. and Gacic, M. (1996) Baroclinic response of the Adriatic Sea to an episode of bora wind. J. Phys. Oceanogr., 26, pp. 1354-1369.
45. Cerovecki, I., Pasaric, Z., Kuzmic, M., Brana, J. and Orlic, M. (1991) Ten day variability of the summer circulation in the North Adriatic. Geofizika, 8, pp. 67-81.
46. Pugnetti, A., Acri, F., Bastianini, M., Aubry, F. Bernardi, Berton, A., Bianchi, F., Noack, P. and Socal, G. (2003) Primary production processes in the north-western Adriatic Sea. Proceedings of the AIOL XV Congress, 16, Genoa
47. Reed, R. (1977) On estimating insolation over the ocean. J. Phys. Oceanogr., 17, pp. 854-871.
48. Lancelot, C., Staneva, J., van Eeckhout, D., Beckers, J.-M. and Stanev, E. (2002) Modelling the Danube-influenced north-western continental shelf of the Black Sea. II: Ecosystem response to changes in nutrient delivery by the Danube river after its damming in 1972. Estuar. Coast. Shelf Sci., 54, pp. 473-499.
49. Fasham, M., Ducklow, H. and McKelvie, S. (1990) A nitrogen-based model of plankton dynamics in the oceanic mixed layer. J. Mar. Res., 48, pp. 591-639.
50. Druon, J.-N. and Fèvre, J. Le (1999) Sensitivity of a pelagic ecosystem model to variations of process parameters within a realistic range. J. Mar. Syst., 19, pp. 1-26.
51. Lee, J. -Y., Tett, P., Jones, K., Jones, S., Luyten, P., Smith, C. and Wild-Allen, K. (2002) The PROWQM physical-biological model with benthic-pelagic coupling applied to the northern North Sea. J. Sea Res., 48, pp. 287-331.
52. Vichi, M., Zavatarelli, M. and Pinardi, N. (1998) Seasonal modulation of microbial-mediated carbon fluxes in the Northern Adriatic Sea. Fish. Oceanogr., 7, pp. 182-190.
53. Ruardij, P., Haren, H. V. and Ridderinkhof, H. (1997) The impact of thermal stratification on phytoplankton and nutrient dynamics in shelf seas: A model study. J. Sea Res., 38, pp. 311-331.
54. Carniel, S., Sclavo, M., Kantha, L. and Clayson, C. (2006) Langmuir cells and mixing in the upper ocean. Il Nuovo Cimento, 28, pp. 33-54.
55. Berges, J. and Falkowsky, P. (1998) Physiological stress and cell death in marine phytoplankton: Induction of proteases in response to nitrogen or light limitation. Limnol. Oceanogr., 43, pp. 129-135.
56. Egge, J. (1998) Are diatoms poor competitors at low phosphate concentrations?. J. Mar. Syst., 16, pp. 191-198.
57. Allen, J. I., Somerfield, P. J. and Gilbert, F. J. (2007) Quantifying uncertainty in high-resolution coupled hydrodynamic-ecosystem models. J. Mar. Systems, 64, pp. 3-14.