ACADIA model:  numerical experiments
 
 

                 In our study we used the ACADIA model version 4, with  3D climatological bi-monthly velocity and temperature/salinity fields used as input. These fields are model generated circulation and temperature/salinity structure fields representing bi-monthly mean conditions. We  focus in detail on the two spring periods, March-April and May-June  and on the summer period July-August to simulate alongshore transport of offshore algal blooms in the Gulf of Main. A finite element formulation of the non-conservative form of the vertically averaged Advection-Diffusion-Reaction equation that tracks depth-averaged single transport variable - Alexandrium tamarense cells concentration was used for  simulation. 
Investigation of the climatological mean seasonal cycle of Alexandrium tamarense consists of  6 separate 6 month long runs. In each experiment, zero cells concentration was used as initial condition, then velocity and temperature/salinity fields  from a particular period were specified (runs 1-2, 5-7 ). In some experiments a  boundary condition 10 cells/l flowing in through the open boundary in the Bay of Fundy was used (runs 3-5). An additional experiment was conducted assuming initial cells concentration equal to 10 cells/l (run 4).  In all the above mentioned experiments it was assumed that the only light is a factor limiting growth rate of the cells. Finally, one more run with nutrient limitation has been performed (run 6).

Below these runs are described and discussed in terms of the Gulf of Main circulation scheme outlined in Lynch et al, 1997. All runs are performed on 'g2s.5b' finite element mesh which includes Bay of Fundy domain.

                                                            Table 1                                             Summary of Model Parameters


      attenuation coeff (water)		                attenk =  0.20                 1/meter

      attenuation coeff  (sedim)		                attens = 3000                  1/meter

  day light averaged irradiance		                  Rad =  280                  watt/m^2

      maximum growth rate		                G_max = 0.60                   1/day

   maintenance respir rate 		                   Gr =  0.05                   1/day

       growth efficiency		                  G_eff = 0.017               m^2/day/watt

        grazing/mortality		                   Graze = 0.1                 1/day

        DIN half-sat constant		                   aksn = 1.5                  mkg/l

        "light" irradiance flux		                   L_light = 2.4               watt/m^2

         "dark" irradiance flux		                   L_dark = 0.024               watt/m^2

 

                           Table 2                                                                                                      Run table


      Time period		    Initial condition     Inflow boundary       Biological model       *.fli movie name   data/obs compares

  March 1 -August 20		                 C = 0           C =   0     germ, growth, mort        cell98_a1.fli      cell98_a1.jpg

          same		                 C = 0           C = 10     growth, mortality        cell98_a3.fli       cell98_a3.jpg

          same		                 C = 10           C = 10      growth, mortality        cell99_a4.fli       cell98_a4.jpg

          same		                 C = 0           C = 10   germ, growth, mort        cell98_a5.fli       cell98_a5.jpg

          same		                 C =  0           C =  0          germ        cell98_a6.fli       cell98_a6.jpg

          same		                 C = 0           C =   0    germ, growth, mort, 
    nutrient limitation		       cell98_a7.fli       cell98_a7.jpg

          same		                 C = 10           C = 10   growth, mort, nutrient
           limitation		        cell98_a8.fli        cell98_a8.jpg

 
 sc98c1.fliis the original Rich Signell's animation.

 run a1.   cell98_a1.fli     Basic run. Initial cells concentration is et to zero,  germination, growth and mortality included.  Initial distribution of Alexandrium cysts in the upper 1 cm of bottom sediments, derived from a survey in October 1997, displayed in init_cyst.jpg. Two maxima in cysts distribution are clearly seen there: approximately between isobaths 75 and 150 m offshore of Kennebec  River and Penobscot Bay. Also, an additional maximum may be tracked in the Bay of Fundy.  Climatological velocity fields for two two bi-monthly periods are displayed here.  Run starts on March 1, 1997 when the endogenous clock is on. 

 run a3.   cell98_a3.fli    Initial cell concentration is set to zero, no germination, the only grows and mortality are included. There is a cell flux 10 cells/l flowing in through the open boundary in the Bay of Fundy. 

run a4.   cell98_a4.fli    Initial cell concentration is set to 10 cell/l;  no germination, the only growth and mortality are included. There is a cell flux 10 cells/l flowing in through the open boundary in the Bay of Fundy.

 run a5.   cell98_a5.fli  Initial cells concentration is set to zero,  germination, growth and mortality included.  There is a cell flux 10 cells/l flowing in through the open boundary in the Bay of Fundy. 

 run a6.   cell98_a6.fli  Initial cells concentration is set to zero,  the only germination included. There is no cell flux  flowing in through the open boundary in the Bay of Fundy. 

 run a7.   cell98_a7.fli     Initial cells concentration is set to zero,  germination, growth, mortality and nutrient limitation are included. NO3 distribution has been derived  from the climatic temperature and salinity fields using a regression formula.  Example of such distribution NO3 field received from the March-April climatology in case of two different regressions (2 and 5) is displayed  here.

 run a8.   cell98_a8.fli    Initial cell concentration is set to 10 cell/l;  no germination, the only growth, mortality, and nutrient limitation are included. There is a cell flux 10 cells/l flowing in through the open boundary in the Bay of Fundy.

A composite of  cell distribution for 3 model runs: a6, a1, and a7 on  May 15,  June 15, July 15, and August 15 is presented in   cell_model_a617.jpg.  A seperate plot displaying results of run a6 may be found here:  cell_model_a6.jpg.   A composite for runs 3, 4 is in    cell_model_a34.jpg.
 
 Cell densities (number of cells / l)  of Alexandrium sp. at 2m, 20m, and the average of these two centered on  June 11, July 11, and August 11 1998 are shown here: cell98_data_ave.jpg.  Cell densities for 2000 survey cruise centered on April 29 and June 9 are shown in   cell2000_data_ave.jpg.
The 100 and 600 cells/l contour lines are given.

 A growth rate diagnosis based on the climatical March-April, May-June, and July-August bi-monthly fields is presented here: cell98_diagn.jpg. 

 Notes on frames.

 Rows 1, 2: Temperature and salinity at the uppermost level.

 Row 3: NO3 field restored from  the climatological temperature and salinity fields using a regression relation.

 Row 4: The growth rate (1/day) depending only on light limitation.

 Row 5: The growth rate (1/day) dependent only on nutrient limitation.

 Note on equations used to compute NO3  field and growth rates.

                                                          NO3 = max(0,NO3'),  NO3' = -144.8 - 0.38 * T + 4.75 * S   (option 2)

                                        R-light = (G_max * G_fac + Gr) * tanh(G_eff * Rad/(G_max * G_fac + Gr))  - Gr ,  light limitation

                                                                       R-no3 = G_max * G_fac * NO3/(NO3 + aksn),  NO3 limitation,

                                                                          R = min(R-light, R-no3) - Graze,  light and NO3 limitation
 where,

                                                     G_fac = T_fac * S_fac, 
                                                     T_fac = -0.000347 * T^3 + 0.0097 * T^2 - 0.0133 * T + 0.131,
                                                     S_fac = -0.0022 * S^2 + 0.103 * S -0.195