# must use DATABASE ex15.dat
TITLE Example 15.--1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
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PLEASE NOTE: This problem requires database file ex15.dat!!
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PRINT
        -reset false
        -echo_input true
		-status false
SOLUTION 0 Pulse solution with NTA and cobalt
        units umol/L
        pH      6
        C       .49
        O(0)    62.5 
        Nta     5.23
        Co      5.23
        Na      1000
        Cl      1000
SOLUTION 1-10 Background solution initially filling column
        units umol/L
        pH      6
        C       .49
        O(0)    62.5 
        Na      1000
        Cl      1000
COPY solution 0 100 # to use with 20 cells
COPY solution 1 101
END
RATES Rate expressions for the four kinetic reactions
#
        HNTA-2
        -start
10 Ks = 7.64e-7
20 Ka = 6.25e-6
30 qm = 1.407e-3/3600
40 f1 = MOL("HNta-2")/(Ks + MOL("HNta-2"))
50 f2 = MOL("O2")/(Ka + MOL("O2"))
60 rate = -qm * KIN("Biomass") * f1 * f2 
70 moles = rate * TIME
80 PUT(rate, 1)   # save the rate for use in Biomass rate calculation
90 SAVE moles
        -end
#
        Biomass
        -start
10 Y = 65.14
20 b = 0.00208/3600
30 rate = GET(1)  # uses rate calculated in HTNA-2 rate calculation
40 rate = -Y*rate -b*M
50 moles = -rate * TIME
60 if (M + moles) < 0 then moles = -M
70 SAVE moles
        -end
#
        Co_sorption
        -start
10 km = 1/3600
20 kd = 5.07e-3
30 solids = 3.75e3
40 rate = -km*(MOL("Co+2") - (M/solids)/kd)
50 moles = rate * TIME
60 if (M - moles) < 0 then moles = M
70 SAVE moles
        -end
#
        CoNta_sorption
        -start
10 km = 1/3600
20 kd = 5.33e-4
30 solids = 3.75e3
40 rate = -km*(MOL("CoNta-") - (M/solids)/kd)
50 moles = rate * TIME
60 if (M - moles) < 0 then moles = M
70 SAVE moles
        -end
KINETICS 1-10 Four kinetic reactions for all cells
        HNTA-2
                -formula C -3.12 H -1.968 O -4.848 N -0.424 Nta 1.
        Biomass
                -formula        H 0.0
                -m              1.36e-4
        Co_sorption
                -formula CoCl2
                -m      0.0
                -tol 1e-11
        CoNta_sorption
                -formula NaCoNta
                -m      0.0
                -tol 1e-11
#        -cvode true; -cvode_order 3 # uncomment with 1000 times higher sorption rates
COPY kinetics 1 101 # to use with 20 cells                
END
SELECTED_OUTPUT
        -file   ex15.sel
        -mol    Nta-3 CoNta- HNta-2 Co+2
USER_PUNCH
        -headings        hours   Co_sorb CoNta_sorb      Biomass
        -start
  10 punch TOTAL_TIME/3600 + 3600/2/3600
  20 punch KIN("Co_sorption")/3.75e3
  30 punch KIN("CoNta_sorption")/3.75e3
  40 punch KIN("Biomass")
        -end
TRANSPORT First 20 hours have NTA and cobalt in infilling solution
        -cells                10
        -lengths              10*1
        -shifts               20
        -time_step            3600
        -flow_direction       forward
        -boundary_conditions  flux flux
        -dispersivities       10*.05
        -correct_disp         true
        -diffusion_coefficient 0.0
        -punch_cells          10
        -punch_frequency      1
        -print_cells          10
        -print_frequency      5
        -warnings false
USER_GRAPH Example 15B
        -headings 10_cells: Co+2 CoNTA- Biomass
        -chart_title "Example 15, Sorbed Species"
        -axis_titles "Time / hours" "nmol / kgw" "Biomass / (mg/L)"
        -axis_scale x_axis 0 75
        -axis_scale y_axis 0 2
        -axis_scale secondary_y_axis 0 0.4
        -plot_concentration_vs t
        -start
  10 x = TOTAL_TIME/3600 + 3600/2/3600
  20 PLOT_XY -1, -1, line_width = 0, symbol_size = 0
  30 PLOT_XY x, KIN("Co_sorption") / 3.75e3 * 1e9, color = Red, line_width = 0, symbol_size = 4
  40 PLOT_XY x, KIN("CoNta_sorption") / 3.75e3 * 1e9, color = Green, line_width = 0, symbol_size = 4
  50 PLOT_XY x, KIN("Biomass") * 1e3, y-axis = 2, color = Magenta, line_width = 0, symbol_size = 4
        -end
COPY solution 101 0
END
TRANSPORT Last 55 hours with background infilling solution
        -shifts               55
COPY cell 100 0
COPY cell 101 1-20
END
USER_PUNCH
        -start
  10 punch TOTAL_TIME/3600 + 3600/4/3600
  20 punch KIN("Co_sorption")/3.75e3
  30 punch KIN("CoNta_sorption")/3.75e3
  40 punch KIN("Biomass")
        -end
TRANSPORT First 20 hours have NTA and cobalt in infilling solution
        -cells                20
        -lengths              20*0.5
        -shifts               40
        -initial_time         0
        -time_step            1800
        -flow_direction       forward
        -boundary_conditions  flux  flux
        -dispersivities       20*.05
        -correct_disp         true
        -diffusion_coefficient 0.0
        -punch_cells          20
        -punch_frequency      2
        -print_cells          20
        -print_frequency      10
USER_GRAPH
        -headings 20_cells: Co+2 CoNTA- Biomass
        -start
  10 x = TOTAL_TIME/3600 + 3600/4/3600
  20 PLOT_XY -1, -1, line_width = 0, symbol_size = 0
  30 PLOT_XY x, KIN("Co_sorption") / 3.75e3 * 1e9, color = Red, symbol_size = 0
  40 PLOT_XY x, KIN("CoNta_sorption") / 3.75e3 * 1e9, color = Green, symbol_size = 0
  60 PLOT_XY x, KIN("Biomass") * 1e3, y-axis = 2, color = Magenta, symbol_size = 0
        -end
COPY cell 101 0
END
TRANSPORT Last 55 hours with background infilling solution
        -shifts               110
END