MbT-Tool: Metabolism based on Thermodynamics
Model was written in NetLogo 5.3.1
•
Viewed 93 times
•
Downloaded 15 times
•
Run 0 times
Download this modelDo you have questions or comments about this model? Ask them here! (You'll first need to log in.)
Info tab cannot be displayed because of an encoding error
Comments and Questions
Please start the discussion about this model!
(You'll first need to log in.)
Click to Run Model
; MbT-tool - Metabolism-based on Thermodynamics by Araujo P., Gras A. and Ginovart M. - 2016 extensions [matrix sound] globals [reactions rd ra rd1 rd2 molecular-weight e-eeq/mol dGpc gamma_cells b-biomass carbon hydrogen oxygen nitrogen b-co2 b-hco3 b-nh4 b-bio b-h2o b-no3- b-no2- b-n2 b-H+ dGp n m dGr A fs fe yc/c to-print gamma_donor reaction energy_reaction synthesis_reaction dGfa dGs p c c2 y_grams_cells/mol_donor y_mol_C_cell/mol_donor row_matrix column_matrix e_d1 e_d2 x_d1 x_d2] to calculate clear-all if Electron_donor = "--- Organic Reactions ---" or Electron_donor = "--- Inorganic Reactions ---" [output-type "Please, select a valid primary electron donor" error-sound stop] if Electron_donor_2 = "--- Organic Reactions ---" and second_electron_donor? = true or Electron_donor_2 = "--- Inorganic Reactions ---" and second_electron_donor? = true [output-type "Please, select a valid second electron donor" error-sound stop] if Electron_acceptor = "--- Organic Reactions ---" or Electron_acceptor = "--- Inorganic Reactions ---" [output-type "Please, select a valid electron acceptor" error-sound stop] if Electron_donor = Electron_acceptor [output-type "It is not possible that the electron donor is equal to the electron acceptor " error-sound stop] setup-reactions setup-electron-donor setup-electron-acceptor setup-microorganism let check (matrix:get ra 0 25) - (matrix:get rd 0 25) if check = 0 [output-type "It is not possible that the electron donor is equal to the electron acceptor " error-sound stop] setup-thermodynamic if fs <= 0 or fe <= 0 [output-print "With this combination of electron-donor and electron acceptor, is not possible write a global reaction" output-print "Please select another combination or change the efficiency value" error-sound stop] setup-reaction yield-prediction setup-output end to error-sound sound:play-note "TRUMPET" 60 64 0.5 end to setup-thermodynamic if Thermodynamics = "TEEM_1" [ set dGp 35.09 - (matrix:get rd 0 25) ifelse dGp > 0 [set n 1][set n -1] set dGr (matrix:get ra 0 25) - (matrix:get rd 0 25) set A -1 * (((dGp / (efficiency ^ n))+(matrix:get b-biomass 0 25 / efficiency))/(efficiency * dGr)) set fs (1 / (1 + A)) set fe (A / (1 + A)) ] if Thermodynamics = "TEEM_2" [ set dGp 30.09 - (matrix:get rd 0 25) ifelse dGp > 0 [set n 1][set n -1] ifelse Electron_donor = "Methane" or Electron_donor = "Methanol" or Electron_donor = "Formate" [set dGfa 46.53][set dGfa 0] ifelse dGfa > 0 [set m 1][set m n] set p abs (1 / (matrix:get rd 0 c)) set dGr (matrix:get ra 0 25) - (matrix:get rd 0 25) - (q / p)* (-219.2) set dGs ((dGfa - (matrix:get rd 0 25)) / (efficiency ^ m)) + ((30.9 - dGfa)/(efficiency ^ n)) + (matrix:get b-biomass 0 25 / efficiency) set A -1 * dGs / (efficiency * dGr) set fs (1 / (1 + A)) set fe (A / (1 + A)) ] end to yield-prediction set y_grams_cells/mol_donor abs(((matrix:get reaction 0 6) * molecular-weight) / (matrix:get reaction 0 c)) let g_donor (matrix:get rd 0 3 + matrix:get rd 0 5) ifelse g_donor <= 0 [ ][set gamma_donor 1 / g_donor set yc/c (gamma_donor / gamma_cells) * fs] set y_mol_C_cell/mol_donor abs(((matrix:get reaction 0 6) * carbon) / (matrix:get reaction 0 c)) end to setup-reaction set energy_reaction ra matrix:- rd set synthesis_reaction b-biomass matrix:- rd set reaction ((fe matrix:* ra) matrix:+ (fs matrix:* b-biomass) matrix:- (rd)) end to setup-microorganism set b-biomass matrix:make-constant 1 column_matrix 0 if Microorganism = "C(n)H(a)O(b)N(c) - Bacteria, Generic" [set carbon c-carbon set hydrogen c-hydrogen set oxygen c-oxygen set nitrogen c-nitrogen] if Microorganism = "C4.17H8O1.75N - Bacteria, Undefined" [set carbon 4.17 set hydrogen 8 set oxygen 1.75 set nitrogen 1] if Microorganism = "C5H9O2.5N - Agrobacterium tumefaciens, succinate" [set carbon 5 set hydrogen 9 set oxygen 2.5 set nitrogen 1] if Microorganism = "C4H7.2O1.93N - Paracoccus denitrificans, succinate" [set carbon 4 set hydrogen 7.2 set oxygen 1.93 set nitrogen 1] if Microorganism = "C3.85H6.69O1.78N - Escherichia coli, glucose" [set carbon 3.85 set hydrogen 6.69 set oxygen 1.78 set nitrogen 1] if Microorganism = "C4.16H8O1.25N - Escherichia coli, undefined" [set carbon 4.16 set hydrogen 8 set oxygen 1.25 set nitrogen 1] if Microorganism = "C4.17H7.21O1.79N - Klebsiella aerogenes, Glycerol, u=0.85 h-1" [set carbon 4.17 set hydrogen 7.21 set oxygen 1.79 set nitrogen 1] if Microorganism = "C4.54H7.91O1.95N - Klebsiella aerogenes, Glycerol, u=0.1 h-1" [set carbon 4.54 set hydrogen 7.91 set oxygen 1.95 set nitrogen 1] if Microorganism = "C4.17H7.42O1.38N - Aerobacter aerogenes, undefined" [set carbon 4.17 set hydrogen 7.42 set oxygen 1.83 set nitrogen 1] if Microorganism = "C4H8O2N - Bacteria, Undefined" [set carbon 4 set hydrogen 8 set oxygen 2 set nitrogen 1] if Microorganism = "C5H8.33O0.81N - Bacteria, Undefined" [set carbon 5 set hydrogen 8.33 set oxygen 0.81 set nitrogen 1] if Microorganism = "C5H8O2N - Bacteria, acetate, aerobic" [set carbon 5 set hydrogen 8 set oxygen 2 set nitrogen 1] if Microorganism = "C5.3H9.1O2.5N - Stahrch, Methanogenic" [set carbon 5.3 set hydrogen 9.1 set oxygen 2.5 set nitrogen 1] if Microorganism = "C5.1H8.5O2.5N - Glucose, Methanogenic" [set carbon 5.1 set hydrogen 8.5 set oxygen 2.5 set nitrogen 1] if Microorganism = "C4.1H6.8O2.2N - Nutrient Broth, Methanogenic" [set carbon 4.1 set hydrogen 6.8 set oxygen 2.2 set nitrogen 1] if Microorganism = "C5H8.8O3.2N - Leucine, Methanogenic" [set carbon 5 set hydrogen 8.8 set oxygen 3.2 set nitrogen 1] if Microorganism = "C4.9H9O3N - Glycine, Methanogenic" [set carbon 4.9 set hydrogen 9 set oxygen 3 set nitrogen 1] if Microorganism = "C4.7H7.7O2.1N - Octanoate, Methanogenic" [set carbon 4.7 set hydrogen 7.7 set oxygen 2.1 set nitrogen 1] if Microorganism = "C4.9H9.4O2.9N - Acetate, Methanogenic" [set carbon 4.9 set hydrogen 9.4 set oxygen 2.9 set nitrogen 1] if Microorganism = "C9H16O5N - Acetate, Nitrite N source aerobic" [set carbon 9 set hydrogen 16 set oxygen 5 set nitrogen 1] if Microorganism = "C9H15O5N - Acetate, Nitrate N source aerobic" [set carbon 9 set hydrogen 15 set oxygen 5 set nitrogen 1] if Microorganism = "C7H12O4N - Acetate, Ammomia N source aerobic" [set carbon 7 set hydrogen 12 set oxygen 4 set nitrogen 1] if Microorganism = "C5H7O2N - Casein, aerobic" [set carbon 5 set hydrogen 7 set oxygen 2 set nitrogen 1] if Microorganism = "C6.33H10.21O3.53N - Saccharomyces cerevisiae, glucose" [set carbon 6.33 set hydrogen 10.21 set oxygen 3.53 set nitrogen 1] set molecular-weight 12.011 * carbon + 1.008 * hydrogen + 16 * oxygen + 14 * nitrogen if N-Source = "NH4+" [ set e-eeq/mol (4 * carbon + hydrogen - 2 * oxygen - 3 * nitrogen) set b-co2 ((carbon - nitrogen) / e-eeq/mol) set b-hco3 (nitrogen / e-eeq/mol) set b-nh4 (nitrogen / e-eeq/mol) set b-H+ (1) set b-bio (1 / e-eeq/mol) set b-h2o ((2 * carbon - oxygen + nitrogen) / e-eeq/mol) set dGpc (3.324 * molecular-weight / e-eeq/mol) set gamma_cells e-eeq/mol / carbon ] if N-Source = "NO3-" [ set e-eeq/mol (4 * carbon + hydrogen - 2 * oxygen + 5 * nitrogen) set b-co2 (carbon / e-eeq/mol) set b-no3- (nitrogen / e-eeq/mol) set b-H+ ((4 * carbon + hydrogen - 2 * oxygen + 6 * nitrogen) / e-eeq/mol) set b-bio (1 / e-eeq/mol) set b-h2o ((3 * nitrogen + 2 * carbon - oxygen) / e-eeq/mol) set dGpc (3.341 * molecular-weight / e-eeq/mol) set gamma_cells e-eeq/mol / carbon ] if N-Source = "NO2-" [ set e-eeq/mol (4 * carbon + hydrogen - 2 * oxygen + 3 * nitrogen) set b-co2 (carbon / e-eeq/mol) set b-no2- (nitrogen / e-eeq/mol) set b-H+ ((4 * carbon + hydrogen - 2 * oxygen + 4 * nitrogen) / e-eeq/mol) set b-bio (1 / e-eeq/mol) set b-h2o ((2 * nitrogen + 2 * carbon - oxygen) / e-eeq/mol) set dGpc (3.333 * molecular-weight / e-eeq/mol) set gamma_cells e-eeq/mol / carbon ] if N-Source = "N2" [ set e-eeq/mol (4 * carbon + hydrogen - 2 * oxygen) set b-co2 (carbon / e-eeq/mol) set b-n2 (nitrogen / (2 * e-eeq/mol)) set b-H+ (1) set b-bio (1 / e-eeq/mol) set b-h2o ((2 * carbon - oxygen) / e-eeq/mol) set dGpc (3.334 * molecular-weight / e-eeq/mol) set gamma_cells e-eeq/mol / carbon ] matrix:set b-biomass 0 13 (b-n2) matrix:set b-biomass 0 9 (b-no3-) matrix:set b-biomass 0 10 (b-no2-) matrix:set b-biomass 0 1 (b-H+) matrix:set b-biomass 0 2 (1) matrix:set b-biomass 0 3 (b-co2) matrix:set b-biomass 0 4 (b-nh4) matrix:set b-biomass 0 5 (b-hco3) matrix:set b-biomass 0 6 (-1 * b-bio) matrix:set b-biomass 0 7 (-1 * b-h2o) matrix:set b-biomass 0 25 (dGpc) end to setup-electron-donor if Electron_donor = "H2O -> O2" [set rd1 matrix:submatrix reactions 0 0 1 column_matrix set c 7] if Electron_donor = "(S2O3)2- -> (SO4)2-" [set rd1 matrix:submatrix reactions 1 0 2 column_matrix set c 21] if Electron_donor = "S -> (SO4)2-" [set rd1 matrix:submatrix reactions 2 0 3 column_matrix set c 22] if Electron_donor = "(SO3)2- -> (SO4)2-" [set rd1 matrix:submatrix reactions 3 0 4 column_matrix set c 18] if Electron_donor = "H2S + HS- -> (SO3)2-" [set rd1 matrix:submatrix reactions 4 0 5 column_matrix set c 19] if Electron_donor = "H2S + HS- -> (SO4)2-" [set rd1 matrix:submatrix reactions 5 0 6 column_matrix set c 19] if Electron_donor = "N2 -> N2O" [set rd1 matrix:submatrix reactions 6 0 7 column_matrix set c 13] if Electron_donor = "N2O -> NO" [set rd1 matrix:submatrix reactions 7 0 8 column_matrix set c 12] if Electron_donor = "N2 -> NO2-" [set rd1 matrix:submatrix reactions 8 0 9 column_matrix set c 13] if Electron_donor = "NO -> NO2-" [set rd1 matrix:submatrix reactions 9 0 10 column_matrix set c 11] if Electron_donor = "N2 -> NO3-" [set rd1 matrix:submatrix reactions 10 0 11 column_matrix set c 13] if Electron_donor = "NO + N2O -> NO3-" [set rd1 matrix:submatrix reactions 11 0 12 column_matrix set c 12] if Electron_donor = "N2O -> NO3-" [set rd1 matrix:submatrix reactions 12 0 13 column_matrix set c 12] if Electron_donor = "NO -> NO3-" [set rd1 matrix:submatrix reactions 13 0 14 column_matrix set c 11] if Electron_donor = "NO2- -> NO3-" [set rd1 matrix:submatrix reactions 14 0 15 column_matrix set c 10] if Electron_donor = "H2 -> H+" [set rd1 matrix:submatrix reactions 15 0 16 column_matrix set c 14] if Electron_donor = "Fe2+ -> Fe3+" [set rd1 matrix:submatrix reactions 16 0 17 column_matrix set c 16] if Electron_donor = "NH4+ -> N2" [set rd1 matrix:submatrix reactions 17 0 18 column_matrix set c 4] if Electron_donor = "NH4+ -> NO3-" [set rd1 matrix:submatrix reactions 18 0 19 column_matrix set c 4] if Electron_donor = "NH4+ -> NO2-" [set rd1 matrix:submatrix reactions 19 0 20 column_matrix set c 4] if Electron_donor = "Acetate" [set rd1 matrix:submatrix reactions 20 0 21 column_matrix set c 8] if Electron_donor = "Alanine" [set rd1 matrix:submatrix reactions 21 0 22 column_matrix set c 23] if Electron_donor = "Benzoate" [set rd1 matrix:submatrix reactions 22 0 23 column_matrix set c 24] if Electron_donor = "Citrate" [set rd1 matrix:submatrix reactions 23 0 24 column_matrix set c 26] if Electron_donor = "Ethanol" [set rd1 matrix:submatrix reactions 24 0 25 column_matrix set c 27] if Electron_donor = "Formate" [set rd1 matrix:submatrix reactions 25 0 26 column_matrix set c 28] if Electron_donor = "Glucose" [set rd1 matrix:submatrix reactions 26 0 27 column_matrix set c 29] if Electron_donor = "Glutamate" [set rd1 matrix:submatrix reactions 27 0 28 column_matrix set c 30] if Electron_donor = "Glycerol" [set rd1 matrix:submatrix reactions 28 0 29 column_matrix set c 31] if Electron_donor = "Glycine" [set rd1 matrix:submatrix reactions 29 0 30 column_matrix set c 32] if Electron_donor = "Lactate" [set rd1 matrix:submatrix reactions 30 0 31 column_matrix set c 33] if Electron_donor = "Methane" [set rd1 matrix:submatrix reactions 31 0 32 column_matrix set c 34] if Electron_donor = "Methanol" [set rd1 matrix:submatrix reactions 32 0 33 column_matrix set c 35] if Electron_donor = "Palmitate" [set rd1 matrix:submatrix reactions 33 0 34 column_matrix set c 36] if Electron_donor = "Propionate" [set rd1 matrix:submatrix reactions 34 0 35 column_matrix set c 37] if Electron_donor = "Pyruvate" [set rd1 matrix:submatrix reactions 35 0 36 column_matrix set c 38] if Electron_donor = "Succinate" [set rd1 matrix:submatrix reactions 36 0 37 column_matrix set c 39] if Electron_donor = "NTA - Acid nitrilotriacetic" [set rd1 matrix:submatrix reactions 37 0 38 column_matrix set c 40] ifelse second_electron_donor? = true [ if Electron_donor_2 = "H2O -> O2" [set rd2 matrix:submatrix reactions 0 0 1 column_matrix set c2 7] if Electron_donor_2 = "(S2O3)2- -> (SO4)2-" [set rd2 matrix:submatrix reactions 1 0 2 column_matrix set c2 21] if Electron_donor_2 = "S -> (SO4)2-" [set rd2 matrix:submatrix reactions 2 0 3 column_matrix set c2 22] if Electron_donor_2 = "(SO3)2- -> (SO4)2-" [set rd2 matrix:submatrix reactions 3 0 4 column_matrix set c2 18] if Electron_donor_2 = "H2S + HS- -> (SO3)2-" [set rd2 matrix:submatrix reactions 4 0 5 column_matrix set c2 19] if Electron_donor_2 = "H2S + HS- -> (SO4)2-" [set rd2 matrix:submatrix reactions 5 0 6 column_matrix set c2 19] if Electron_donor_2 = "N2 -> N2O" [set rd2 matrix:submatrix reactions 6 0 7 column_matrix set c2 13] if Electron_donor_2 = "N2O -> NO" [set rd2 matrix:submatrix reactions 7 0 8 column_matrix set c2 12] if Electron_donor_2 = "N2 -> NO2-" [set rd2 matrix:submatrix reactions 8 0 9 column_matrix set c2 13] if Electron_donor_2 = "NO -> NO2-" [set rd2 matrix:submatrix reactions 9 0 10 column_matrix set c2 11] if Electron_donor_2 = "N2 -> NO3-" [set rd2 matrix:submatrix reactions 10 0 11 column_matrix set c2 13] if Electron_donor_2 = "NO + N2O -> NO3-" [set rd2 matrix:submatrix reactions 11 0 12 column_matrix set c2 12] if Electron_donor_2 = "N2O -> NO3-" [set rd2 matrix:submatrix reactions 12 0 13 column_matrix set c2 12] if Electron_donor_2 = "NO -> NO3-" [set rd2 matrix:submatrix reactions 13 0 14 column_matrix set c2 11] if Electron_donor_2 = "NO2- -> NO3-" [set rd2 matrix:submatrix reactions 14 0 15 column_matrix set c2 10] if Electron_donor_2 = "H2 -> H+" [set rd2 matrix:submatrix reactions 15 0 16 column_matrix set c2 14] if Electron_donor_2 = "Fe2+ -> Fe3+" [set rd2 matrix:submatrix reactions 16 0 17 column_matrix set c2 16] if Electron_donor_2 = "NH4+ -> N2" [set rd2 matrix:submatrix reactions 17 0 18 column_matrix set c2 4] if Electron_donor_2 = "NH4+ -> NO3-" [set rd2 matrix:submatrix reactions 18 0 19 column_matrix set c2 4] if Electron_donor_2 = "NH4+ -> NO2-" [set rd2 matrix:submatrix reactions 19 0 20 column_matrix set c2 4] if Electron_donor_2 = "Acetate" [set rd2 matrix:submatrix reactions 20 0 21 column_matrix set c2 8] if Electron_donor_2 = "Alanine" [set rd2 matrix:submatrix reactions 21 0 22 column_matrix set c2 23] if Electron_donor_2 = "Benzoate" [set rd2 matrix:submatrix reactions 22 0 23 column_matrix set c2 24] if Electron_donor_2 = "Citrate" [set rd2 matrix:submatrix reactions 23 0 24 column_matrix set c2 26] if Electron_donor_2 = "Ethanol" [set rd2 matrix:submatrix reactions 24 0 25 column_matrix set c2 27] if Electron_donor_2 = "Formate" [set rd2 matrix:submatrix reactions 25 0 26 column_matrix set c2 28] if Electron_donor_2 = "Glucose" [set rd2 matrix:submatrix reactions 26 0 27 column_matrix set c2 29] if Electron_donor_2 = "Glutamate" [set rd2 matrix:submatrix reactions 27 0 28 column_matrix set c2 30] if Electron_donor_2 = "Glycerol" [set rd2 matrix:submatrix reactions 28 0 29 column_matrix set c2 31] if Electron_donor_2 = "Glycine" [set rd2 matrix:submatrix reactions 29 0 30 column_matrix set c2 32] if Electron_donor_2 = "Lactate" [set rd2 matrix:submatrix reactions 30 0 31 column_matrix set c2 33] if Electron_donor_2 = "Methane" [set rd2 matrix:submatrix reactions 31 0 32 column_matrix set c2 34] if Electron_donor_2 = "Methanol" [set rd2 matrix:submatrix reactions 32 0 33 column_matrix set c2 35] if Electron_donor_2 = "Palmitate" [set rd2 matrix:submatrix reactions 33 0 34 column_matrix set c2 36] if Electron_donor_2 = "Propionate" [set rd2 matrix:submatrix reactions 34 0 35 column_matrix set c2 37] if Electron_donor_2 = "Pyruvate" [set rd2 matrix:submatrix reactions 35 0 36 column_matrix set c2 38] if Electron_donor_2 = "Succinate" [set rd2 matrix:submatrix reactions 36 0 37 column_matrix set c2 39] if Electron_donor_2 = "NTA - Acid nitrilotriacetic" [set rd2 matrix:submatrix reactions 37 0 38 column_matrix set c2 40] set e_d1 abs ( 1 / matrix:get rd1 0 c) set e_d2 abs ( 1 / matrix:get rd2 0 c2) let total_electrons (e_d1 + e_d2) set x_d1 (e_d1 / total_electrons) set x_d2 (e_d2 / total_electrons) set rd (x_d1 matrix:* rd1) matrix:+ (x_d2 matrix:* rd2) ] [set rd rd1 matrix:+ rd2] end to setup-electron-acceptor if Electron_acceptor = "O2 -> H2O" [set ra matrix:submatrix reactions 0 0 1 column_matrix ] if Electron_acceptor = "(SO4)2- -> (S2O3)2-" [set ra matrix:submatrix reactions 1 0 2 column_matrix ] if Electron_acceptor = "(SO4)2- -> S" [set ra matrix:submatrix reactions 2 0 3 column_matrix ] if Electron_acceptor = "(SO4)2- -> (SO3)2-" [set ra matrix:submatrix reactions 3 0 4 column_matrix ] if Electron_acceptor = "(SO3)2- -> H2S + HS-" [set ra matrix:submatrix reactions 4 0 5 column_matrix ] if Electron_acceptor = "(SO4)2- -> H2S + HS-" [set ra matrix:submatrix reactions 5 0 6 column_matrix ] if Electron_acceptor = "N2O -> N2" [set ra matrix:submatrix reactions 6 0 7 column_matrix ] if Electron_acceptor = "NO -> N2O" [set ra matrix:submatrix reactions 7 0 8 column_matrix ] if Electron_acceptor = "NO2- -> N2" [set ra matrix:submatrix reactions 8 0 9 column_matrix ] if Electron_acceptor = "NO2- -> NO" [set ra matrix:submatrix reactions 9 0 10 column_matrix ] if Electron_acceptor = "NO3- -> N2" [set ra matrix:submatrix reactions 10 0 11 column_matrix ] if Electron_acceptor = "NO3- -> NO + N2O" [set ra matrix:submatrix reactions 11 0 12 column_matrix ] if Electron_acceptor = "NO3- -> N2O" [set ra matrix:submatrix reactions 12 0 13 column_matrix ] if Electron_acceptor = "NO3- -> NO" [set ra matrix:submatrix reactions 13 0 14 column_matrix ] if Electron_acceptor = "NO3- -> NO2-" [set ra matrix:submatrix reactions 14 0 15 column_matrix ] if Electron_acceptor = "H+ -> H2" [set ra matrix:submatrix reactions 15 0 16 column_matrix ] if Electron_acceptor = "Fe3+ -> Fe2+" [set ra matrix:submatrix reactions 16 0 17 column_matrix ] if Electron_acceptor = "N2 -> NH4+" [set ra matrix:submatrix reactions 17 0 18 column_matrix ] if Electron_acceptor = "NO3- -> NH4+" [set ra matrix:submatrix reactions 18 0 19 column_matrix ] if Electron_acceptor = "NO2- -> NH4+" [set ra matrix:submatrix reactions 19 0 20 column_matrix ] if Electron_acceptor = "Acetate" [set ra matrix:submatrix reactions 20 0 21 column_matrix ] if Electron_acceptor = "Alanine" [set ra matrix:submatrix reactions 21 0 22 column_matrix ] if Electron_acceptor = "Benzoate" [set ra matrix:submatrix reactions 22 0 23 column_matrix ] if Electron_acceptor = "Citrate" [set ra matrix:submatrix reactions 23 0 24 column_matrix ] if Electron_acceptor = "Ethanol" [set ra matrix:submatrix reactions 24 0 25 column_matrix ] if Electron_acceptor = "Formate" [set ra matrix:submatrix reactions 25 0 26 column_matrix ] if Electron_acceptor = "Glucose" [set ra matrix:submatrix reactions 26 0 27 column_matrix ] if Electron_acceptor = "Glutamate" [set ra matrix:submatrix reactions 27 0 28 column_matrix ] if Electron_acceptor = "Glycerol" [set ra matrix:submatrix reactions 28 0 29 column_matrix ] if Electron_acceptor = "Glycine" [set ra matrix:submatrix reactions 29 0 30 column_matrix ] if Electron_acceptor = "Lactate" [set ra matrix:submatrix reactions 30 0 31 column_matrix ] if Electron_acceptor = "Methane" [set ra matrix:submatrix reactions 31 0 32 column_matrix ] if Electron_acceptor = "Methanol" [set ra matrix:submatrix reactions 32 0 33 column_matrix ] if Electron_acceptor = "Palmitate" [set ra matrix:submatrix reactions 33 0 34 column_matrix ] if Electron_acceptor = "Propionate" [set ra matrix:submatrix reactions 34 0 35 column_matrix ] if Electron_acceptor = "Pyruvate" [set ra matrix:submatrix reactions 35 0 36 column_matrix ] if Electron_acceptor = "Succinate" [set ra matrix:submatrix reactions 36 0 37 column_matrix ] if Electron_acceptor = "NTA - Acid nitrilotriacetic" [set ra matrix:submatrix reactions 37 0 38 column_matrix ] end to setup-output output-print " " ifelse second_electron_donor? = true [output-type "(rd) Electron donor(s) --> " output-type Electron_donor output-type " + " output-type Electron_donor_2 output-print " : "] [output-type "(rd) Electron donor --> " output-type Electron_donor output-print " : "] set to-print matrix:copy rd output-all output-print " " output-type "(ra) Electron acceptor --> " output-type Electron_acceptor output-print " : " set to-print matrix:copy ra output-all output-print " " output-type "(rc) Biomass half reaction : " output-type Microorganism output-type " , N-Source : " output-print N-source ifelse (matrix:get b-biomass 0 3) = 0 [ ][output-type precision (matrix:get b-biomass 0 3) 4 output-type " CO2 + "] ifelse (matrix:get b-biomass 0 5) = 0 [ ][output-type precision (matrix:get b-biomass 0 5) 4 output-type " HCO3- + "] ifelse (matrix:get b-biomass 0 4) = 0 [ ][output-type precision (matrix:get b-biomass 0 4) 4 output-type " NH4+ + "] ifelse (matrix:get b-biomass 0 9) = 0 [ ][output-type precision (matrix:get b-biomass 0 9) 4 output-type " NO3- + "] ifelse (matrix:get b-biomass 0 10) = 0 [ ][output-type precision (matrix:get b-biomass 0 10) 4 output-type " NO2- + "] ifelse (matrix:get b-biomass 0 13) = 0 [ ][output-type precision (matrix:get b-biomass 0 13) 4 output-type " N2 + "] ifelse (matrix:get b-biomass 0 1) = 0 [ ][output-type precision (matrix:get b-biomass 0 1) 4 output-type " H+ + "] ifelse (matrix:get b-biomass 0 2) = 0 [ ][output-type precision (matrix:get b-biomass 0 2) 4 output-type " e- --> "] output-type precision abs (matrix:get b-biomass 0 6) 4 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type nitrogen output-type " + " output-type precision abs (matrix:get b-biomass 0 7) 4 output-type " H2O " output-type "[ ∆G = " output-type precision (matrix:get b-biomass 0 25) 4 output-print " KJ/e-eq ]" output-print " " output-print "Energy reaction : " set to-print matrix:copy energy_reaction output-all output-print " " output-print "Synthesis reaction : " set to-print matrix:copy synthesis_reaction output-all output-print " " output-type "Balanced equation using " output-type Thermodynamics output-print " : " output-type "[ fe = " output-type precision fe 2 output-type " ] [ fs = " output-type precision fs 2 output-type " ] [ e = " output-type efficiency output-print " ]" set to-print matrix:copy reaction output-all output-print " " output-print "Yield prediction :" output-type "Yg/m = " output-type precision y_grams_cells/mol_donor 3 if Electron_donor = "H2S + HS- -> (SO3)2-" or Electron_donor = "H2S + HS- -> (SO4)2-" [output-print " [ grams_cells/mol_H2S ]"] ifelse Electron_donor = "NO + N2O -> NO3-" [output-print " [ grams_cells/mol_N2O ]"][output-print " [ grams_cells/mol_donor ]"] output-type "Yc/m = " output-type precision y_mol_C_cell/mol_donor 3 if Electron_donor = "H2S + HS- -> (SO3)2-" or Electron_donor = "H2S + HS- -> (SO4)2-" [output-print " [ mol_C_cell/mol_H2S ]"] ifelse Electron_donor = "NO + N2O -> NO3-" [output-print " [ mol_C_cells/mol_N2O ]"][output-print " [ mol_C_cells/mol_donor ]"] ifelse yc/c = 0 [ ][output-type "Yc/c = " output-type precision yc/c 3 output-print " [ mol_C_cell/mol_C_donor ]"] end to output-all ifelse (matrix:get to-print 0 8) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 8) 4 output-type " CH3COO- "] ifelse (matrix:get to-print 0 23) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 23) 4 output-type " CH3CHNH2COO- "] ifelse (matrix:get to-print 0 24) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 24) 4 output-type " C6H5COO- "] ifelse (matrix:get to-print 0 26) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 26) 4 output-type " (COO-)CH2COH(COO-)CH2COO- "] ifelse (matrix:get to-print 0 27) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 27) 4 output-type " CH3CH2OH "] ifelse (matrix:get to-print 0 28) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 28) 4 output-type " HCOO- "] ifelse (matrix:get to-print 0 29) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 29) 4 output-type " C6H12O6 "] ifelse (matrix:get to-print 0 30) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 30) 4 output-type " COOHCH2CH2CHNH2COO- "] ifelse (matrix:get to-print 0 31) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 31) 4 output-type " CH2OHCHOHCH2OH "] ifelse (matrix:get to-print 0 32) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 32) 4 output-type " CH2NH2COOH "] ifelse (matrix:get to-print 0 33) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 33) 4 output-type " CH3CHOHCOO- "] ifelse (matrix:get to-print 0 34) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 34) 4 output-type " CH4 "] ifelse (matrix:get to-print 0 35) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 35) 4 output-type " CH3OH "] ifelse (matrix:get to-print 0 36) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 36) 4 output-type " CH3(CH2)14COO- "] ifelse (matrix:get to-print 0 37) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 37) 4 output-type " CH3CH2COO- "] ifelse (matrix:get to-print 0 38) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 38) 4 output-type " CH3COCOO- "] ifelse (matrix:get to-print 0 39) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 39) 4 output-type " (C4H4O4)2- "] ifelse (matrix:get to-print 0 40) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 40) 4 output-type " (C6H6O6N)3- "] ifelse (matrix:get to-print 0 0) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 0) 4 output-type " O2 "] ifelse (matrix:get to-print 0 3) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 3) 4 output-type " CO2 "] ifelse (matrix:get to-print 0 4) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 4) 4 output-type " NH4+ "] ifelse (matrix:get to-print 0 5) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 5) 4 output-type " HCO3- "] ifelse (matrix:get to-print 0 6) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 6) 4 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type nitrogen output-type " "] ifelse (matrix:get to-print 0 7) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 7) 4 output-type " H2O "] ifelse (matrix:get to-print 0 9) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 9) 4 output-type " NO3- "] ifelse (matrix:get to-print 0 10) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 10) 4 output-type " NO2- "] ifelse (matrix:get to-print 0 11) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 11) 4 output-type " NO "] ifelse (matrix:get to-print 0 12) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 12) 4 output-type " N2O "] ifelse (matrix:get to-print 0 13) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 13) 4 output-type " N2 "] ifelse (matrix:get to-print 0 14) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 14) 4 output-type " H2 "] ifelse (matrix:get to-print 0 15) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 15) 4 output-type " Fe3+ "] ifelse (matrix:get to-print 0 16) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 16) 4 output-type " Fe2+ "] ifelse (matrix:get to-print 0 17) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 17) 4 output-type " (SO4)2- "] ifelse (matrix:get to-print 0 18) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 18) 4 output-type " (SO3)2- "] ifelse (matrix:get to-print 0 19) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 19) 4 output-type " H2S "] ifelse (matrix:get to-print 0 20) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 20) 4 output-type " HS- "] ifelse (matrix:get to-print 0 21) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 21) 4 output-type " (S2O3)2- "] ifelse (matrix:get to-print 0 22) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 22) 4 output-type " S "] ifelse (matrix:get to-print 0 1) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 1) 4 output-type " H+ "] ifelse (matrix:get to-print 0 2) <= 0 [ ][output-type "+ " output-type precision (matrix:get to-print 0 2) 4 output-type " e- "] output-type "--> " ifelse (matrix:get to-print 0 6) >= 0 [ ][output-type precision abs (matrix:get to-print 0 6) 4 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type nitrogen output-type " "] ifelse (matrix:get to-print 0 8) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 8) 4 output-type " CH3COO- "] ifelse (matrix:get to-print 0 23) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 23) 4 output-type " CH3CHNH2COO- "] ifelse (matrix:get to-print 0 24) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 24) 4 output-type " C6H5COO- "] ifelse (matrix:get to-print 0 26) >= 0 [ ][output-type "+ " output-type precision abs(matrix:get to-print 0 26) 4 output-type " (COO-)CH2COH(COO-)CH2COO- "] ifelse (matrix:get to-print 0 27) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 27) 4 output-type " CH3CH2OH "] ifelse (matrix:get to-print 0 28) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 28) 4 output-type " HCOO- "] ifelse (matrix:get to-print 0 29) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 29) 4 output-type " C6H12O6 "] ifelse (matrix:get to-print 0 30) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 30) 4 output-type " COOHCH2CH2CHNH2COO- "] ifelse (matrix:get to-print 0 31) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 31) 4 output-type " CH2OHCHOHCH2OH "] ifelse (matrix:get to-print 0 32) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 32) 4 output-type " CH2NH2COOH "] ifelse (matrix:get to-print 0 33) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 33) 4 output-type " CH3CHOHCOO- "] ifelse (matrix:get to-print 0 34) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 34) 4 output-type " CH4 "] ifelse (matrix:get to-print 0 35) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 35) 4 output-type " CH3OH "] ifelse (matrix:get to-print 0 36) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 36) 4 output-type " CH3(CH2)14COO- "] ifelse (matrix:get to-print 0 37) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 37) 4 output-type " CH3CH2COO- "] ifelse (matrix:get to-print 0 38) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 38) 4 output-type " CH3COCOO- "] ifelse (matrix:get to-print 0 39) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 39) 4 output-type " (C4H4O4)2- "] ifelse (matrix:get to-print 0 40) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 40) 4 output-type " (C6H6O6N)3- "] ifelse (matrix:get to-print 0 0) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 0) 4 output-type " O2 "] ifelse (matrix:get to-print 0 1) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 1) 4 output-type " H+ "] ifelse (matrix:get to-print 0 2) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 2) 4 output-type " e- "] ifelse (matrix:get to-print 0 3) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 3) 4 output-type " CO2 "] ifelse (matrix:get to-print 0 4) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 4) 4 output-type " NH4+ "] ifelse (matrix:get to-print 0 5) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 5) 4 output-type " HCO3- "] ifelse (matrix:get to-print 0 9) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 9) 4 output-type " NO3- "] ifelse (matrix:get to-print 0 10) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 10) 4 output-type " NO2- "] ifelse (matrix:get to-print 0 11) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 11) 4 output-type " NO "] ifelse (matrix:get to-print 0 12) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 12) 4 output-type " N2O "] ifelse (matrix:get to-print 0 13) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 13) 4 output-type " N2 "] ifelse (matrix:get to-print 0 14) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 14) 4 output-type " H2 "] ifelse (matrix:get to-print 0 15) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 15) 4 output-type " Fe3+ "] ifelse (matrix:get to-print 0 16) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 16) 4 output-type " Fe2+ "] ifelse (matrix:get to-print 0 17) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 17) 4 output-type " (SO4)2- "] ifelse (matrix:get to-print 0 18) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 18) 4 output-type " (SO3)2- "] ifelse (matrix:get to-print 0 19) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 19) 4 output-type " H2S "] ifelse (matrix:get to-print 0 20) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 20) 4 output-type " HS- "] ifelse (matrix:get to-print 0 21) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 21) 4 output-type " (S2O3)2- "] ifelse (matrix:get to-print 0 22) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 22) 4 output-type " S "] ifelse (matrix:get to-print 0 7) >= 0 [ ][output-type "+ " output-type precision abs (matrix:get to-print 0 7) 4 output-type " H2O "] ifelse to-print = reaction or to-print = energy_reaction or to-print = synthesis_reaction[ ][ifelse (matrix:get to-print 0 25) = 0 [ ][output-type "[ ∆G = " output-type precision (matrix:get to-print 0 25) 4 output-type " KJ/e-eq ]"]] output-print " " end to setup-reactions set column_matrix 41 ; type here the number of chemical species involved set row_matrix (column_matrix - 1) ; this number is the number of reduction-half-reactions in this version of the tool. set reactions matrix:make-constant row_matrix column_matrix 0 matrix:set reactions 0 0 (1 / 4) ; O2 matrix:set reactions 0 1 (1) ; H+ matrix:set reactions 0 2 (1) ; e- matrix:set reactions 0 7 (-1 / 2) ; H2O matrix:set reactions 0 25 (-78.72) ; ∆G matrix:set reactions 1 17 (1 / 4) ; (SO4)2- matrix:set reactions 1 1 (5 / 4) ; H+ matrix:set reactions 1 2 (1) ; e- matrix:set reactions 1 7 (-5 / 8) ; H2O matrix:set reactions 1 21 (-1 / 8) ; (S2O3)2- matrix:set reactions 1 25 (23.58) ; ∆G matrix:set reactions 2 17 (1 / 6) ; (SO4)2- matrix:set reactions 2 1 (4 / 3) ; H+ matrix:set reactions 2 2 (1) ; e- matrix:set reactions 2 7 (-2 / 3) ; H2O matrix:set reactions 2 22 (-1 / 6) ; S matrix:set reactions 2 25 (19.15) ; ∆G matrix:set reactions 3 17 (1 / 2) ; (SO4)2- matrix:set reactions 3 1 (1) ; H+ matrix:set reactions 3 2 (1) ; e- matrix:set reactions 3 7 (-1 / 2) ; H2O matrix:set reactions 3 18 (-1 / 2) ; (SO3)2- matrix:set reactions 3 25 (50.30) ; ∆G matrix:set reactions 4 18 (1 / 6) ; (SO3)2- matrix:set reactions 4 1 (5 / 4) ; H+ matrix:set reactions 4 2 (1) ; e- matrix:set reactions 4 7 (-1 / 2) ; H2O matrix:set reactions 4 19 (-1 / 12) ; H2S matrix:set reactions 4 20 (-1 / 12) ; HS- matrix:set reactions 4 25 (11.03) ; ∆G matrix:set reactions 5 17 (1 / 8) ; (SO4)2- matrix:set reactions 5 1 (19 / 16) ; H+ matrix:set reactions 5 2 (1) ; e- matrix:set reactions 5 7 (-1 / 2) ; H2O matrix:set reactions 5 19 (-1 / 16) ; H2S matrix:set reactions 5 20 (-1 / 16) ; HS- matrix:set reactions 5 25 (20.85) ; ∆G matrix:set reactions 6 12 (1 / 2) ; N2O matrix:set reactions 6 1 (1) ; H+ matrix:set reactions 6 2 (1) ; e- matrix:set reactions 6 7 (-1 / 2) ; H2O matrix:set reactions 6 13 (-1 / 2) ; N2 matrix:set reactions 6 25 (-133.469) ; ∆G matrix:set reactions 7 11 (1) ; NO matrix:set reactions 7 1 (1) ; H+ matrix:set reactions 7 2 (1) ; e- matrix:set reactions 7 7 (-1 / 2) ; H2O matrix:set reactions 7 12 (-1 / 2) ; N2O matrix:set reactions 7 25 (-115.829) ; ∆G matrix:set reactions 8 10 (1 / 3) ; NO2- matrix:set reactions 8 1 (4 / 3) ; H+ matrix:set reactions 8 2 (1) ; e- matrix:set reactions 8 7 (-2 / 3) ; H2O matrix:set reactions 8 13 (-1 / 6) ; N2 matrix:set reactions 8 25 (-92.56) ; ∆G matrix:set reactions 9 10 (1) ; NO2- matrix:set reactions 9 1 (2) ; H+ matrix:set reactions 9 2 (1) ; e- matrix:set reactions 9 7 (-1) ; H2O matrix:set reactions 9 11 (-1) ; NO matrix:set reactions 9 25 (-33.718) ; ∆G matrix:set reactions 10 9 (1 / 5) ; NO3- matrix:set reactions 10 1 (6 / 5) ; H+ matrix:set reactions 10 2 (1) ; e- matrix:set reactions 10 7 (-3 / 5) ; H2O matrix:set reactions 10 13 (-1 / 10) ; N2 matrix:set reactions 10 25 (-72.20) ; ∆G matrix:set reactions 11 9 (7 / 24) ; NO3- matrix:set reactions 11 1 (31 / 24) ; H+ matrix:set reactions 11 2 (1) ; e- matrix:set reactions 11 7 (-31 / 48) ; H2O matrix:set reactions 11 11 (-1 / 6) ; NO matrix:set reactions 11 12 (-1 / 16) ; N2O matrix:set reactions 11 25 (-48.274) ; ∆G matrix:set reactions 12 9 (1 / 4) ; NO3- matrix:set reactions 12 1 (5 / 4) ; H+ matrix:set reactions 12 2 (1) ; e- matrix:set reactions 12 7 (-5 / 8) ; H2O matrix:set reactions 12 12 (-1 / 8) ; N2O matrix:set reactions 12 25 (-57.54) ; ∆G matrix:set reactions 13 9 (1 / 3) ; NO3- matrix:set reactions 13 1 (4 / 3) ; H+ matrix:set reactions 13 2 (1) ; e- matrix:set reactions 13 7 (-2 / 3) ; H2O matrix:set reactions 13 11 (-1 / 3) ; NO matrix:set reactions 13 25 (-39.00) ; ∆G matrix:set reactions 14 9 (1 / 2) ; NO3- matrix:set reactions 14 1 (1) ; H+ matrix:set reactions 14 2 (1) ; e- matrix:set reactions 14 7 (-1 / 2) ; H2O matrix:set reactions 14 10 (-1 / 2) ; NO2- matrix:set reactions 14 25 (-41.65) ; ∆G matrix:set reactions 15 1 (1) ; H+ matrix:set reactions 15 2 (1) ; e- matrix:set reactions 15 14 (-1 / 2) ; H2 matrix:set reactions 15 25 (39.87) ; ∆G matrix:set reactions 16 15 (1) ; Fe3+ matrix:set reactions 16 2 (1) ; e- matrix:set reactions 16 16 (-1) ; Fe2+ matrix:set reactions 16 25 (-74.27) ; ∆G matrix:set reactions 17 13 (1 / 6) ; N2 matrix:set reactions 17 1 (4 / 3) ; H+ matrix:set reactions 17 2 (1) ; e- matrix:set reactions 17 4 (-1 / 3) ; NH4+ matrix:set reactions 17 25 (26.70) ; ∆G matrix:set reactions 18 9 (1 / 8) ; NO3- matrix:set reactions 18 1 (5 / 4) ; H+ matrix:set reactions 18 2 (1) ; e- matrix:set reactions 18 7 (-3 / 8) ; H2O matrix:set reactions 18 4 (-1 / 8) ; NH4+ matrix:set reactions 18 25 (-35.11) ; ∆G matrix:set reactions 19 10 (1 / 6) ; NO2- matrix:set reactions 19 1 (4 / 3) ; H+ matrix:set reactions 19 2 (1) ; e- matrix:set reactions 19 4 (-1 / 6) ; NH4+ matrix:set reactions 19 7 (-1 / 3) ; H2O matrix:set reactions 19 25 (-32.93) ; ∆G matrix:set reactions 20 1 (1) ; H+ matrix:set reactions 20 2 (1) ; e- matrix:set reactions 20 3 (1 / 8) ; CO2 matrix:set reactions 20 5 (1 / 8) ; HCO3- matrix:set reactions 20 7 (-3 / 8) ; H2O matrix:set reactions 20 8 (-1 / 8) ; Acetate matrix:set reactions 20 25 (27.40) ; ∆G matrix:set reactions 21 1 (11 / 12) ; H+ matrix:set reactions 21 2 (1) ; e- matrix:set reactions 21 3 (1 / 6) ; CO2 matrix:set reactions 21 4 (1 / 12) ; NH4+ matrix:set reactions 21 5 (1 / 12) ; HCO3- matrix:set reactions 21 7 (-5 / 12) ; H2O matrix:set reactions 21 23 (-1 / 12) ; Alanine matrix:set reactions 21 25 (31.37) ; ∆G matrix:set reactions 22 1 (1) ; H+ matrix:set reactions 22 2 (1) ; e- matrix:set reactions 22 3 (1 / 5) ; CO2 matrix:set reactions 22 5 (1 / 30) ; HCO3- matrix:set reactions 22 7 (-13 / 30) ; H2O matrix:set reactions 22 24 (-1 / 30) ; Benzoate matrix:set reactions 22 25 (27.34) ; ∆G matrix:set reactions 23 1 (1) ; H+ matrix:set reactions 23 2 (1) ; e- matrix:set reactions 23 3 (1 / 6) ; CO2 matrix:set reactions 23 5 (1 / 6) ; HCO3- matrix:set reactions 23 7 (-4 / 9) ; H2O matrix:set reactions 23 26 (-1 / 18) ; Citrate matrix:set reactions 23 25 (33.08) ; ∆G matrix:set reactions 24 1 (1) ; H+ matrix:set reactions 24 2 (1) ; e- matrix:set reactions 24 3 (1 / 6) ; CO2 matrix:set reactions 24 7 (-1 / 4) ; H2O matrix:set reactions 24 27 (-1 / 12) ; Ethanol matrix:set reactions 24 25 (31.18) ; ∆G matrix:set reactions 25 1 (1) ; H+ matrix:set reactions 25 2 (1) ; e- matrix:set reactions 25 5 (1 / 2) ; HCO3- matrix:set reactions 25 7 (-1 / 2) ; H2O matrix:set reactions 25 28 (-1 / 2) ; Formate matrix:set reactions 25 25 (39.19) ; ∆G matrix:set reactions 26 1 (1) ; H+ matrix:set reactions 26 2 (1) ; e- matrix:set reactions 26 3 (1 / 4) ; CO2 matrix:set reactions 26 7 (-1 / 4) ; H2O matrix:set reactions 26 29 (-1 / 24) ; Glucose matrix:set reactions 26 25 (41.35) ; ∆G matrix:set reactions 27 1 (1) ; H+ matrix:set reactions 27 2 (1) ; e- matrix:set reactions 27 3 (1 / 6) ; CO2 matrix:set reactions 27 4 (1 / 18) ; NH4+ matrix:set reactions 27 5 (1 / 9) ; HCO3- matrix:set reactions 27 7 (-4 / 9) ; H2O matrix:set reactions 27 30 (-1 / 18) ; Glutamate matrix:set reactions 27 25 (30.93) ; ∆G matrix:set reactions 28 1 (1) ; H+ matrix:set reactions 28 2 (1) ; e- matrix:set reactions 28 3 (3 / 14) ; CO2 matrix:set reactions 28 7 (-3 / 14) ; H2O matrix:set reactions 28 31 (-1 / 14) ; Glycerol matrix:set reactions 28 25 (33.88) ; ∆G matrix:set reactions 29 1 (1) ; H+ matrix:set reactions 29 2 (1) ; e- matrix:set reactions 29 3 (1 / 6) ; CO2 matrix:set reactions 29 4 (1 / 6) ; NH4+ matrix:set reactions 29 5 (1 / 6) ; HCO3- matrix:set reactions 29 7 (-1 / 2) ; H2O matrix:set reactions 29 32 (-1 / 6) ; Glycine matrix:set reactions 29 25 (39.80) ; ∆G matrix:set reactions 30 1 (1) ; H+ matrix:set reactions 30 2 (1) ; e- matrix:set reactions 30 3 (1 / 6) ; CO2 matrix:set reactions 30 5 (1 / 12) ; HCO3- matrix:set reactions 30 7 (-1 / 3) ; H2O matrix:set reactions 30 33 (-1 / 12) ; Lactato matrix:set reactions 30 25 (32.29) ; ∆G matrix:set reactions 31 1 (1) ; H+ matrix:set reactions 31 2 (1) ; e- matrix:set reactions 31 3 (1 / 8) ; CO2 matrix:set reactions 31 7 (-1 / 4) ; H2O matrix:set reactions 31 34 (-1 / 8) ; Methane matrix:set reactions 31 25 (23.53) ; ∆G matrix:set reactions 32 1 (1) ; H+ matrix:set reactions 32 2 (1) ; e- matrix:set reactions 32 3 (1 / 6) ; CO2 matrix:set reactions 32 7 (-1 / 6) ; H2O matrix:set reactions 32 35 (-1 / 6) ; Methanol matrix:set reactions 32 25 (36.84) ; ∆G matrix:set reactions 33 1 (1) ; H+ matrix:set reactions 33 2 (1) ; e- matrix:set reactions 33 3 (15 / 19) ; CO2 matrix:set reactions 33 5 (1 / 92) ; HCO3- matrix:set reactions 33 7 (-31 / 92) ; H2O matrix:set reactions 33 36 (-1 / 92) ; Palmitate matrix:set reactions 33 25 (27.26) ; ∆G matrix:set reactions 34 1 (1) ; H+ matrix:set reactions 34 2 (1) ; e- matrix:set reactions 34 3 (1 / 7) ; CO2 matrix:set reactions 34 5 (1 / 14) ; HCO3- matrix:set reactions 34 7 (-5 / 14) ; H2O matrix:set reactions 34 37 (-1 / 14) ; Propionate matrix:set reactions 34 25 (27.63) ; ∆G matrix:set reactions 35 1 (1) ; H+ matrix:set reactions 35 2 (1) ; e- matrix:set reactions 35 3 (1 / 5) ; CO2 matrix:set reactions 35 5 (1 / 10) ; HCO3- matrix:set reactions 35 7 (-2 / 5) ; H2O matrix:set reactions 35 38 (-1 / 10) ; Pyruvate matrix:set reactions 35 25 (35.09) ; ∆G matrix:set reactions 36 1 (1) ; H+ matrix:set reactions 36 2 (1) ; e- matrix:set reactions 36 3 (1 / 7) ; CO2 matrix:set reactions 36 5 (1 / 7) ; HCO3- matrix:set reactions 36 7 (-3 / 7) ; H2O matrix:set reactions 36 39 (-1 / 14) ; Succinate matrix:set reactions 36 25 (29.09) ; ∆G matrix:set reactions 37 1 (20 / 18) ; H+ matrix:set reactions 37 2 (1) ; e- matrix:set reactions 37 4 (1 / 18) ; NH4+ matrix:set reactions 37 5 (6 / 18) ; HCO3- matrix:set reactions 37 7 (-12 / 18) ; H2O matrix:set reactions 37 40 (-1 / 18) ; NTA - Acid nitrilotriacetic matrix:set reactions 37 25 (68.889) ; ∆G end to download ifelse second_electron_donor? = true [export-output (word (word behaviorspace-run-number"_rd_("Electron_donor"+"Electron_donor_2")_ra_("Electron_acceptor")_rc_("Microorganism")_N-soruce_("N-Source")_with_"Thermodynamics"_with_"efficiency)".txt")] [export-output (word (word behaviorspace-run-number"_rd_("Electron_donor")_ra_("Electron_acceptor")_rc_("Microorganism")_N-soruce_("N-Source")_with_"Thermodynamics"_with_"efficiency)".txt")] ; Outputfile name with .txt extension and Behaviorspace numering end
There is only one version of this model, created over 4 years ago by Pablo Alejandro Araujo Granda.
Attached files
| File | Type | Description | Last updated | |
|---|---|---|---|---|
| MbT-Tool: Metabolism based on Thermodynamics.png | preview | Preview for 'MbT-Tool: Metabolism based on Thermodynamics' | over 4 years ago, by Pablo Alejandro Araujo Granda | Download |
This model does not have any ancestors.
This model does not have any descendants.