Expressions of process rates and stoichiometric factors used to simulate the dynamics of all state variables from Table 2 between distinct transfer events.
| . | . | Stoichiometry matrix Q (State variables as column headers) . | ||||||
|---|---|---|---|---|---|---|---|---|
| Process . | Process rate expressions (vector r) . | R . | Bo . | Bx . | Bfs . | Bff . | F . | X . |
| Bacterial growth (Bo) | m · monod(R, hB, zB) · Bo | α | 1 | |||||
| Bacterial growth (Bx) | m · cBx · monod(R, hB, zB) · Bx | α | 1 | |||||
| Bacterial growth (Bfs) | m · cBf · monod(R, hB, zB) · Bfs | α | −1 | 1 | ||||
| Bacterial growth (Bff) | m · cBf · monod(R, hB, zB) · Bff | α | p | 1-p | ||||
| Flagellate grazing | g · monod(Bo + Bx + Bfs, hF, zF) · F · inh(X, micX) | -Bo/β | -Bx/β | -Bfs/β | yF | |||
| Upregulation of metabolite production | ku · Bo · on(Bo, tuB) · on(F, tuF) | −1 | 1 | |||||
| Downregulation of metabolite production | kd · Bx · max(off(Bo, tuB), off(F, tuF)) | 1 | −1 | |||||
| Excretion of metabolites | kx · Bx | 1 | ||||||
| Filamentation | kf · (Bx + Bo) · on(X, tf) | -Bo/γ | -Bx/γ | 1 | ||||
| . | . | Stoichiometry matrix Q (State variables as column headers) . | ||||||
|---|---|---|---|---|---|---|---|---|
| Process . | Process rate expressions (vector r) . | R . | Bo . | Bx . | Bfs . | Bff . | F . | X . |
| Bacterial growth (Bo) | m · monod(R, hB, zB) · Bo | α | 1 | |||||
| Bacterial growth (Bx) | m · cBx · monod(R, hB, zB) · Bx | α | 1 | |||||
| Bacterial growth (Bfs) | m · cBf · monod(R, hB, zB) · Bfs | α | −1 | 1 | ||||
| Bacterial growth (Bff) | m · cBf · monod(R, hB, zB) · Bff | α | p | 1-p | ||||
| Flagellate grazing | g · monod(Bo + Bx + Bfs, hF, zF) · F · inh(X, micX) | -Bo/β | -Bx/β | -Bfs/β | yF | |||
| Upregulation of metabolite production | ku · Bo · on(Bo, tuB) · on(F, tuF) | −1 | 1 | |||||
| Downregulation of metabolite production | kd · Bx · max(off(Bo, tuB), off(F, tuF)) | 1 | −1 | |||||
| Excretion of metabolites | kx · Bx | 1 | ||||||
| Filamentation | kf · (Bx + Bo) · on(X, tf) | -Bo/γ | -Bx/γ | 1 | ||||
See Tables 4 and 5 for the declaration of additional symbols representing functions and parameters, respectively. Greek symbols encode auxiliary expressions as follows: α = −1 / (yB · (1 + iyB · on(X, ty))); β = Bo + Bx + Bfs; γ = Bo + Bx. See Fig. 4 for a graphical representation of the simultaneous ODE.
Expressions of process rates and stoichiometric factors used to simulate the dynamics of all state variables from Table 2 between distinct transfer events.
| . | . | Stoichiometry matrix Q (State variables as column headers) . | ||||||
|---|---|---|---|---|---|---|---|---|
| Process . | Process rate expressions (vector r) . | R . | Bo . | Bx . | Bfs . | Bff . | F . | X . |
| Bacterial growth (Bo) | m · monod(R, hB, zB) · Bo | α | 1 | |||||
| Bacterial growth (Bx) | m · cBx · monod(R, hB, zB) · Bx | α | 1 | |||||
| Bacterial growth (Bfs) | m · cBf · monod(R, hB, zB) · Bfs | α | −1 | 1 | ||||
| Bacterial growth (Bff) | m · cBf · monod(R, hB, zB) · Bff | α | p | 1-p | ||||
| Flagellate grazing | g · monod(Bo + Bx + Bfs, hF, zF) · F · inh(X, micX) | -Bo/β | -Bx/β | -Bfs/β | yF | |||
| Upregulation of metabolite production | ku · Bo · on(Bo, tuB) · on(F, tuF) | −1 | 1 | |||||
| Downregulation of metabolite production | kd · Bx · max(off(Bo, tuB), off(F, tuF)) | 1 | −1 | |||||
| Excretion of metabolites | kx · Bx | 1 | ||||||
| Filamentation | kf · (Bx + Bo) · on(X, tf) | -Bo/γ | -Bx/γ | 1 | ||||
| . | . | Stoichiometry matrix Q (State variables as column headers) . | ||||||
|---|---|---|---|---|---|---|---|---|
| Process . | Process rate expressions (vector r) . | R . | Bo . | Bx . | Bfs . | Bff . | F . | X . |
| Bacterial growth (Bo) | m · monod(R, hB, zB) · Bo | α | 1 | |||||
| Bacterial growth (Bx) | m · cBx · monod(R, hB, zB) · Bx | α | 1 | |||||
| Bacterial growth (Bfs) | m · cBf · monod(R, hB, zB) · Bfs | α | −1 | 1 | ||||
| Bacterial growth (Bff) | m · cBf · monod(R, hB, zB) · Bff | α | p | 1-p | ||||
| Flagellate grazing | g · monod(Bo + Bx + Bfs, hF, zF) · F · inh(X, micX) | -Bo/β | -Bx/β | -Bfs/β | yF | |||
| Upregulation of metabolite production | ku · Bo · on(Bo, tuB) · on(F, tuF) | −1 | 1 | |||||
| Downregulation of metabolite production | kd · Bx · max(off(Bo, tuB), off(F, tuF)) | 1 | −1 | |||||
| Excretion of metabolites | kx · Bx | 1 | ||||||
| Filamentation | kf · (Bx + Bo) · on(X, tf) | -Bo/γ | -Bx/γ | 1 | ||||
See Tables 4 and 5 for the declaration of additional symbols representing functions and parameters, respectively. Greek symbols encode auxiliary expressions as follows: α = −1 / (yB · (1 + iyB · on(X, ty))); β = Bo + Bx + Bfs; γ = Bo + Bx. See Fig. 4 for a graphical representation of the simultaneous ODE.
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