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Table 2 Reaction network capturing synthetic ecosystem’s behavior

From: Stochastic simulations of a synthetic bacteria-yeast ecosystem

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Reaction

Reaction rate

Kinetic constant

1

−−→ k 1 c 1

k 1 · c 1 1− c 1 + c 2 c max

k 1 = 0 . 234 h , c max =1 0 9 cells[18, 21]

2

−−→ k 2 c 2

k 2 · c 2 1− c 1 + c 2 c max

k 2 = 0 . 936 h [19], c max =1 0 9 cells[18, 21]

3

c 1 +Gc −−→ k 3 Gc

k 3 ″ · c 1 1 + α · Res 1

k 3 = 4 · 1 0 6 M · h [19],α= 5 · 1 0 4 Molecules

4

c 2 +Gc −−→ k 3 Gc

k 3 ″ · c 2 1 + α · Res 2

k 3 = 4 · 1 0 6 M · h [19],α= 5 · 1 0 4 Molecules

5

c 1 −−→ k 4 AHL1+ c 1

k4·c1

k 4 =5·1 0 − 6 1 h [18]

6

c 2 −−→ k 5 AHL2+ c 2

k5·c2

k 5 =5·1 0 − 6 1 h [18]

7

2AHL2+2AHLR2 −−→ k 6 AHL2:AHLR2

k 6 ″ · AHL 2 2 V 1 · Na

k 6 = 3 · 1 0 19 M 3 · h [26], V 1 =3.7·1 0 − 14 L[49],

   

Na = 6.023 · 1023

8

AHL2:AHLR2 −−→ k 7 preRes1

k 7 · AHL 2 : AHLR 2 n 1 k 7 b n 1 + AHL 2 : AHLR 2 n 1

k 7 =6·1 0 − 5 M h , k 7 b =1 0 − 8 M, n 1 =1[26]

9

preRes1 −−→ k 8 Res1

k8·preRes 1

k 8 = 5 h

10

2AHL1+2AHLR1 −−→ k 9 AHL1:AHLR1

k 9 ″ · AHL 1 2 V 2 · Na

k 9 = 3 · 1 0 19 M 3 · h [26], V 2 =1 0 − 15 L[50]

11

AHL1:AHLR1 −−→ k 10 Res2

k 10 · AHL 1 : AHLR 1 n 2 k 10 b n 2 + AHL 1 : AHLR 1 n 2

k 10 =6·1 0 − 5 M h , k 10 b =1 0 − 8 M, n 2 =1[26]

12

AHL1 −−→ k 11 ∅

k11·AHL 1

k 11 = 1 . 19 h [19]

13

AHL2 −−→ k 12 ∅

k12·AHL 2

k 12 = 1 . 19 h [19]

14

AHL1:AHLR1 −−→ k 13 ∅

k13·AHL 1:AHLR 1

k 13 = 1 . 386 h [26]

15

AHL2:AHLR2 −−→ k 14 ∅

k14·AHL 2:AHLR 2

k 14 = 1 . 386 h [26]

16

Res1 −−→ k 15 ∅

k15·Res 1

k 15 = 4 h [20]

17

Res2 −−→ k 16 ∅

k16·Res 2

k 16 = 4 h [20]