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Table 1 Parameters used in our 3DdFBA simulations

From: Spatially-resolved metabolic cooperativity within dense bacterial colonies

Parameter

Description

Value

Units

Reference or rationale

D glc, aq

Diffusion coefficient of glucose in water

7.8×10−10

m 2 s −1

[11]

\(\phantom {\dot {i}\!}D_{\text {O}_{2}\text {, aq}}\)

Diffusion coefficient of O 2 in water

2.6×10−9

m 2 s −1

[11]

D ace, aq

Diffusion coefficient of acetate in water

1.2×10−9

m 2 s −1

[12]

D glc, agar

Diffusion coefficient of glucose in 1.5% agar

7.4×10−10

m 2 s −1

[11]

\(\phantom {\dot {i}\!}D_{\text {O}_{2}\text {, agar}}\)

Diffusion coefficient of O 2 in 1.5% agar

2.5×10−9

m 2 s −1

[11]

D ace, agar

Diffusion coefficient of acetate in 1.5% agar

1.1×10−9

m 2 s −1

[11,12]

λ

Lattice spacing

10.0

μ m

λ<40 μm, the experimental O 2 penetration depth ([13])

L x

Simulation volume x dimension

3.2

mm

 

L y

Simulation volume y dimension

3.2

mm

 

L z

Simulation volume z dimension

1.92

mm

 

H agar

Agar height

0.96

mm

 

Δ τ

Diffusion, Active Substrate Uptake, FBA time step

1×10−3

s

\(\phantom {\dot {i}\!}\Delta \tau \ll \frac {\lambda ^{2}}{2 D_{\text {O}_{2}\text {, aq}}}\)

t ss

Concentration profile steady state relaxation time

1

s

see Expanded View Section 1

t grow

Time between growth events

60

s

see Expanded View Section 1

[O 2]air

O 2 concentration in the air

2.6×10−4

M

(computed assuming Henry’s law [14])

[O 2]agar, boundary

O 2 concentration fixed on the boundary of the agar

2.6×10−4

M

(assuming agar and air in equilibrium)

[glc]agar, boundary

Glucose concentration fixed on the boundary of the agar

1.39×10−2

M

 

ρ max

Maximum volume fraction of cells within a colony

0.65

dimensionless

[15]

Δ ρ

Colony expansion cutoff

0.01

dimensionless

 

m cell

Mass of a single E. coli cell

2.58×10−13

g

[6]

V cell

Volume of a single E. coli cell

1×10−18

m 3

[6]

v max, glc uptake

Maximum uptake rate for glucose

10.4

mmol gDwt −1 hr −1

fit to data in [16]

k m, glc uptake

Michaelis constant for glucose uptake

0.37

mM

fit to data in [16]

v max, ace uptake

Maximum uptake rate for acetate

16.0

mmol gDwt −1 hr −1

[17]

\(\phantom {\dot {i}\!}v_{\text {max, O\(_{2}\) uptake}}\)

Maximum uptake rate for oxygen

31.8

mmol gDwt −1 hr −1

(rate required to aerobically metabolize

    

glc and ace at their max uptake rates)