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 | |
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) |