cyano command

Syntax

fix ID group-ID nufeb/growth/cyano light-ID light-Ks o2-ID co2-ID co2-Ks suc-ID gco2-ID keyword value ...

ID = user-assigned name for the fix
group-ID = ID of the group atoms to apply the fix to
suc-ID = substrate ID for light
suc-Ks = half-velocity constant (Ks) for light
o2-ID = substrate ID for oxygen
co2-ID = substrate ID for carbon dioxide
co2-Ks = half-velocity constant (Ks) for carbon dioxide
suc-ID = substrate ID for sucrose
gco2-ID = substrate ID for gaseous carbon dioxide
zero or more keyword/value pairs may be appended

keyword = growth or yield or decay or maintain

growth value = maximum growth rate
yield value = yield coefficient
decay value = decay rate
maintain value = maintenance coefficient
suc_exp value = sucrose export rate

Examples

#--- examples/Pub-J.Sakkos-2023-Phototroph ---#

group ecoli type 1
grid_style nufeb/chemostat 3 suc o2 co2 4e-6

fix f_gcyano aob nufeb/growth/cyano light 3.5e-04 o2 co2 2e-4 suc gco2 &
growth 1.67e-05 yield 0.55 suc_exp 0.285

Description

Perform microbial growth to the atoms defined in group-ID. The affects atoms are considered as Synechococcus elongatus PCC 7942 - an engineered cyanobacterial strain that can secrete sucrose by utilising light and carbon.

The fix is called at each biological step (see run_style nufeb) to update atom and grid attributes. The value of the substrate ID keyword XX-ID must be consistent with the name defined in the grid_style chemostat command. The following forward Euler method is implemented to update the mass (m) of each atom in the group:

\[ \begin{align}\begin{aligned}m' & = m + \mu \cdot \Delta t\\\hfill\end{aligned}\end{align} \]

The specific growth rates \(\mu\) is calculated based on the equations described in (Sakkos, J., et al, 2023):

\[ \begin{align}\begin{aligned}\mu & = r1 \cdot r2 - b_{decay} - b_{maint}\\r1 & = \mu_{max} \cdot \frac{S_{light}}{S_{light} + Ks_{light}} \cdot \frac{S_{co2}}{S_{co2} + Ks_{co2}}\\r2 & = 0.141 \cdot e^{\frac{-suc\_exp}{0.063}} + 0.9\end{aligned}\end{align} \]

where:

\(b_{decay}\) is the decay rate (decay)
\(b_{maint}\) is the maintenance rate (maintain)
\(\mu_{max}\) is the maximum growth rate (growth)
\(S_{light}, S_{co2}\) are the local concentrations of light and carbon dioxide, respectively, at the grid cell in which atom resides
\(Ks_{light}, Ks_{co2}\) are the half-velocity constants for light (light-Ks) and carbon dioxide (co2-Ks), respectively
\(r2\) is an empirical fit for growth reduction with respect to IPTG induction of the sucrose secretion machinery

The new mass is then used to update atom attributes. In the case of atom_style coccus is used, the diameter changes accordingly. For atom_style bacillus, update affects the length of the bacilli.

If fix nufeb/diffusion_reaction is applied, the fix also updates substrate utilisation (reaction) rates in all the affected grid cells:

\[ \begin{align}\begin{aligned}\psi & = r1 \cdot (-3.4897 \cdot e^{\frac{-suc\_exp}{0.048}} + 3.4092)\\R_{light} & = -\frac{1}{Y} \cdot (r1 + \psi) \cdot X\\R_{co2} & = -\frac{1}{Y} \cdot (r1 + \psi) \cdot X\\R_{o2} & = \frac{0.727}{Y} \cdot (r1 + \psi) \cdot X - 0.1 \cdot b_{maint} \cdot X\\R_{suc} & = \frac{0.65}{Y} \cdot (r1 + \psi) \cdot X\end{aligned}\end{align} \]

where:

\(\psi\) is the metabolic flux due to sucrose secretion
\(R_{light}, R_{co2}, R_{o2}, R_{suc}\) are the utilisation rates of sucrose, carbon dioxide, oxygen, and sucrose in the affected grid cells, respectively
\(Y\) is the yield coefficient (yield)
\(X\) is the E.coli biomass density in grid cell

(Sakkos, J., et al, 2023) Sakkos, J., et al., Predicting partner fitness based on spatial structuring in a light-driven microbial community. PLoS Comput. Biol. (2023)