Skip to content

Commit

Permalink
fix headings
Browse files Browse the repository at this point in the history
  • Loading branch information
exaexa committed Jan 30, 2024
1 parent fb4a55f commit 0fd58ed
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions docs/src/examples/05-enzyme-constrained-models.jl
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ end
#md #!!! warning "Turnover number units"
#md # Take care with the units of the turnover numbers. In literature they are usually reported in 1/s. However, flux units are typically mmol/gDW/h, suggesting that you should rescale the turnover numbers to 1/h if you want to use the conventional flux units.

### Enzyme molar masses
# ## Enzyme molar masses

# We also require the mass of each enzyme, to properly weight the contribution
# of each flux/isozyme in the capacity bound(s). These data can typically be
Expand Down Expand Up @@ -309,14 +309,14 @@ ecoli_core_gene_product_masses
#md # !!! warning "Molar mass units"
#md # Take care with the units of the molar masses. In literature they are usually reported in Da or kDa (g/mol). However, as noted above, flux units are typically mmol/gDW/h. Since the enzyme kinetic equation is `v = k * e`, where `k` is the turnover number, it suggests that the enzyme variable will have units of mmol/gDW. The molar masses come into play when setting the capacity limitations, e.g. usually a sum over all enzymes weighted by their molar masses: `e * mm`. Thus, if your capacity limitation has units of g/gDW, then the molar masses must have units of g/mmol (= kDa).

### Capacity limitation
# ## Capacity limitation

# The capacity limitation usually denotes an upper bound of protein available to
# the cell.

total_enzyme_capacity = 50.0 # mg of enzyme/gDW

### Running a basic enzyme constrained model
# ## Running a basic enzyme constrained model

# With all the parameters specified, we can directly use the enzyme constrained
# convenience function to run enzyme constrained FBA in one shot:
Expand Down

0 comments on commit 0fd58ed

Please sign in to comment.