### Toolbox: degrad

Biodegradation of chemical compounds in batch cultures.
The theory for the models can be found in the DEB-book.

The Marr-Pirt model is a special case of the DEB model, and has the Monod model as special case.
It concerns V1-morphs in a batch culture.
Two data sets are required to estimate all parameters using routines
`nmregr`

, or
`nrregr`

: time-substrate-weight and time-biomass-weight matrices.
The weight coefficients can be suppressed, in which case value one is inserted for all weight coefficients.
The single data set time-substrate-weight is sufficient if the initial biomass concentration, the yield and maintenance rate coefficients are kept fixed.
Input:

- 6-vector with parameters:
- initial concentration of substrate
- initial concentration of biomass
- saturation constant
- max spec uptake rate
- yield of substrate on biomass
- maintenance rate coefficient

- (n,k)-matrix with times for concentrations of substrate in column 1
- (m,k)-matrix with times for biomass in column 1

Output:

- n-vector with concentrations of substrate
- m-vector with biomass

An example of application of `pirt`

in regression and plotting routines is given in the script-file `mydata_pirt`

.

The DEB model concerns 1-structure, 1-reserve V1-morphs in a batch culture.
The reserve density is treated as a hidden variable, and the measured biomass is taken to quantify structure.
Two data sets are required to estimate all parameters using routines
`nmregr`

, or
`nrregr`

:
time-substrate-weight and time-biomass-weight matrices.
The weight coefficients can be suppressed, in which case value one is inserted for all weight coefficients.
Input:

- 6-vector with parameters:
- initial concentration of substrate
- initial concentration of structure
- saturation constant
- max spec uptake rate
- yield of substrate on structure
- reserve turnover rate
- maintenance rate coefficient

- (n,k)-matrix with times for concentrations of substrate in column 1
- (m,k)-matrix with times for biomass in column 1

Output:

- n-vector with concentrations of substrate
- m-vector with biomass

An example of application of `DEB`

in regression and plotting routines is given in the script-file `mydata_deb`

.

Back to the DEBtool page