SIMSPEC files included in the SimuPlot toolbox
Press the links below to see simulation examples and further descriptions (The suffix .fig of all SIMSPEC file names is omitted.)

Fed-batch simulations
fedbatch_demoSimple fedbatch model for illustration of common principles of a fedbatch process.
fedbatch_Cmole Fedbatch simulation based on the use of stoichiometric analysis (C- and degree-of-reduction balancing) to improve the simple model in
demo_fedbatch. In this way also the CO2 production is obtained and RQ can be calculated.
fedbatch_kla Includes a common model for KLa as function of RPM and aeration, which makes DOT dependent on these control parameters.
fedbatch_ecoli An overflow metabolism model is used to simulate the acetate formation/consumption by E. coli W3110 in a process started as batch,
followed by first exponential feed to resorb the acetate and then constant feed to reach high cell density.
yeast_fedbatch This simulation utilizes exponential feed to control ethanol production by overflow metabolism in a fed-batch culture of S. cerevisiae. The model used is described in the SIMSPEC file yeast_model.

Chemostat simulations
chemostat_demo Simulation of steady-state values of concentrations in a chemostat as function of dilution rate.
chemostat_dyn Dynamic simulation of a chemostat. Illustrates how to start and control a chemostat.
yeast_chemostat_ss This simulation shows steady state concentrations of cells, glucose, ethanol, and DOT in a S. cerevisiae chemostat.
chemostat_mutant Dynamic simulation that illustrates take-over by a single plasmid free cell at the start of a continuous culture of a recombinant
protein producer.

Other applications
monod_inhibition This simulation is used to illustrate different inhibition types (competitive, non-competitive, etc.) in Monod plots.
yeast_model The overflow model used in the yeast simulations above is illustrated as Monod plots of specific rates of glucose and oxygen uptake and
cell and ethanol production.
exp_growth Shows how mu-max determines the maximum cell density obtained in an (aerobic) batch bioreactor (at constant KLa).
Sconsumption Illustrates how fast the limiting substrate is exhausted in a fed-batch if the feed is interrupted.
Sgradient_bead This application simulatesthe substrate concentration profile in a homogeneous bead/floc at different concentration of S and biocatalyst.
The effectiveness factor is also calculated for the bead.
HTST_sterilisation The sterilisation time is calculated as function of temperature in a continuous sterilisation process.
Batch_sterilisation The lethal rate and accumulated sterilisation dose is calculated during a batch autoclaving process.
Astat This file simulates an accelerostate, i.e. a pseudo-chemostat in which the dilution rate is constantly increased or reduced with time.
yeast_Astat The Astat simulation is applied on a S. cerevisiae culture.

The models used in the simulations above assume that oxygen does not become limiting. If process control settings result in oxygen limitation the results may become completely wrong. Most fed-batch models above are based on parameters typical for E. coli without overflow metabolism (as if grown on glycerol).
Some of the applications above include links to student exercises.

To download SimuPlot 6 : Send an (empty) email to and you will immediately get an email with a link for downloading.
The toolbox is compressed (.zip). Unpack with suitable software in your computer. Set MATLABs path to the folder SimuPlot6 and its subfolders. Start command is simuplot.

Page updated Oct. 29, 2018