simulation instuction

7/26/2019 Simulation Instuction

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Simulation exercises- BEC 2014

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The folder SimExerciseBEC contains two sets of bioprocess simulations forMATLAB.The frst set includes the examples in Appendix 1- in the BEC course boo!.

The" are m-les for a chemostat at stead" states# a p$-auxostat %at stead"state or d"namicall"&# and a d"namic simulation of a fedbatch process.

To run these simulations# start MATLAB. 'rom the Command (indow) Set#and sa*e# MATLABs search path to the folder SimExercisesBEC # and itssubfolders. %This path settin+ is needed onl" the ,rst time "ou run this on acomputer# if the path has been sa*ed&. un the simulation pro+ram b"enterin+ the command lename exclusive the .m extension. 'or instance)

The command app1_chemostat will run the simulation of a chemostat atstead" state which is included in appendix 1 of the course boo!.

This mode of simulations ha*e man" restrictions# especiall" for the d"namicsimulations) The" can not %easil"& permit interacti*e simulations where "ouinterrupt and chan+e control *ariable li!e feed rate# the" can onl" include*ariables sol*ed from the dierential e/uations %the mass balances&# andonl" one %relati*e& scale can be used for all plots.

The second set of exercises are based on the toolbox Simu0lot# which sol*esthe limitations with the simple m-,les and also oers man" con*enienteditin+ functions and plottin+ of experimental data superimposed on thesimulations.

The SimuPlotBEC2014 folder contains a folder %S2MS0EC,les& whichcontains se*eral applications for simulation of chemostat and fedbatchprocesses. The" ha*e the MATLAB ,le format .g# and the" must be openedand run from a Simu0lot pa+e.

chemostat_dyn runs a d"namic simulation of a chemostat. 2t starts as abatch and at the end of this batch "ou must start and control the chemostatb" means of the medium 3ow rate %F & and the inlet limitin+ substrateconcentration %Si&. 4ou can also use cell recirculation %56delta61# pleaserefer to the course boo!&. The time scale of this simulation automaticall"switches from 5-75 hrs to 5-755 hours to *isuali8e the batch phase

fedbatch also starts as a batch culture and at the end "ou must start asuitable feed rate %F &. 4ou can +et hints for how to calculate a feed in theComments of this S2M0SEC ,le.

yeast_fedbatch is an example of an exponential fed-batch in which thespeci,c +rowth rate# and thereb" the o*er3ow metabolism %ethanolproduction&# can be controlled. 2t starts with a low and limitin+ +lucoseconcentration and a low F which balances the +lucose %S& consumption rate.

This F is increased with the exponent SF %speci,c feed rate& and !eeps S and mu relati*el" constant. The parameters can be set to completel" a*oidethanol formation# but for producti*it" reasons some ethanol is usuall"

permitted initiall". B" switchin+ from exponential to constant feed rate%9Fmax & the +lucose concentration declines and e*entuall" all ethanol isresorbed. :ote how the metabolic phases are re3ected b" the respirator"

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/uotient %!&# and the hi+h ox"+en consumption rate as lon+ as ethanol isconsumed.

These simulations are d"namic simulations which "ou can interrupt b"pressin+ the mouse in the simulation +raph %not on a plot;&# chan+eparameters which ha*e been speci,ed as chan+eable# and resume thesimulation.

The other simulations %chemosta_ss" yeast_chemostat_ss# and yeast_model#are not interacti*e. The result appears immediatel" after pressin+ the buttonCompile<un. The two chemostat applications plot the stead" state *aluesof the *ariables a+ainst the dilution rate %#$F%& & and the yeast_model plotsMonod t"pe !inetics of the speci,c rates for substrate upta!e %rS&# +rowth%mu&# ox"+en upta!e %r'&# and ethanol production %r(&

The S2MS0EC-,le of each simulation contains sections for speci,cation. Seenext pa+e

&ariables and plotted constants %top&# )onstants % tables in the middle&#

and *lgorithm with e/uations %bottom&)

- The ,rst row in the =ariables must specif" the x-*ariable %usuall" time or >&.

- 2f the simulation is d"namic %ode7s based& all di#-e/uation *ariables%usuall" x" s" #'+ # and & & must be located after the x-*ariable %time&# the"?>E buttons must be acti*ated# and initial *alues must be entered. Axes andplot *isibilit" are optional. See next pa+e.

- The remainin+ list ma" contain other *ariables from theal+orithm %e.+. mu& and constants %e.+. '& if the" shall beincluded in the +raph.

-Constants located in the left table can be chec!ed and if sothe" appear and can be chan+ed in the list of constantwhich appears after a mouse-clic! in the +raph. esume thesimulation with the button ?@. The cancel button interruptsthe simulation and +i*es error messa+es "ou can ne+lect.

-The units are onl" for information- ha*e no eect on the simulation.

- 4ou can scroll updown amon+ =ariables and Constant if needed. 2f there aremore than *ariables % constants& in a table the th %th& row is mar!edwith red.

- The Al+orithm is one sin+le multi-line ,eld. The ,eld si8e can be increasedwith the D button. A*oid chan+in+ the window si8e; 2t ma" chan+e the roworder;

-?pen a new S2MS0EC ,le onl" from a Simu0lot window. Two open S2MS0EC-,les creates an error messa+e.

- 0ress the button Sho, comments for explanation of the parameters andal+orithm.

-un the simulation with the button un)ompile.

The simulation runs with the present specifcation even i the

change has not been save! " #ou want to save a change$ give thefle a new name!

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+he plot ,indo,- To identif" a plot# ri+ht-clic! on it and "ou +et its identit"#and the options to edit it %color# linest"le# scale&# delete orhide it# or +et the coordinates at the point "ou clic!edprinted in the Command (indow. 2f hidden# "ou can retrie*ethe plot from the plot window menu EditraphEdit plots.

-There are three Simu0lot speci,c menus) Editraph# >ata# and Simulation.Fse the $EL0 function in these menus to +et explanations in the Commandwindow.



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