BIOL398-04/S15:Week 5

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BIOL398-04: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Tuesday, February 17 at midnight PST (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

NOTE: this page is under construction.

Individual Journal Assignment

  • Store this journal entry as "username Week 5" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL398-04/S15" category to the end of your wiki page.

MATLAB model creation

  • create two matlab files, YourNameDE.m and YourNameScript.m (replace YourName with your first and last names).
  • in the YourNameDE.m file, create a function that defines the differential equations

ds/dt = -V*s/(K+s) dp/dt = V*s/(K+s)

  • in the YourNameScript.m file,
    • put a global statement with the two parameters V, K in it.
    • set the variables V = 2, K = 1.
    • define a time sequence from 0 to 10 by steps of 0.1
    • set the initial value of s to 8 and the initial value of p to 0
    • use the MATLAB function ODE45 to solve the differential equation system you put in the file YourNameDE.m
    • plot the solutions s and p vs time.
    • upload the two MATLAB files and the resulting graph to your individual journal.

Shared Journal Assignment

  • Store your shared journal entry in the shared Class Journal Week 5 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL398-04/S15" category to the end of the wiki page (if someone has not already done so).

Group Assignment

  • Create a chemical reaction graph that defines the five enzyme reactions in yeast's nitrogen metabolism. Include a rate constant for each reaction arrow. The three product/substrate quantities are alpha-ketogluterate, glutamate, and glutamine. Get the enzymes from the slides Dr. Dahlquist prepared on myLMUconnect.
  • Answer this question: what do yeast do in the lag phase of growth that is related to the reaction graph you just drew?