BIOL398-01/S11:Week 6

This journal entry is due on Tuesday, February 22 at midnight PST (Monday night/Tuesday morning). NOTE new due date and that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

Individual Journal Assignment

• Store this journal entry as "username Week 6" (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: you can do all of this easily by adding them to your template and then using the template on your pages.)
  • 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 "BIOL398-01/S11" category to the end of your wiki page.

A Quantitative Look at Nitrogen Metabolism

• List the state variables needed to model the process of interest.
• Propose at least one system of differential equations you think will model the dynamics.
• Discuss the terms in your equation(s) in order to justify your choices.
• List all parameters your model requires for numerical simulation.
• Discuss the relationship between the data in the papers by ter Schure et al and the state variables (and parameters).

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 6 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 "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).

Reflection on a Quantitative Look at Nitrogen Metabolism

1. What was the purpose of this assignment?
2. What aspect of this assignment came most easily to you?
3. What aspect of this assignment was the most challenging for you?
4. What (yet) do you not understand?

Read and Reflect

• Compare the current ter Schure et al paper (Microbiology, 1995, 141, pp1101-1108) with the previously discussed J. Bacteriology (1995) 177, no. 22, pp6672-6675, paper.
  1. In what ways are the goals of the papers different?
  2. What things in the Microbiology paper help clarify methods in the Bacteriology paper?
  3. Do you feel anything is lacking for the purposes of developing a math model and simulating nitrogen metabolism? If so, what?