BIOL398-01/S11:Week 3

This journal entry is due on Monday, January 31 at midnight PST (Sunday night/Monday morning). NOTE 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 3" (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.

Terminology

• Look up the following terms and provide definitions. For each definition, three elements are required: you must quote a source, reference the source, and interpret the definition in your own words.

1. dynamical system
2. law of mass action
3. homeostasis
4. equilibrium
5. oscillation
6. autocatalysis

Applying the Law of Mass Action

• Construct differential equations that model the following reactions. Be sure to define your state variables and rate constants.

1. A + B → C
2. A + B ↔ C
3. A + B ↔ 2C
4. 2A + 3B ↔ C+D

Please note that the symbol ↔ is used to denote arrows (reactions) in both directions.

Simulating Reaction Kinetics

• Use the matlab code provided at my lionshare folder to study the simple reaction

1. E + S ↔ ES → E + P

that we have studied in class. Set the parameters as follows:

• [S₀] = 1.0
• [E₀] = 0.2
• [ES₀] = 0.0
• [P₀] = 0.0
• k₁ = 2.0
• k_-1 = 0.0
• k₂ = 10

Plot the output, and save the plot as an image. Post the image on the wiki as the answer to the question.

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 3 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

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?
5. What is the relationship between homeostasis and equilibrium?