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
Please note that the symbol &harr; is used to denote arrows (reactions) in both directions.
 * Construct differential equations that model the following reactions. Be sure to define your state variables and rate constants.
 * 1) A + B &rarr; C
 * 2) A + B &harr; C
 * 3) A + B &harr; 2C
 * 4) 2A + 3B &harr; C+D

Simulating Reaction Kinetics
that we have studied in class. Set the parameters as follows: Plot the output, and save the plot as an image. Post the image on the wiki as the answer to the question.
 * Use the matlab code provided at my lionshare folder to study the simple reaction
 * 1) E + S &harr; ES &rarr; E + P
 * [ S0 ] = 1.0
 * [ E0 ] = 0.2
 * [ ES0 ] = 0.0
 * [ P0 ] = 0.0
 * k1 = 2.0
 * k-1 = 0.0
 * k2 = 10

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?