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 Assignment

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 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?