# BIOL398-01/S11:Class Journal Week 3

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## Contents

## Instructions

### Formatting

- 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

- What was the purpose of this assignment?
- What aspect of this assignment came most easily to you?
- What aspect of this assignment was the most challenging for you?
- What (yet) do you not understand?
- What is the relationship between homeostasis and equilibrium?

## Class Responses

### Sarah Carratt's Journal Entry

- The purpose of this assignment was to give us practice with matlab and see if we could create a simple model on our own.
- The easiest part of this assignment was understanding the technical definitions.
- The hardest aspect of this assignment was working with matlab and creating differential equations. It was particularly difficult to understand the matlab program without comments. Example, x0 represents s0, e0, es0/c0, p0.
- I am really struggling with formatting in matlab. "CS" is graphing at figures that are effectively zero and I am confused by just about everything within the program except the plots that are produced. At least the graphs are easy enough to interpret.
*Homeostasis*is the term for the ability to maintain a good balance in an internal environment even as the external environment changes, and*equilibrium*is the point in time when a reaction is completely balanced.

Sarah Carratt 20:17, 30 January 2011 (EST)

### Carmen E. Castaneda's Journal Entry

- The purpose of this assignment was to engage us in the world of math modeling. That is to say after being introduced to the idea of finding a model to fit our experiment, we were put to the test to do the same with the information we were given. As well as introduce us to MATLAB.
- Finding the mathematical models was the easiest part of the assignment, I just don't know how correct they are.
- The most challenging aspect was trying to make MATLAB run. Eventhough we played with a little before, I still don't fully understand how to use this program.
- As I stated earlier, I don't quite understand how to use MATLAB and I think I might need some more clarification on writing my equations, since I'm second guessing myself a little.
- Homeostasis is what the body, or in our case cells, has to have to be in equilibrium. Meaning that through homeostasis, which is the state of adapting and working toward equilibrium, which is a balance, we can reach equilibrium.

Carmen E. Castaneda 02:58, 31 January 2011 (EST)

### James C. Clements' Journal Entry

- The purpose of this assignment was to gain a better understanding of catalytic reaction kinetics and to understand a basic method for modeling them.
- The MatLab portion of the assignment came most easily to me. Just changing a couple of numbers out from the given code felt too easy; I almost feel like I was missing something. I understand this is also serving as an introduction to the program for those who have not been exposed to it, hopefully the MatLab portions will become more involved in the future (I've been using MatLab since 2006...).
- The application of the Law of Mass Action was most difficult with me. I wasn't too sure on what to do for parts 3 and 4.
- I still don't understand what the advantage of using the Michaelis Menten method is.
- Homeostasis is the process by which equilibrium is maintained within a cell.

James C. Clements 00:50, 31 January 2011 (EST)

### Nicholas A. Rohacz's Journal Entry

- The purpose of this assignment is to let us practice matlab as well as writing out differential equations.
- Having to describe the chemical processes in words came easiest because I have had a lot of practice in that field over my years as a lab tech.
- The matlab was confusing to use at first but I managed it with some help from a few engineers.
- I, personally, am still confused about what happens to the coefficients in front of the reactants, and exactly where it goes in the differential equation.
- Homeostasis and Equilibrium are similiar in that homeostasis manages the functions in the cells to keep them at a constant, thus creating an equilibrium throughout several parts of the body.

Nicholas A. Rohacz 01:52, 31 January 2011 (EST)

### Alondra Vega's Journal Entry

- The purpose of this assignment was to know how to write and understand differential equations. Also, how matlab works with differential equations. The simulation allows us to understand how an ordinary differential equation works and how it applies to modeling different areas of biology.
- The part of this assignment that came easily to me was working with the simulation. It was easy since we did not have to write the actual program.
- The part of this assignment that came most difficult was writing the ordinary differential equations. I was using the example from class, but it was hard to know when we needed to subtract the concentrations and when it was needed to be added, or even included.
- What I still do not understand is the writing of a differential equation. Specifically, what I mentioned in number 3. I feel that I wrote the differential equations in the wrong order, as in I subtracted a number when it was supposed to be added. Also, in the first reaction I only wrote one rate of change equation and I was wondering if I needed one for the elements A and B. I did not write any, but am I supposed to have d[A]/dt = -k
_{1}[A][B]? The same equation would be d[B]/dt. I just was not sure to include them, since the reaction is only going in one direction. It makes sense that they would have an equation, since they are also changing over time. I am just not sure. - The relationship between homeostasis and equilibrium is that homeostasis focuses on having a stable internal environment, which also means to be in equilibrium.

Alondra Vega 12:53, 30 January 2011 (EST)