# BIOL398-03/S13:Class Journal Week 4

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(→James P. McDonald Week 4 Journal: answered last question) |
(Added all of Anthony J. Wavrin reflection and read and reflect) |
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[[User:Salman Ahmad|Salman Ahmad]] 00:14, 8 February 2013 (EST) | [[User:Salman Ahmad|Salman Ahmad]] 00:14, 8 February 2013 (EST) | ||

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+ | ==Anthony J. Wavrin Week 4 Journal== | ||

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+ | [[User:Anthony J. Wavrin|Anthony J. Wavrin]] | ||

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+ | ===Reflection=== | ||

+ | #What was the purpose of this assignment? | ||

+ | #*The purpose of this assignment is for us to do the algebra by hand, so we understand how the constants and state variables are interrelated. This is similar to doing limits by hand before learning derivative rules. | ||

+ | #What aspect of this assignment came most easily to you? | ||

+ | #*The matlab portion because the script and function were already written, thus it was simply changing the parameters. | ||

+ | #What aspect of this assignment was the most challenging for you? | ||

+ | #*The first question was extremely difficult for me. Not doing any math, let alone algebra, since highschool put me in a strange position in which I struggled. | ||

+ | #What (yet) do you not understand? | ||

+ | #*How we are supposed to derive the steady states. I understand the idea of it but, I was unable to deal with the intense algebra. | ||

+ | |||

+ | ===Read and Reflect=== | ||

+ | #Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper? | ||

+ | #* In the ter Schure paper, they give us three of the parameters: ammonia concentration (26, 44, 61, 66, 78, 90, 96, 114, 118 mM), glucose concentration (100 mM), and dilution rate (0.15 per hour). That means that we must find the conversion factor (r), reaction maximum (v), and reaction constants (kn, kc). Since the data in the paper is supposedly measured during the equilibrium, all of the data should be representative of steady states. However, there is no description of a function of constants that could be used to determine any of the steady states. | ||

+ | |||

+ | [[User:Anthony J. Wavrin|Anthony J. Wavrin]] 01:32, 8 February 2013 (EST) |

## Revision as of 02:32, 8 February 2013

## Contents |

## Paul Magnano Class Journal Week 4

### Reflection on Work

- What was the purpose of this assignment? To help us become more familiar with matlab, as well as to help us better understand the relationships between various parameters and state variables in the equations we are using to model chemostats.
- What aspect of this assignment came most easily to you? The inital graph using matlab.
- What aspect of this assignment was the most challenging for you? The 3 questions were very confusing for me because I wasn't in class on tuesday, so for the most part I kind of had to guess my way through it.
- What (yet) do you not understand? Why we had to do pages of algebra..

### Read and Reflect

- Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper? You could extract the rate of nutrient inflow namely ammonia (q in our model), net growth rate namely the rate of biomass increase (y in our model), nutrient saturation rate namely ammonia flux (K in our model). You could determine V, the nutrient consumption rate by using the rate of ammonia going into the cell and the residual ammonia left, but it is not explicitly listed in the paper. The steady state for ammonia concentration is given (calculated as ammonia flux into biomass) and is shown to be 1.1 mmol/(gh).

## Kevin McKay Class Journal Week 4

### Reflection

- What was the purpose of this assigment?
- Well other than making us suffer through heavy algebra, it helped us see the relationship between certain parameters in equations that we defied i class. It allowed us to model a system and compare our results to an actual experiment.

- What aspect of the assignment was easiest?
- Doing the actual math.

- What was most challenging?
- Being patient with how tedious using the computer is for me.

- What do you not understand?
- Why we had to do all of the algebra why not just give us the steady states.

## Kasey E. O'Connor Class Journal Week 4

#### Reflection

- What was the purpose of this assigment?
- What aspect of the assignment was easiest?
- What was most challenging?
- What do you not understand?

#### Read and Reflect

- Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?

## James P. McDonald Week 4 Journal

### Reflection on Work

- What was the purpose of this assignment?
- Once purpose was to further our practice and experience using matlab to plot functions. It was also done to improve our understanding of the math of the chemostat and its parameters.

- What aspect of this assignment came most easily to you?
- I had an easy time inputting the function and script into matlab and producing different graphs by altering parameter values.

- What aspect of this assignment was the most challenging for you?
- Finding the steady states was challenging. I had trouble using math to manipulate the equations into the final steady state values.

- What (yet) do you not understand?
- I am not sure how to come up with the functions and use all the proper notations, from scratch, that can be put into matlab and executed.

### Read and Reflect

- Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
- The first parameter that can be extracted from the ter Schure paper is the dilution rate, what we label as q, which was kept constant in the paper. Another parameter was the nitrogen feed rate, what we label as u
_{n}, in the paper it is the feed concentration of NH_{4}^{+}. The last parameter found in the paper was the carbon rate, what we label as u_{c}, it is constant in the paper as the glucose concentration. The conversion rate, r, reaction rate, V, and reaction constant, K, are not provided in the paper but could be found by other methods. In the paper the levels of ammonia flux are kept in steady state.

- The first parameter that can be extracted from the ter Schure paper is the dilution rate, what we label as q, which was kept constant in the paper. Another parameter was the nitrogen feed rate, what we label as u

## Salman Ahmad Week 4 Journal

### 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?

### Read and Reflect

- Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?

Salman Ahmad 00:14, 8 February 2013 (EST)

## Anthony J. Wavrin Week 4 Journal

### Reflection

- What was the purpose of this assignment?
- The purpose of this assignment is for us to do the algebra by hand, so we understand how the constants and state variables are interrelated. This is similar to doing limits by hand before learning derivative rules.

- What aspect of this assignment came most easily to you?
- The matlab portion because the script and function were already written, thus it was simply changing the parameters.

- What aspect of this assignment was the most challenging for you?
- The first question was extremely difficult for me. Not doing any math, let alone algebra, since highschool put me in a strange position in which I struggled.

- What (yet) do you not understand?
- How we are supposed to derive the steady states. I understand the idea of it but, I was unable to deal with the intense algebra.

### Read and Reflect

- Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
- In the ter Schure paper, they give us three of the parameters: ammonia concentration (26, 44, 61, 66, 78, 90, 96, 114, 118 mM), glucose concentration (100 mM), and dilution rate (0.15 per hour). That means that we must find the conversion factor (r), reaction maximum (v), and reaction constants (kn, kc). Since the data in the paper is supposedly measured during the equilibrium, all of the data should be representative of steady states. However, there is no description of a function of constants that could be used to determine any of the steady states.

Anthony J. Wavrin 01:32, 8 February 2013 (EST)