# BIOL398-03/S13:Class Journal Week 4

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(→James P. McDonald Week 4 Journal: answered last question) |
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*What do you not understand? | *What do you not understand? | ||

**Why we had to do all of the algebra why not just give us the steady states. | **Why we had to do all of the algebra why not just give us the steady states. | ||

+ | |||

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

+ | *Steady states given in the paper were concentration of nitrogen and amount of biomass. Flux was held constant. Dilution rate was held constant. Steady state value of carbon (glucose) was held constant. We had to figure out or assume rate constants and V and r. | ||

+ | |||

+ | [[User:Kevin Matthew McKay|Kevin Matthew McKay]] 01:33, 8 February 2013 (EST) | ||

==Kasey E. O'Connor Class Journal Week 4== | ==Kasey E. O'Connor Class Journal Week 4== | ||

Line 29: | Line 34: | ||

====Reflection==== | ====Reflection==== | ||

*What was the purpose of this assigment? | *What was the purpose of this assigment? | ||

- | ** | + | **This assignment allowed us to see the interactions between the parameters and state variables, without needing to depend on actual values. We were better able to understand the concept of equilibrium, and how the state variables interact with each other. It also gave us a more accurate depiction of the way chemostats work, because yeast are not actually only dependent on one nutrient. |

*What aspect of the assignment was easiest? | *What aspect of the assignment was easiest? | ||

- | ** | + | **Running the script and understanding the state variables and parameters were the easiest part of the assignment. |

*What was most challenging? | *What was most challenging? | ||

- | ** | + | **All of the algebra was the most difficult. Not because it was hard to do, just because keeping all of the different variables and letters straight without making a stupid mistake was challenging. |

*What do you not understand? | *What do you not understand? | ||

- | ** | + | **I am having a little difficulty trying to figure out how the product term affects it, and the actual changes that would be made in the state variables if it was changed to an addition term. |

+ | |||

====Read and Reflect==== | ====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? | *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? | ||

- | ** | + | **Both our work and the paper contain nutrient inflow rate, net growth rate (looking at biomass specifically), the nitrogen feed rate, and the carbon rate. However, in the paper, carbon rate was kept constant, but we treated it as a state variable. In reading the paper, we had to work to figure out all of the rate constants, the conversion factor, and the reaction maximum. The ammonia flux (steady state concentration of ammonia) was given in the paper, since all the data was assumed to be taken when the chemostat was at equilibrium. |

+ | |||

+ | '''[[User:Kasey E. O'Connor|Kasey E. O'Connor]] 01:43, 8 February 2013 (EST)''' | ||

==James P. McDonald Week 4 Journal== | ==James P. McDonald Week 4 Journal== | ||

Line 65: | Line 73: | ||

===Reflection=== | ===Reflection=== | ||

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

- | #* | + | #*Practice solving differential equations and deal with multiple variables. |

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

- | #* | + | #*The MATLAB part of the assignment was the easiest for me. |

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

- | #* | + | #*Doing all of the math. |

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

- | #* | + | #*I'm still not sure if I did my math right. |

===Read and Reflect=== | ===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 parameters from the paper were the ammonia concentration, carbon (glucose) concentration, and and the dilution. The only two rate constants that are not give to us are V and r. |

[[User:Salman Ahmad|Salman Ahmad]] 00:14, 8 February 2013 (EST) | [[User:Salman Ahmad|Salman Ahmad]] 00:14, 8 February 2013 (EST) | ||

+ | |||

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

+ | |||

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

+ | |||

+ | ===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) | ||

+ | |||

+ | |||

+ | ==Ashley Rhoades Week 4== | ||

+ | |||

+ | [[User: Ashley Rhoades | Ashley Rhoades]] | ||

+ | |||

+ | ===Reflection on Work=== | ||

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

+ | #*The purpose of this assignment was to get more comfortable with differential equations in matlab and the chemostat models. | ||

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

+ | #*Running the functions in matlab was easy. | ||

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

+ | #*It was difficult keeping track of all the parameters in the mathematics of this assignment | ||

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

+ | #*I probably couldn't put those functions into matlab very easily. There is a lot of formatting that we learned that still hasn't stuck with me. | ||

+ | |||

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

+ | |||

+ | |||

+ | **Parameters that were extracted from the paper were the dilution rate, the nitrogen feed, and the carbon feed. What had to be found through other methods were the net growth, nutrient consumption, and nutrient saturation. The paper does not go to steady state values. The experiments stop before the steady states are reached. | ||

+ | |||

+ | [[User:Ashley Rhoades|Ashley Rhoades]] 01:48, 8 February 2013 (EST) | ||

+ | |||

+ | ==Elizabeth Polidan Class Journal Week 4== | ||

+ | [[User:Elizabeth Polidan|Elizabeth Polidan]] | ||

+ | |||

+ | ===Reflection on Work=== | ||

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

+ | ##To help us understand how these mathematical equations create information we can analyze and assess. | ||

+ | ##To help us understand the ideas of parameters and constants and get us used to using them. | ||

+ | ##To give us practice using Matlab. | ||

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

+ | ##Playing around with Matlab and understanding parameters and constants vs. state variables. | ||

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

+ | ##Remembering my algebra! I sure hope some of that work is correct. | ||

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

+ | ##Just waiting to see where we go from here. | ||

+ | |||

+ | [[User:Elizabeth Polidan|Elizabeth Polidan]] 01:51, 8 February 2013 (EST) | ||

+ | |||

+ | ==Helena M. Olivieri Week 4 Journal== | ||

+ | [[User:Helena M. Olivieri|Helena M. Olivieri]] | ||

+ | ===Questions=== | ||

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

+ | #*The purpose was to further delve into the functions of Matlab, as well as to fully understand the algebraic functions and derivatives behind the Matlab inputs. | ||

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

+ | #*The matlab aspect was the easiest because the most difficult part, the code writing, was already done. | ||

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

+ | #*The algebra was slightly less than pleasant. | ||

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

+ | #*How to develop the codes in Matlab... as well as how to make algebra pleasant (haha). | ||

+ | |||

+ | ===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? | ||

+ | #*By looking at the Schure paper, the parameters that can be extracted are concerned with growth rate, carbon rate, and nitrogen feed. The paper emphasized that ammonia flux was constant. We will need to determine V and r. | ||

+ | [[User:Helena M. Olivieri|Helena M. Olivieri]] 02:00, 8 February 2013 (EST) | ||

+ | |||

+ | ==Laura Terada Week 4 Journal== | ||

+ | [[User:Laura Terada|Laura Terada]] | ||

+ | ===Questions=== | ||

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

+ | #*The purpose of this assignment was for us to be able to mathematically understand the model of steady state conditions in terms of the yeast, carbon, and nitrogen state variables. It also tested our ability to do algebra. | ||

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

+ | #*Inserting the script and running the graph in MATLAB was the easiest. | ||

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

+ | #*Being able to derive the steady state for the state variables was the most challenging. After introducing the assignment in today's class, I was not comfortable deriving the equations. I worked on the equations for an extremely long time, and was still unable to fully complete the first question to the homework assignment. | ||

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

+ | #*I still don't understand how to derive the steady state equations. | ||

+ | ===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 paper provided the nitrogen concentration, carbon concentration, and dilution rate. The values of V, r, and K, which are the reaction maximum, the rate of conversion and reaction rate constant, respectively. The only steady state provided in the paper was ammonia concentration. | ||

+ | [[User:Laura Terada|Laura Terada]] 02:15, 8 February 2013 (EST) | ||

+ | |||

+ | ==Matthew E. Jurek Week 4== | ||

+ | [[User:Matthew E. Jurek|Matthew E. Jurek]] | ||

+ | ===Questions=== | ||

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

+ | **The purpose of this assignment was to explore what we studied in the most recent journal club. This was done by expressing the chemostat in the experiment as a function on MatLab. Furthermore, this assignment required us to explore the math behind these functions. | ||

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

+ | **Running the given script and manipulating the already established function. However, there was an error in the given script, but I was able to correct it and run it properly. | ||

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

+ | **Working through the math. I haven't studied math in a while and this part was extremely difficult. I'm not sure what I did is correct, but I tried to work through as many variables as possible. | ||

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

+ | **I still don't understand how to work through the steady state equations. I want to figure this out as I know we will continue to use these skills as the semester continues. | ||

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

+ | |||

+ | **The ter Schure paper stated the dilution rate, the nitrogen feed rate, the carbon rate, and the glucose concentration. All of these are found in our model. The conversion rate and reaction rate must be found by some other method. The ammonia flux was kept steady in the paper. | ||

+ | *'''[[User:Matthew E. Jurek|Matthew E. Jurek]] 02:35, 8 February 2013 (EST)''': |

## Current revision

## 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.

### Read and Reflect

- Steady states given in the paper were concentration of nitrogen and amount of biomass. Flux was held constant. Dilution rate was held constant. Steady state value of carbon (glucose) was held constant. We had to figure out or assume rate constants and V and r.

Kevin Matthew McKay 01:33, 8 February 2013 (EST)

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

#### Reflection

- What was the purpose of this assigment?
- This assignment allowed us to see the interactions between the parameters and state variables, without needing to depend on actual values. We were better able to understand the concept of equilibrium, and how the state variables interact with each other. It also gave us a more accurate depiction of the way chemostats work, because yeast are not actually only dependent on one nutrient.

- What aspect of the assignment was easiest?
- Running the script and understanding the state variables and parameters were the easiest part of the assignment.

- What was most challenging?
- All of the algebra was the most difficult. Not because it was hard to do, just because keeping all of the different variables and letters straight without making a stupid mistake was challenging.

- What do you not understand?
- I am having a little difficulty trying to figure out how the product term affects it, and the actual changes that would be made in the state variables if it was changed to an addition term.

#### 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?
- Both our work and the paper contain nutrient inflow rate, net growth rate (looking at biomass specifically), the nitrogen feed rate, and the carbon rate. However, in the paper, carbon rate was kept constant, but we treated it as a state variable. In reading the paper, we had to work to figure out all of the rate constants, the conversion factor, and the reaction maximum. The ammonia flux (steady state concentration of ammonia) was given in the paper, since all the data was assumed to be taken when the chemostat was at equilibrium.

**Kasey E. O'Connor 01:43, 8 February 2013 (EST)**

## 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?
- Practice solving differential equations and deal with multiple variables.

- What aspect of this assignment came most easily to you?
- The MATLAB part of the assignment was the easiest for me.

- What aspect of this assignment was the most challenging for you?
- Doing all of the math.

- What (yet) do you not understand?
- I'm still not sure if I did my math right.

### 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 parameters from the paper were the ammonia concentration, carbon (glucose) concentration, and and the dilution. The only two rate constants that are not give to us are V and r.

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)

## Ashley Rhoades Week 4

### Reflection on Work

- What was the purpose of this assignment?
- The purpose of this assignment was to get more comfortable with differential equations in matlab and the chemostat models.

- What aspect of this assignment came most easily to you?
- Running the functions in matlab was easy.

- What aspect of this assignment was the most challenging for you?
- It was difficult keeping track of all the parameters in the mathematics of this assignment

- What (yet) do you not understand?
- I probably couldn't put those functions into matlab very easily. There is a lot of formatting that we learned that still hasn't stuck with me.

### 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?
- Parameters that were extracted from the paper were the dilution rate, the nitrogen feed, and the carbon feed. What had to be found through other methods were the net growth, nutrient consumption, and nutrient saturation. The paper does not go to steady state values. The experiments stop before the steady states are reached.

Ashley Rhoades 01:48, 8 February 2013 (EST)

## Elizabeth Polidan Class Journal Week 4

### Reflection on Work

- What was the purpose of this assignment?
- To help us understand how these mathematical equations create information we can analyze and assess.
- To help us understand the ideas of parameters and constants and get us used to using them.
- To give us practice using Matlab.

- What aspect of this assignment came most easily to you?
- Playing around with Matlab and understanding parameters and constants vs. state variables.

- What aspect of this assignment was the most challenging for you?
- Remembering my algebra! I sure hope some of that work is correct.

- What (yet) do you not understand?
- Just waiting to see where we go from here.

Elizabeth Polidan 01:51, 8 February 2013 (EST)

## Helena M. Olivieri Week 4 Journal

### Questions

- What was the purpose of this assignment?
- The purpose was to further delve into the functions of Matlab, as well as to fully understand the algebraic functions and derivatives behind the Matlab inputs.

- What aspect of this assignment came most easily to you?
- The matlab aspect was the easiest because the most difficult part, the code writing, was already done.

- What aspect of this assignment was the most challenging for you?
- The algebra was slightly less than pleasant.

- What (yet) do you not understand?
- How to develop the codes in Matlab... as well as how to make algebra pleasant (haha).

### 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?
- By looking at the Schure paper, the parameters that can be extracted are concerned with growth rate, carbon rate, and nitrogen feed. The paper emphasized that ammonia flux was constant. We will need to determine V and r.

Helena M. Olivieri 02:00, 8 February 2013 (EST)

## Laura Terada Week 4 Journal

### Questions

- What was the purpose of this assignment?
- The purpose of this assignment was for us to be able to mathematically understand the model of steady state conditions in terms of the yeast, carbon, and nitrogen state variables. It also tested our ability to do algebra.

- What aspect of this assignment came most easily to you?
- Inserting the script and running the graph in MATLAB was the easiest.

- What aspect of this assignment was the most challenging for you?
- Being able to derive the steady state for the state variables was the most challenging. After introducing the assignment in today's class, I was not comfortable deriving the equations. I worked on the equations for an extremely long time, and was still unable to fully complete the first question to the homework assignment.

- What (yet) do you not understand?
- I still don't understand how to derive the steady state equations.

### 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 paper provided the nitrogen concentration, carbon concentration, and dilution rate. The values of V, r, and K, which are the reaction maximum, the rate of conversion and reaction rate constant, respectively. The only steady state provided in the paper was ammonia concentration.

Laura Terada 02:15, 8 February 2013 (EST)

## Matthew E. Jurek Week 4

### Questions

- What was the purpose of this assignment?
- The purpose of this assignment was to explore what we studied in the most recent journal club. This was done by expressing the chemostat in the experiment as a function on MatLab. Furthermore, this assignment required us to explore the math behind these functions.

- What aspect of this assignment came most easily to you?
- Running the given script and manipulating the already established function. However, there was an error in the given script, but I was able to correct it and run it properly.

- What aspect of this assignment was most challenging for you?
- Working through the math. I haven't studied math in a while and this part was extremely difficult. I'm not sure what I did is correct, but I tried to work through as many variables as possible.

- What (yet) do you not understand?
- I still don't understand how to work through the steady state equations. I want to figure this out as I know we will continue to use these skills as the semester continues.

### 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 ter Schure paper stated the dilution rate, the nitrogen feed rate, the carbon rate, and the glucose concentration. All of these are found in our model. The conversion rate and reaction rate must be found by some other method. The ammonia flux was kept steady in the paper.

**Matthew E. Jurek 02:35, 8 February 2013 (EST)**: