BIOL398-05/S17:Class Journal Week 7

Lauren M. Kelly Reflection

Lauren M. Kelly

1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • By performing this research, I learned that models must take into account a large number of variables and it is easy to get caught up in figuring out how to connect everything. I also learned that, while a connection between two different papers may seem obvious, it may be difficult to model. In terms of my technical skills, performing this research improved my MATLAB skills and showed me how to put together a professional presentation. In terms of personal or teamwork qualities, working with my classmates showed me that collaboration and support is necessary in the scientific community.
2. What is still not clear to you after having concluded this project?
   • It is still not clear to me whether or not my model accurately represented the population. The model did not behave like I hoped it would, and I am unsure if this is due to the connection between nitrogen and CO2 production being irrelevant or my equations being inaccurate.
3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?

1. • If I had more time, I would like to more thoroughly develop my system of differential equations to ensure that everything fits together properly. I would also like to see how other variables that affect the environment of the yeast interact.

Lauren M. Kelly 18:49, 26 February 2017 (EST)

Cameron M. Rehmani Seraji Reflection

1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).

• After finishing this assignment I believe I now have a better knowledge of generating functions and scripts in MATLAB, I have improved my syntax and ability to create and edit my OpenWetWare pages, and I have developed skills that will make me a better problem solver.

1. What is still not clear to you after having concluded this project?

• I am not sure how to correctly calculate and find the steady state values for my system of equations. Some of my equations looked very similar to those from previous assignments so I was able to figure those out, but I am unsure if I correctly solved the other equations I included in my powerpoint.

1. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?

• If I had more time for this project, I would further study how changing the different concentrations of ammonia and glucose affect the production of yeast. Another idea would be to see how much yeast is produced when it's nutrients are genetically modified.
• Cameron M. Rehmani Seraji 02:54, 2 March 2017 (EST):

Conor Keith Reflection

1. I learned that in order to understand the mathematics behind biological processes you need a very solid foundation of biological knowledge. Its not possible to rely on one or the other when constructing your own project.
2. I'm still unsure about glycolysis and all of the different enzymes that play a role.
3. I would do many more simulations using different controls and more state variables. The oversimplified model I used does not best represent that complex fermentation process.

Conor Keith 02:55, 2 March 2017 (EST)

Nika Vafadari Reflection Questions

Nika Vafadari

1. By performing this research project I was able to gain a better understanding of the importance alcohol fermentation, which occurs in yeast, such as S. cerevisiae. More specifically, I was able to gain a better understanding of the specific factors that affect alcohol fermentation and the various ways that the rate of alcohol fermentation can be increased by studying the relationship between fermentation kinetics and the population dynamics of yeast. However, the greatest piece of knowledge I gained from this project, was a better understanding of how differential equations can represent a specific relationship and how they can be used to model that relationship and look into various predictions. It was very interesting learning how to build a differential equation to represent our hypotheses and predictions. Some of the technical skills I gained from this experience, include learning how to better use the matlab software to create a model and test the various outcomes and learning how to write a differential equation that incorporates all aspects of a hypothesis. Overall, this experience taught me that in order to succeed as a scientist, working with others and asking questions are vital skills. Without the help of Dr. Fitzpatrick in relating my differential equations to my hypothesis and plotting my data in matlab or the help of Dr. Dahlquist in properly presenting our data, this project would not be possible.
2. As for my results, the complete set of the factors that affect the rate and time of alcohol fermentation still remain unclear. However my results did confirm the results of the Albertin et. al paper, which concluded that population size of yeast drive alcohol fermentation.
3. If I had more time I would look into some of the other factors that could affect the duration of alcohol fermentation in yeast, such as the rate of glucose consumption and compare them to my results on the effects of the rate of nitrogen consumption. In addition I would look further into factors that may affect the rate of nitrogen consumption since it plays a role in the duration of alcohol consumption.

• I certify that this individual journal entry was completed by me and not copied from another source.
• Nika Vafadari 03:00, 2 March 2017 (EST):