Desireegonzalez Week 15
- The purpose of this assignment was to work with the given chemostat equations and the Arrhenius equation to edit the model simulations and MATLAB files for chemostat reactions that depicted a temperature dependence and also modeled efficiency and waste.
- To begin the Arrhenius equation (rate = A*exp(-B/(R*T)) was used to model the temperature dependence of the chemostat reaction.
- This was then used to figure out the constants A and B from the rate data in the TaiParamsRevised.m file.
- MATLAB was then used to simulate the chemostat for T = 15,20, 25 degrees C conditions and graph the time courses of the biomass and nutrients.
- Afterwards, the glucose efficiency/waste constant (that is not really a constant?) was investigated for the glucose-limited and ammonium-limited conditions. Making sure to note the values of E for glucose-limited and ammonium-limited conditions.
- For each temperature (12, 30), a function E(y) that matches the two points of (y,E) data was then found.
- These functions were then used to modify the chemostat_2nutrient_dynamics.m file.The resulting simulations were then compared.
- A 15 minute presentation was then created with the information below.
- A brief intro to the chemostat problem of Tai et al (2007).
- The data we've extracted from the paper and other sources.
- The temperature investigation.
- The efficiency/waste investigation.
- A discussion and reflection on your findings.
Data Files and Calculations
Results for Temperature Dependency Using Arrhenius Equation
Figure 1: Temperature dependency graph of Glucose limited trial at 15 degrees C.
Figure 2: Temperature dependency graph of Glucose limited trial at 20 degrees C.
Figure 3: Temperature dependency graph of Glucose limited trial at 25 degrees C.
Figure 4: Temperature dependency graph of Glucose limited trial at 12 degrees C.
Results for Efficiency and Waste Modeling
- The purpose of this assignment, to edit the model simulations and MATLAB files for chemostat reactions that depicted a temperature dependence and also modeled efficiency and waste, was fulfilled.
- The experiment looking at temperature dependency model depicted that residual glucose levels decrease as the temperature increases.
- The experiment looking at the efficiency and waste model revealed that there was not a significant difference in the models use of efficiency as E=1/Y or as E=my+b.
- I communicated in person with my homework partner, Leanne to go over the calculations and MATLAB simulations that we were going to put into our 15 minute final presentation.
- The MATLAB files needed for the completion of this assignment were provided by Dr. Dahlquist and Dr. Fitzpatrick.
Dahlquist, K. & Fitzpatrick, B.G. (2019, May 6). BIOL388/S19:Week 14/15. Retrieved from https://openwetware.org/wiki/BIOL388/S19:Week_14/15 on 7 May 2019.
MATLAB (Version R2014b) [Computer software]. (n.d.). Retrieved 7 May 2019.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., Winde, J. H., & Daran, J. (2005). Two-dimensional Transcriptome Analysis in Chemostat Cultures Combinational Effects of Oxygen Availability and Macronutrient Limitation in Saccharomyces cerevisiae. Retrieved April 22, 2019, from http://www.jbc.org/content/280/1/437.long
Tai, S. L., Daran-Lapujade, P., Walsh, M. C., Pronk, J. T., & Daran, J. (2007). Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analysis. Molecular Biology of the Cell, 18(12), 5100-5112. doi:10.1091/mbc.e07-02-0131
Below are the links to all the Assignments and Journal Entries of the Spring 2019 Semester.
User Page: user:desireegonzalez
Template Page: template:desireegonzalez
Weekly Assignment Pages:
Individual Journal Entry Pages:
- desireegonzalez Week 1
- desireegonzalez Week 2
- desireegonzalez Week 3
- desireegonzalez Week 4/5
- desireegonzalez Week 6
- desireegonzalez Week 7
- desireegonzalez Week 9
- desireegonzalez Week 10
- desireegonzalez Week 11
- desireegonzalez Week 12
- desireegonzalez Week 15
Shared Journal Pages: