Angela C Abarquez Week 15
The purpose is to use MATLAB to create models of the temperature dependence of the chemostat reaction demonstrated in the Tai et al. (2007) paper. Additionally the glucose efficiency constant was further investigated and modified to account for the differing metabolization processes that yeast undergo under different conditions.
The MATLAB files provided by Dr. Fitzpatrick linked (here) were used.
Modeling Temperature Dependence
- The Arrhenius equation (rate = A*e^(-B/(R*T)) was used on each of the four cases (glucose-limited and ammonium-limited for 12 and 30 degrees C) to solve for A and B.
- The r and T values were taken from the "taiParamsRevised" MATLAB file and input into the equation, along with the universal gas constant R, to solve for A and B.
- The rates for then found for T = 15, 20, and 25 degrees C.
- The chemostat was then simulated for T = 15, 20, and 25 degrees C conditions. The time courses of the biomass and nutrients were graphed.
Investigating the Efficiency 'Constant'
- The y and E values were taken from the "taiParamsRevised" MATLAB file for all four cases.
- Using the point-slope and slope-intercept formulas, an equation for each temperature E(y) was created to relate the two points, (y,E).
- The "chemostat_2nutrient_dynamics.m" file was modified to use the two developed equations.
- Results were compared to the previous ones.
Variables found in "taiParamsRevised" file:
12 degree C Glucose-Limited:
30 degree C Glucose-Limited:
12 degree C Ammonium-Limited:
30 degree C Ammonium-Limited:
Variables calculated using Arrhenius equation:
A = 4.979 * 10^11
B = 69,840.58946
r(15 degrees C) = 0.1087
r(20 degrees C) = 0.1787
r(25 degrees C) = 0.289
Equations developed using point-slope and slope-intercept formulas:
12 degree C: E = 0.3637y + 14.1022
30 degree C: E = 0.7012y + 14.2483
Presentation: File:Biomathmatical Modeling Final Presentation .pdf
I worked with my homework partner, Ava on this assignment. We texted throughout the week and met on Monday 5/7 and Wednesday 5/8 to discuss the assignment and make and practice our presentation.
Dr. Fitzpatrick also helped in class on 5/2 and in office hours on 5/8 with MATLAB and how to input our new variables and functions.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Loyola Marymount University (6 May 2019) BIOL388/S19:Week 14/15. Retrieved from https://openwetware.org/wiki/BIOL388/S19:Week_14/15 on 6 May 2019.
Tai, S. L., Daran-Lapujade, P., Walsh, M. C., Pronk, J. T., & Daran, J. M. (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
User Page: Angela Abarquez