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Biology / Computation / Data analysis / Math Modeling / Teaching

Introduction to modeling: parameter estimation in R

This code introduces how to perform parameter estimation for a system of differential equations in R. First, the necessary packages and data are imported using code previously introduced in a previous post. R code available here.  Due to computational constraints, the mathematical model we are using to fit to the data includes product inhibition. If product inhibition doesn’t … Continue reading

Introduction to modeling and coding in R
Computation / Math Modeling / Teaching

Introduction to modeling and coding in R

After introducing students to a simple mathematical model describing enzyme kinetics, I introduced them to coding and modeling in R. Coding is traditionally done by first describing some coding ‘rules’, including ending the line with semicolons or how to define a variable. Personally I found these methods ineffective and frustrating. I took a few classes … Continue reading

Modeling demo: photosynthesis
Biology / Computation / Math Modeling / Teaching

Modeling demo: photosynthesis

This demo is intended to help students understand the connection between photosynthetic pigment function, light energy, and plant growth. The relative absorption of 8 wavelength ranges can be modified to represent an absorption spectra. These absorption spectra could be simplified to include one or two specific colors, or approximate an absorption spectra obtained in lab. … Continue reading

Modeling demo: enzyme kinetics
Biology / Math Modeling / Teaching

Modeling demo: enzyme kinetics

When using this demo, students can alter the reaction rate, substrate, or enzyme concentrations. The simulation motivates understanding what a basic mechanistic model of enzyme kinetics would consist of. After running a simulation, the predicted dynamics of the product and substrate are plotted. The model behind the simulation is: First I ask them a series of … Continue reading