interactive notebooks for teaching biochemistry concepts

Notebook Explores free energy, enthalpy, and entropy in the context of dice rolling

Notebook Explores differential scanning calorimetry data to learn about protein folding. Covers $\Delta G$, $\Delta H$, $\Delta S$, $\Delta C_p$, and $T_m$.

Notebook Graphical exploration of Michaelis-Menten kinetics.

Notebook Graphical exploration of the difference between a binding curve that gives access to $K_{D}$ versus binding stoichiometry.

Notebook Fit binding models to experimental data to extract $K_{D}$. Covers basics of of regression, residuals, and bootstrapping to estimate parameter uncertainty.

Notebook Run simulations of complicated reaction schemes using deterministic Markov matrices and stochastic Gillespie simulations. Uses actin filament formation as a model reaction.