biochem-jupyter-notebooks

interactive notebooks for teaching biochemistry concepts

Free energy as a bet

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

Differential scanning calorimetry

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

Michaelis Menten Kinetics

Notebook Graphical exploration of Michaelis-Menten kinetics.

Stoichiometric binding curves

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

Nonlinear regression to extract equilibrium constants

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

Chemical kinetics simulations

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