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biochem-jupyter-notebooks

interactive notebooks for teaching biochemistry concepts

Free energy as a bet

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

Differential scanning calorimetry

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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

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Notebook Graphical exploration of Michaelis-Menten kinetics.

Stoichiometric binding curves

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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

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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

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

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interactive notebooks for teaching biochemistry concepts

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