Physical Chemistry Python Practice

Author: AJ Book
Date: 02/02/2025
Notebook Name: Physical_Chemistry_Notebook.ipynb

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Objective

Demonstrate Physical Chemistry concepts by implementing Python code for all the problems from the provided list using the given datasets.

Table of Contents

1. Distance Formula

   • Compute Euclidean distances between points in 3D space.

2. Root Mean Square Deviation (RMSD)

   • Calculate RMSD between two sets of points in 3D space.

3. Ramachandran Plot Calculation

   • Analyze and visualize phi (ϕ) and psi (ψ) angles for a peptide chain.

4. Lennard-Jones Potential Calculation

   • Compute and plot the potential energy as a function of interatomic distance.

5. Michaelis-Menten Equation (Enzyme Kinetics)

   • Model enzymatic reaction rates as a function of substrate concentration.

6. Boltzmann Distribution

   • Compute and plot the Boltzmann factor for energy levels at a given temperature.

7. Force Field Energy Equation

   • Compute the total energy of a molecular system using bond and angle terms.

8. Poisson-Boltzmann Equation

   • Solve the 1D Poisson-Boltzmann equation numerically using finite differences.

9. Binding Free Energy Calculation (ΔG)

   • Calculate binding free energies using thermodynamic principles.

10. References

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