Describe using no more than 200 words what is a protein and

Question

1. Describe using no more than 200 words what is a protein and how could we model and simulate it using classical mechanics and computer programs.

2. Write down the formula of the Hamiltonian used in a typical classical atomistic molecular dynamics simulation. Describe the potential energy terms using only one simple sentence for each term.

3. Plot on a single graph the Lennard-Jones potential using the parameters σ=3, and ε₁=2, ε₂=3 and ε₃=4. State in one short sentence what is the interpretation of the parameter ε. Please remember to label your axes properly.

4. Plot on a single graph the Lennard-Jones potential using the parameters ε=3, σ₁=2, σ₂=3 and σ₃=4. State in one short sentence what is the interpretation of the parameter σ. Please remember to label your axes properly.