1. Quick review of thermodynamic definition of temperature
2. Introduction of the Boltzmann distribution and the partition function
3. Thermodynamic derivation of the Boltzmann distribution
4. Using Lagrange multipliers to maximize Entropy
5. Boltzmann distribution through Entropy maximization
6. Determination of β from the ideal gas
7. Application to ligand binding equilibrium
8. Practical: Ligand binding and dimerization in BioNetGen
1. Free energy of a dilute solution.
2. Law of mass action.
3. ATP hydrolysis in a cell.
4. Simple binding.
5. The Hill function.
6. Practical: Ligand-receptor binding in BioNetGen
PBOC2, chapter 6.3-6.5
1. Assessing cooperativity using the Hill number.
2. Generalized law of mass action - the Gibbs distribution.
3. Simple ligand-receptor binding revisited (again).
4. Two-site binding model with equivalent sites.
5. Application to ligand-induced dimerization.
6. Competitive binding (not in notes).
PBOC2, chapter 7.