BIOC 651 Macromolecular Interactions and Forces
Instructor: Qi Zhang; 919-966-5710, qi_zhang@med.unc.edu
Meeting Dates/Times and Locations: Late September – Early November; MWF 11:00 AM; 3007 GMB. Registration limited to 12 except with permission Course Director. (Recitation TBD).
Readings
- Hermans & Lentz, “Equilibria & Kinetics of Biological Macromolecules”.
Chapter 3: Molecular Structure and Interactions
Chapter 7: Sampling Molecular Systems with Simulations
Chapter 14: Charged Groups: Binding of Hydrogen Ions, Solvation, and Charge-Charge Interactions - Dill & Bromberg, “Molecular Driving Forces”
- Eisenberg & Crothers “Physical Chemistry with Applications to the Life Sciences” 1979,
Energy Landscape of Macromolecules
- Overview of macromolecular interaction (Forces in protein and nucleic acid)
- Free energy: microstate and macrostate
- Radial distribution function (RDF)
- Potential of mean force (PMF)
Electrostatic and Hydrophobic Interactions
- Elements of electrostatics
- Poisson-Boltzmann equation
- Debye-Huckel equation
- Electrostatic potential of polyelectrolytes
- Water and special properties
- Hydrophobic interactions
Computer Simulation of Macromolecules
- Overview of computer simulations
- Molecular mechanics force field and calculation of free energy
- Molecular Dynamics and Monte Carlo techniques
- Solvent and computation (Guest lecture by Patrick McCarter)
- Solvent based DFT (Guest lecture by Patrick McCarter)