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Instructor: Qi Zhang; 919-966-5710,

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).


  • 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)