Lecture Notes

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Thermodynamics and Statistical Thermodynamics (CCB 425/525), Spring, 2017

  1. Course syllabus.

  2. Notes on thermodynamics, from J.C. Slater, Introduction to Chemical Physics, chapters 1-3.

  3. Entropy and the Boltzmann distribution.

  4. Homework #1, due in class, Feb. 1: Problems 1.15, 4.5, 5.6 and 6.2.

  5. Build-up procedure for partition functions, by Herschbach, Johnston and Rapp.

  6. Homework #2, due in class, Feb. 8: Problems 10.7, 10.18, 11.6, 11.11 and 11.16.

  7. Homework #3, due in class, Feb. 20: Problems 8.18, 10.16, 12.3, 13.2, and 13.8.

  8. Getting free energies from simulation (revised, 24 Feb.)..

  9. Proton binding to proteins: pKa calculations with explicit and implicit solvent models, by Simonson, Carlsson and Case.

  10. Homework #4/#5, due in class on March 1 and March 8.

  11. Dynamics of ligand escape from the heme pocket of myoglobin, by Kottalam and Case.

  12. Notes on molecular dynamics and force fields..

  13. Notes on electrostatics and continuum solvent models.

  14. Homework #6, due in class, Mar. 29: Problems 20.11, 22.6, 22.13, 23.2 and 23.13.

  15. Homework #7, due in class on April 5.

  16. Notes on ligand binding and allostery (revised on 5 April).

  17. Homework #8, due in class, Apr. 12: Problems 26.12, 28.2, 28.3 and 29.1.

  18. Notes on ligand binding kinetics to myoglobin.

  19. Classical derivation of transition state theory.

  20. Fitting models to data.

  21. Instructions for the final project.



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Updated on October 25, 2017. Comments to case@biomaps.rutgers.edu