Lecture Notes

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Statistical Thermodynamics and Kinetics (CCB 425/525), Spring, 2019

  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. 4: Problems 1.15, 5.1, 5.6 and 6.2.

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

  6. Homework #2, due in class, Feb. 11: Problems 10.7, 10.18, 11.6 and 11.16.

  7. Getting free energies from simulation.

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

  9. Notes on molecular dynamics and force fields.

  10. Homework #3, due in class on February 25.

  11. Notes on electrostatics and continuum solvent models.

  12. Homework #4, due in class, Mar. 4: Problems 20.7, 20.11, 22.6, and 22.13.

  13. Review on Generalized Born models.

  14. Homework #5, due in class, Mar. 25: Problems 22.2, 23.1, 23.2.

  15. Instructions for the final project. (Updated with the presentation schedule.)

  16. Slides from guest lecture by Mikolai Fajer.

  17. Homework #6, due by Monday, April 7: choose a paper for your term project, as described in the Instructions above. Send an email to david.case@rutgers.edu with your choice.

  18. Lecture notes on kinetics.

  19. Notes on ligand binding and allostery.

  20. Homework #7, due in class, April 22: Problems 23.13, 23.16, 19.9 and 19.12.

  21. Notes on distance geometry.

  22. Notes on fitting models to data.

  23. Notes on Singular Value Decomposition.



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Updated on July 5, 2019. Comments to case@biomaps.rutgers.edu