Ron Levy group

Exploring
molecular
landscapes

Statistical Thermodynamics

Chemistry 5302

Fall 2015

Time and Location:

  • Tues/Thurs, 5:30PM, SERC 702

Contacts:

Syllabus:

  • pdf
  • MQ = Donald McQuarrie, "Statistical Mechanics" (Harper Collins 1976)
  • KD = Ken Dill and Sarina Bromberg, "Molecular Driving Forces" (Garland Science 2nd ed, 2011)

I. Equilibrium

Date Topic Lecture Slides
1. 8/25 Thermodynamics review - MQ Chapter 1 pdf ppt
2. 8/27, 9/1 Canonical ensemble - MQ Chapter 2 pdf ppt
Problem Set 1 pdf
Problem Set 1 Solutions pdf
3. 9/3, 9/8 Fluctuations and other ensembles - MQ Chapter 3 pdf ppt
Problem Set 2 pdf
Problem Set 2 Solutions pdf
4. 9/10 Classical statistical mechanics - MQ Chapter 7 pdf ppt
Problem Set 3 pdf
Problem Set 3 Solutions pdf
5. 9/10, 9/15 Ideal Gas - MQ Chapter 5 pdf ppt
6. 9/15, 9/17 Imperfect gases - MQ Chapter 12 pdf ppt
7. 9/22 Chemical Equilibria - MQ Chapter 9, KD Chapter 13 pdf ppt
8. 9/29, 10/1 Binding Equilibria - Notes pdf ppt
9. 10/6, 10/8 Liquids - MQ Chapter 13 pdf ppt
10. 10/13 Ionic Solutions and Debye-Huckel Theory - MQ Chapter 15 pdf ppt


II. Computational Methods

Date Topic Lecture Slides
11. 10/15 Intermolecular interactions, potential energy functions - Notes pdf ppt
12. 10/20 Solvation Models - Notes pdf ppt
13. 10/22 Simulation Methods (MD, MC) - Notes pdf ppt
14. 10/27 Advanced conformational sampling - Notes pdf ppt


III. Computer Labs with Lectures

Date Topic Lecture Slides
15. 10/29 Introduction to Maestro and Impact pdf
16. 10/29,11/3,11/5 Lab 1 - Water pdf
17. 11/10 Kinetics, transition state theory, and Markov State Models pdf ppt
18. 11/12,11/17,11/19 Lab 2 - Protein Folding pdf
19. 11/19 Free Energy calculations - Notes pdf ppt mpeg
20. 12/1 Free Energy calculations (cont.) - Notes pdf ppt
21. 12/1,12/3 Lab 3 - Binding pdf data