Computational Chemistry and Biophysics

CHEM 6670: Special Topics in Physical Chemistry: Computational Chemistry & Biophysics

Syllabus
Location and time: PHSC 356 (TU/TH 12:00-1:15 pm)

Date	Topics	Reading	Lecture notes
week 1 Jan 20, 22	Review of HF, Density functional and CI methods, MP, and CC methods	Jensen Chap. 4	Notes 1, Notes 2
week 2 Jan 29	Paper discussion: intermolecular potential, surface scattering	Paper 1, 2
week 3 Feb 3, 5	Semi-empirical methods, calculation of electronic properties; paper discussion: limitations of DFT	Paper 3	Notes 3
week 4 Feb 10, 12, makeup class	Paper discussion: modeling material properties; quantum dynamics; Introduction to statistical mechanics; Tutorial for simulations	Paper 4, 5	Notes 4
week 5 Feb 17, 19	Statistical ensemble, simple thermodynamic averages: temperature and pressure	Allen&Tildesley Chapt 1, 2	Notes 5,Notes 6 Homework 1
week 6 Feb 24, 26	Fluctuations; Monte-Carlo method	Allen&Tildesley Chapt. 2, 4	Notes 7,Notes 8 Homework 2
week 7 Mar 5	Markov chain	Allen&Tildesley Chapt. 4	Notes 9
week 8 Mar 10, 12	Metropolis MC method; free energy methods	Allen&Tildesley Chapt. 4 Kollman, Chem Rev, 1993	Notes 10,Notes 11 Homework 3
week 9 Mar 24, 26	Free energy methods, replica-exchange method	Roux, Comput Phys Commun 1995; Sugita and Okamoto, Chem Phys Lett, 1999; Nymeyer et al, Methods Enzymol, 2004	Notes 12
week 10 Mar 31, April 2	Molecular dynamics; l dynamics, CPHMD method; Implicit solvent models	Allen&Tildesley Chapt. 3, 7; MacKerell, J Comput Chem 2004; Kong and Brooks, J Chem Phys 1995; Khandogin and Brooks, Biophys J 2005; Lee, Salsbury and Brooks, J Chem Phys 2002;	Notes 13,Notes 14
week 11 April 7, 9	GB solvent model;normal mode analysis	Lee, Feig, Salsbury and Brooks, J Comput Chem 2003; Tama et al, Protein Eng 2000
week 12 April 14, 16	Free energy from non-equilibrium processes; CHARMM tutorial	Hummer and Szabo, PNAS 2001; Liphardt et al, Science 2002
week 13 April 21, 23	Constant temperature and pressure molecular dynamics	Allen&Tildesley Chapt. 7	Notes 15
week 14 April 28,30	Projects
week 15 May 5, 7	Projects
week 16 May 12, 14	Presentations

Grading scheme

Paper discussions (20 pts each):
- presenter/discussion leader: main points of the paper (10 pts); current status of the field (5 pts); main challenges (5 pts)
- participants: ask questions (10 pts max); contribute to understanding of the paper (5-10 pts extra)
- blogger (rotation basis): write up a summary of discussions and publish (10-25 pts)

Hands-on practice and home work (20 pts each task)

Projects (100 pts each)