- Course syllabus.
- Notes on thermodynamics, from J.C.
Slater,
*Introduction to Chemical Physics*, chapters 1-3. - Entropy and the Boltzmann distribution.
**Homework #1**, due in class, Feb. 4: Problems 1.15, 5.1, 5.6 and 6.2.- Build-up procedure for partition
functions, by Herschbach, Johnston and Rapp.
**Homework #2**, due in class, Feb. 11: Problems 10.7, 10.18, 11.6 and 11.16.- Getting free energies from
simulation.
- Proton binding to proteins: pKa calculations
with explicit and implicit solvent models, by Simonson, Carlsson and
Case.
- Notes on molecular dynamics and force fields.
**Homework #3**, due in class on February 25.- Notes on electrostatics and
continuum solvent models.
**Homework #4**, due in class, Mar. 4: Problems 20.7, 20.11, 22.6, and 22.13.- Review on Generalized Born
models.
**Homework #5**, due in class, Mar. 25: Problems 22.2, 23.1, 23.2.- Instructions for the final
project.
*(Updated with the presentation schedule.)* - Slides from guest lecture by Mikolai
Fajer.
**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.- Lecture notes on
kinetics.
- Notes on ligand binding and
allostery.
**Homework #7**, due in class, April 22: Problems 23.13, 23.16, 19.9 and 19.12.- Notes on distance geometry.
- Notes on fitting models to data.
- Notes on Singular Value Decomposition.

- Course syllabus.
- Notes on thermodynamics, from J.C.
Slater,
*Introduction to Chemical Physics*, chapters 1-3. - Entropy and the Boltzmann distribution.
**Homework #1**, due in class, Feb. 1: Problems 1.15, 4.5, 5.6 and 6.2.- Build-up procedure for partition
functions, by Herschbach, Johnston and Rapp.
**Homework #2**, due in class, Feb. 8: Problems 10.7, 10.18, 11.6, 11.11 and 11.16.**Homework #3**, due in class, Feb. 20: Problems 8.18, 10.16, 12.3, 13.2, and 13.8.- Getting free energies from
simulation (revised, 24 Feb.)..
- Proton binding to proteins: pKa calculations
with explicit and implicit solvent models, by Simonson, Carlsson and
Case.
**Homework #4/#5**, due in class on March 1 and March 8.- Dynamics of ligand escape from the heme
pocket of myoglobin, by Kottalam and Case.
- Notes on molecular dynamics and force fields..
- Notes on electrostatics and
continuum solvent models.
**Homework #6**, due in class, Mar. 29: Problems 20.11, 22.6, 22.13, 23.2 and 23.13.**Homework #7**, due in class on April 5.- Notes on ligand binding and
allostery (revised on 5 April).
**Homework #8**, due in class, Apr. 12: Problems 26.12, 28.2, 28.3 and 29.1.- Notes on ligand binding kinetics to
myoglobin.
- Classical derivation of transition state
theory.
- Fitting models to data.
- Instructions for the final
project.

- Course syllabus.
**Homework #1**, due in class on Feb. 2: Problems 10.3, 10.13, 10.16 and 10.26.**Homework #2**, due in class on Feb. 9: Problems 11.8, 11.9 and 11.11.**Homework #3**, due in class on Feb. 16: Problems 11.13, 11.16 and 11.19.- Study guide for the first exam, which
is Friday, Feb. 19, in class. Here is the key for the exam.
- Simple guide to force fields.
- Notes on MD and free energies.
- Notes on molecular orbital theory.
**Homework #4**, due in class on Mar. 8: Problems 12.1, 12.5, 12.9, and 12.12.**Homework #5**, due in class on Mar. 22: Problems 13.1, 13.5, 13.6, and 13.8. (For problem 13.1, see the hint at the back of the book, and Eq. 9.74)**Homework #6**, due in class on Mar. 29: Problems 13.11, 13.12, 13.19, and 13.21.- Notes on normal modes..
- Study guide for the second exam, which
is Friday, Apr. 1, in class.
Here is the key for the exam.
**Homework #7**, due in class on Apr. 19: Problems 14.2, 14.5, 14.11c, 14.16.**Homework #8**, due in class on Apr. 26: Problems 15.3, 15.7, 15.12, 15.16a-e.- X-ray refinement strategies..
- Figures for cryoEM single particle
reconstruction.
- Study guide for the final exam, which
will be May 11, 8-11am. Please note that there will be no office hours on
Friday, May 6.

- Course syllabus.
**Homework #1:**(due in class, Sep. 15): Chapter 2, problems 4,8,11,12.**Homework #2:**(due in class, Sep. 24): Chapter 2, problems 21,32; Chapter 3, problems 13,19.- Exam1 study guide. (Note: the first
mid-term will be Mon., Sept. 29, in class). Key for Exam 1.
**Homework #3:**(due in class, Oct. 13): Chapter 4, problems 3, 4, 13, 16.- Notes on the Boltzmann distribution
- Notes on ligand binding and allostery
**Homework #4:**(due in class, Oct. 27): Chapter 5, problems 4, 11, 12, 20.- Notes on lipids and their assemblies
**Homework #5:**(due in class, Nov. 3): Chapter 6, problems 4, 9, 11, 23.- Exam2 study guide.
Key for Exam 2.
- Notes on electrochemistry
**Homework #6:**(due in class, Nov. 24): Chapter 7, problems 3, 5, 11, 23.- Notes on biomolecular
hydrodynamics
**Homework #7:**(due in class, Dec. 8): Chapter 8, problems 10, 18; Chapter 9, problems 16, 20.- Notes on electron transfer rates
- Final exam study guide.

- Course syllabus.
- Lecture 1: Isolation of proteins and DNA
- Lecture 2: Chromatography
- Lecture 3: Biomolecular hydrodynamics
- Lecture 4: Thermodynamics and calorimetry
- Lecture 5: Spectroscopy
- Lecture 6: Circular dichroism
- Lecture 7: Crystallography, Part I
- Lecture 8: Scattering by X-rays
- Lecture 9: X-ray data collection
- Lecture 10: Phases in crystallography
- Lecture 11: Electron densities
- Lecture 12: Introduction to SAXS
- Lecture 13: SAXS applications
- Sample questions for the midterm
- Lectures 14-19 Molecular dynamics simulations
- Instructions for the term paper
- Lectures 20-21: Introduction to NMR
- Lecture 22: NMR short course, part I.
- Lecture 23: NMR short course, part II.
- Lecture 23: NMR short course, part III.
- Lecture 24: Biological mass spectrometry
- Lecture 25: Biological mass
spectrometry, part II

- Course syllabus.
- Lecture 1: Principles of protein structure
- Lecture 2: Exploring nucleic acid structures"; PyMol file for helical forms of DNA
- Lecture 3: Membrane proteins
- Lecture 4: Post-translational modifcations
- Lecture 5: Read pp. 151-165 in the text plus additional lecture notes on the Boltzmann distribution
- Lectures 6,7: Read pp. 173-190 plus additional lecture notes on binding
polynomials.

**Homework #1**(due in class on Monday, Sep. 30): Problems 5.11, 5.14, 5.20. - Lectures 8,9: Read pp. 305-345 plus additional lecture notes on Marcus theory.

**Homework #2**(due in class on Monday, Oct. 7): Problems 9.6, 9.13, 9.16, 9.20. - Lectures 10,11: Read Chapter 10.

**Homework #3**(due in class on Monday, Oct. 14): Problems 9.10, 9.29, 10.1, 10.6 **First midterm exam**is Wednesday, Oct. 16. Here is a Study Guide.- Lecture 12: X-ray lecture notes, part I
- Lecture 13: X-ray lecture notes, part II
**Homework #4**(due in class on Monday, Oct. 28): Symmetry homework- Lecture 14: X-ray lecture notes, part III
- Lectures 15,16: read Chapter 11.

**Homework #5**(due in class on Monday, Nov. 4): Problems 11.2, 11.8, 11.9, 11.15. - Lectures 17,18: read Chapter 12.

**Homework #6**(due in class on Monday, Nov. 11): Problems 12.1, 12.8a, 12.9a, 12.12. **Second midterm exam**is Wednesday, Nov. 13. Here is a Study Guide. And here are some partial answers.- Lecture 19: Slides for absorbance.
- Lecture 20: Slides for fluorescence.
- Lecture 21: Slides for circular dichroism.
- Lecture 22: Small-angle X-ray scattering.
- Lecture 23: NMR, Part I.
- Lecture 24: NMR, Part II.
- Lecture 25: NMR, Part III;
NMR Problem set;

- Course syllabus.
**Week 1 reading:**Prolog, Fundamentals, and Chap. 1.**Week 2 reading:**Chap. 2.**Homework assignment #1**(due in class, Wed. Feb. 6): Exercises 1.18, 1.26, 1.35 (a,b only), 1.46.- Notes on the Boltzmann distribution.
**Week 3 reading:**Chap. 3.**Homework assignment #2**(due in class, Wed. Feb. 13): Exercises 2.3, 2.14, 2.16 and 2.23.**Week 4 reading:**Chap. 4.**Homework assignment #3**(due in class, Wed. Feb. 20): Exercises 3.21 (a,b), 3.25, 3.27, 3.34.**Homework assignment #4**(due in class, Fri. Mar. 1): Exercises 4.10, 4.15, 4.19, 4.38.- Study guide for exam 1. (Exam is on Wednesday, Mar. 13.) (You might want to look at last year's exam and exam key.) This year's exam key.
- Notes on ligand binding and allostery..
**Reading:**Chaps. 5,6,7.**Homework assignment #5**(due in class, Fri. Mar. 29): Exercises 5.22, 5.23, 5.31, 5.41.**Reading:**Chap. 8.**Homework assignment #6**(due in class, Fri. Apr. 5): Exercises 6.13, 6.16, 6.36, 7.21.- Study guide for exam 2. (Exam is on Wednesday, Apr. 17.) (You might want to also look at last year's exam and exam key; note that Chap. 8 was not covered in last year's second exam.) This year's exam key.
**Reading:**Chap. 9.**Homework assignment #7**(due in class, Fri. Apr. 12): Exercises 7.20, 8.12, 8.16, 8.26.**Reading:**Chap. 10, pp. 364-382, 387-391.**Homework assignment #8**(due in class, Fri. Apr. 26): Exercises 9.22, 9.23, 9.30, 9.33**Reading:**Chap. 11, pp. 425-438, 443-444, 451-455; Chap. 12, pp. 463-481, 490-493.**Final exam**will be Friday, May 10, 8am to 11am. Here are a study guide, and last year's exam. I will be out of town on May 7 and 8, but will be available to answer questions on May 6 (morning) and May 9.

- Course syllabus.
**Homework assignment #1,**(due in class, Tuesday, Jan 31): Problems 1.12, 1.15, 1.26, 1.35 (a and b only), 1.46 and 1.47 (parts a,b,c,d only). Be sure to show your work.- Notes on the Boltzmann distribution.
**Homework assignment #2,**(due in class, Tuesday, Feb 7): Problems 2.3, 2.14, 2.16 and 2.21. As always, be sure to show your work.**Homework assignment #3,**(due in class, Tuesday, Feb 14): Problems 3.14, 3.20, 3.25 and 3.34.**Homework assignment #4,**(due in class, Tuesday, Feb 21): Problems 4.8, 4.15, 4.20, 4.37(a).- Study guide for exam 1. (Exam is on Friday, Feb. 24.) Exam key.
- Stat. mech. approach to ligand binding.
**Homework assignment #5,**(due in class, Tuesday, Mar 6): Problems 5.8, 5.21, 5.22, 5.24(a).**Homework assignment #6,**(due in class, Tuesday, Mar 20): Problems 6.13, 6.16, 6.27, 6.36.- Study guide for exam 2. (Exam is on Tuesday, Mar. 27.) Exam key.
**Homework assignment #7,**(due in class, Tuesday, Apr 10): Problems 9.22, 9.23, 9.32(a), 9.33.**Homework assignment #8,**(due in class, Tuesday, Apr 24): Problems 11.32, 11.34, 11.35, 11.40.**Final exam**will be Wednesday, May 9, 8am to 11am. Here is a study guide. I will be out of town from April 30 to May 3, but will be available to answer questions on May 4,6,7.

- Lac repressor structure, from Feb. 7,9, 2012
- Notes on the Boltzmann distribution.
- Notes on thermodynamics, from J.C.
Slater,
*Introduction to Chemical Physics*, chapters 1-3. - Intro. to molecular modeling of DNA.

- Course syllabus.
**Homework assignment #1:**Download and install the VMD visualization program, and work through the Using VMD tutorial. There is nothing to hand in, but you will need to be able to use the program later in the course.- Basics of protein structure.
**Homework assignment #2:**(due Sept. 21) is here.- Thermodyanmics; protein-protein
interactions.

Notes on statistical mechanics, from J.C. Slater,*Introduction to Chemical Physics*, chapter 3. **Homework assignment #3:**(due Sept. 30) is here.- Protein phosphorylation.
- Protein folding (from Babis Kalodimos).
- Basics of nucleic acid structure (Updated 10/14).
**Homework assignment #4:**(due Oct. 21) is here. Also available: the paper you need for question 5.- Protein-DNA interactions (from Babis Kalodimos).
**Homework assignment #5:**(due Nov. 9) is here.- Lipids and membrane proteins.
- Enzymes and mechanisms. Also: reading material on blood substitutes.
**Instructions for the final presentation and report**are here.**Homework assignment #6:**(due Nov. 23) is here.- The immune system.
- Virus structures.

- Course syllabus.
- Introduction, 1/19/10 (DAC).
- Notes on thermodynamics, from J.C.
Slater,
*Introduction to Chemical Physics*, chapters 1-3. - Thermodynamics and calorimetry, 1/26/10 (BK).
- Hydrodynamics and centrifugation, 2/2/10 (DAC).
- Rotational motion, flucutations and fluorescence, 2/9/10 (DAC).
- Crystallography and cryo-EM spectroscopy, 2/16/10 (DAC).
- Biomolecular vibrational spectroscopy, 2/16/10 (DAC).
- Molecular modeling and theory,
2/23/10, 3/2/10 (DAC).

- Course syllabus.
- Week 1, Introduction (Olson).
(Homework assignment is on the final page.)

Spreadsheet for PDB analysis.

CA-only PDB file. - Lecture notes for weeks 2 and 3 (Case).
[Updated on 9/17].

**Homework:**Download and install the VMD visualization program, and work through the Using VMD tutorial. There is nothing to hand in, but you will need to be able to use the program later in the course. - Protein-protein interactions, (Olson, 9/22).
- Phosphorylation, (Dr. Joachim Latzer, 9/24).
- DNA structure, (Olson, 9/29, 10/1). Homework assignment is on the last page.
- Protein/DNA interactions, (Olson, 10/6, 10/8).
- DNA condensation and packaging, (Olson, 10/13, 10/15).
- RNA and the ribosome, (Olson, 10/20, 10/22).

Structural data for tRNA. - Lipids and membranes, (Case, 10/27, 10/29).
- Membrane proteins, (Case, 11/10, 11/12).
- Enzymes, (Case, 11/17, 11/19).
- The immune system, (Case, 11/24, 12/1).
- Virus structures, (Case, 12/3).
- Final student presentations, 12/5, 12/8,
12/10.

- Introduction to Biophysics Methods, from Jan. 20, 2009. Lecture by Babis Kalodimos.
- Thermodynamics, from Jan. 27, 2009. Lecture by Babis Kalodimos.
- Hydrodynamics, from Feb. 3, 2009.
- Rotational motion and fluorescence, from Feb. 10, 2009.
- Biomolecular NMR, from Feb. 24, Mar. 3, 10, 24, 2009. Lectures by Babis Kalodimos.
- Biomolecular NMR, from Mar. 24, 31, 2009. Lectures by Dave Case.
- Protein vibrational spectroscopy, from Mar. 31, 2009.
- Molecular dynamics simulations, from Apr. 7,14, 2009.
- Dynamics from NMR, from Apr. 21, 2009. Lecture by Babis Kalodimos.
- Cryo-electron microscopy, from
Apr. 28, 2009.

- Lac repressor structure, from Jan. 27,29, 2009.
- Intro. to modeling of DNA, from Feb. 10,12, 2009.
- Notes on distance geometry, from
Mar. 26, 2009.