- Course syllabus.
- Lecture 1: The Schrodinger equation.
See also the
slides in PDF format.
- Lecture 2: Quantum operator algebra.
See also the
slides in PDF format.
- Homework #1: Problems 1-23, 2-16, 2-31, 2-34 and 3-11 in EQC.
Due in class on Thurs., Feb. 3.
- Lecture 3: Some simple systems.
See also the
slides in PDF format.
- Homework #2. Assignment is here.
Due in class on Thurs., Feb. 10.
- Homework #3. Assignment is here.
Due in class on Thurs., Feb. 17.
- Homework #4. Assignment is here.
Due in class on Thurs., Feb. 23.
- Term paper/project instructions Due on May 5; instructions are here.
- Homework #5. Assignment is here.
Due in class on Thurs., March 31.
- Lecture notes on
matrices. Discussed in class on March 24.
- Homework #6. Assignment is here.
Due in class on Thurs., April 7.
- Course syllabus.
- Getting an Amarel account: If you don't already have one,
request a user account on Amarel by visiting https://oarc.rutgers.edu/access.
Use a terminal application (the Terminal app in MaxOSX or something like putty on Windows) to carry out a trial
login.
- Lecture 1: The high performance computing environment.
See also the
slides in PDF format.
- Homework #1 Go through the following self-guided tutorials:
- Lecture 2: The AWK programming language.
See also the
slides in PDF format. (Scroll
down to see the AWK material.)
- Lecture 3: Relational databases.
See also the
slides in PDF format.
- Here is the documentation for RDB;
concentrate on the operators highlighted in yellow.
- Here is the XrayPrep script
discussed in class on Jan. 31.
- Homework #2, due Feb. 9 Assignment is here.
- Homework #3, due Feb. 16 Assignment is here.
- Homework #4, now due Feb. 28 Assignment is here.
- Homework #5, due Mar. 11 Assignment is here.
- Homework #6, due Mar. 25 Assignment is here.
- Term paper/project instructions Due on May 5; instructions are here.
- Getting ready for class on March 24: Dr. Martin Calvino will be
a guest lecturer on March 24, giving an introduction to data analysis
using R. We are going to experiment with having students try analyses
during class. If can bring a laptop to class that day, please download
the material described here. If you
cannot bring a computer to the class, come anyway and take some notes.
- Homework #7, due April 8 Assignment is here.
- The R code for March 24 presentation is available
here.
- Homework #8, due April 22 Assignment is here.
- Generalized Born theory reprint is here.
- The MM-PBSA approach to free energies reprint is here.
- Course syllabus.
- Notes on thermodynamics, from J.C.
Slater, Introduction to Chemical Physics, chapters 1-3.
- Lecture 1: Classical thermodynamics.
See also the
slides in PDF format.
[Note: if you get spinning colored lines,
click on pause, then again on play. You will probably need to hit the
"unmute" button,
and may wish to expand to full screen using the arrows
at the lower right, next to the Rutgers logo.]
- Lecture 2: The Boltzmann distribution.
See also the
slides in PDF format.
- Lecture 3: Molecular partition functions.
See also the slides from Lecture 2 plus
new slides in PDF format.
- Homework #1: Problems 1.15, 5.1, 5.6 and 8.8 in MDF. Please email me
your answers by Wed., Feb. 3.
- Build-up procedure for partition
functions, by Herschbach, Johnston and Rapp.
- Lecture 4: Free energies from simulations.
See also the
slides in PDF format.
- Lecture 5: Free energies from simulations (continued).
See also the
slides in PDF format.
- Homework #2: Problems 10.7, 10.18, 11.6 and 11.16. Please email
me your answers by Wed., Feb 10.
- Proton binding to proteins: pKa calculations
with explicit and implicit solvent models, by Simonson, Carlsson and
Case.
- Lecture 6: Free energies from simulations (continued).
See also the
slides in PDF format.
- Lecture 7: Force fields, minimization and dynamics.
See also the slides in PDF format.
- Homework #3 is here.
Please email me your answers by Mon., Feb. 22; (more time since this is
a longer problem set than the first two.)
- Lecture 8: Force fields.
See also the slides in PDF format.
- Lecture 9: Continuum solvent models.
See also the slides in PDF format.
- Lecture 10: Continuum solvent models, continued.
See also the slides in PDF format.
- Lecture 11: Electrostatics and salt water.
See also the slides in PDF format.
- Homework #4 is here.
Please email me your answers by Mon., Mar 8.
- Lecture 12: Born theory.
See also the slides in PDF format.
- Lecture 13: Ligand binding and allostery.
See also the slides in PDF format.
- Lecture 14: Linkage relations.
See also the slides in PDF format.
- Lecture 15: Master equations.
See also the slides in PDF format.
- Lecture 16: More master equations.
See also the slides in PDF format.
- Instructions for the final project are
here,
including the presentation schedule.
- Homework #5 is here.
Please email me your answers by Wed., Mar 31.
- Lecture 17: Transition-state theory.
See also the slides in PDF format.
- Lecture 18: Normal modes.
See also the slides in PDF format.
- Hints for Exam 1 are here.
- Lecture 19: Vibrational energy transfer.
See also the slides in PDF format.
- Homework #6: Choose a paper for your class project. (See the
instructions above.)
Please email me your choices by Fri., April 9 (deadline has been
extended).
- Lecture 20: Forced harmonic oscillator.
See also the slides in PDF format.
- Lecture 21: Integral equations models for liquids.
See also the slides in PDF format.
- Lecture 22: Integral equations models for liquids, part 2.
See also the slides in PDF format.
- Jun Wang: Are you getting course emails? Please check your spam/junk
folders. Send me email (I get yours), or send a text, with possible
alternative ways of communicating. Thanks...dac.
- Lecture 23: Hydrodynamics and diffusion.
See also the slides in PDF format.
- Lecture 24: Rotational diffusion.
See also the slides in PDF format.
- Lecture 25: NMR relaxation; linear regression.
See also the slides in PDF format.
- Exam 2: Please monitor your email to get the second exam, which
will be distributed on April 22.
- Lecture 26: Singular value decomposition.
See also the slides in PDF format.
- Student presentations: Please monitor your email to get the Zoom
links for the student presentations, on April 28 and May 3.
- Course syllabus.
- Getting an Amarel account: If you don't already have one,
request a user account on Amarel by visiting https://oarc.rutgers.edu/access.
Use a terminal application (or something like putty on Windows) to carry out a trial
login.
- Homework #1 Go through the following self-guided tutorials:
- Here is the XrayPrep script discussed in class on Jan.
27.
- Here is the documentation for RDB;
concentrate on the operators highlighted in yellow.
- Homework #2, due Feb. 12 Assignment is here.
- Homework #3, due Feb. 19 Assignment is here.
- Homework #4, due Mar. 4 Assignment is here.
- Notes on the COSMO solvation model.
- Homework #5, now due Mar. 30 Assignment is here.
- Remote Lecture 1: force fields.
[Note: if you get spinning colored lines,
click on pause, then again on play.]
See also the
slides in PDF format.
- Remote Lecture 2: MD and TI.
See also the
slides in PDF format.
- Homework #6, due Apr. 1 Assignment is here.
- Project and Term Paper
Instructions, (updated on 4/11).
- Remote Lecture 3: Amber.
See also the
slides in PDF format.
- Remote Lecture 4: MD. (There are no slides for this
lecture.)
- Homework #7, due Apr. 8 Assignment is here.
- Remote Lecture 5: small molecules.
See also the
slides in PDF format.
- Remote Lecture 6: free energies.
See also the
slides in PDF format.
- Remote Lecture 7: more free energies.
See also the
slides in PDF format.
- Homework #8, due Apr. 22 Assignment is here.
- Remote Lecture 8: cycles and experiments.
See also the
slides in PDF format.
- Remote Lecture 9: generalized Born models.
See also the
slides in PDF format.
- Homework #9, no due date Assignment is here.
- Remote Lecture 10: normal modes.
See also the
slides in PDF format.
- Remote Lecture 11: normal modes plus QM/MM.
See also the
slides in PDF format.
- Remote Lecture 12: more QM/MM.
See also the
slides in PDF format.
- Remote Lecture 13: final thoughts.
See also the
slides in PDF format.
- 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.
Updated on September 19, 2022. Comments to david.case@rutgers.edu