Graduate course in Biomolecular Geometry (Math 728A, Summer II, 2001)

- Course announcement: Three Dimensional Geometry of Biological Molecules
- Syllabus
- RASMOL: a program for molecular visualization.
- BABEL: a program for molecular structure file conversion.
- Corrections and Clarifications, updated 7-26-01.
- Homework: Methane, Ethane, Stereo Viewing
- Homework: Improper wedge angles, Stereoisomers of Methane, Free Rotation
- Homework: Rotation matrices, Quaternions for rotations, Internal coordinates via coordinate transformations
- Solution to Homework: Rotation matrices
- Homework: Identities, spherical coordinates via coordinate transformations, spherical trigonometry: Law of Cosines and Law of Sines, tetrahedronometry
- Homework: Z-system to Z-matrix, Proline ring conformations, exocyclic bond and wedge angles, complete proline conformations
- MAPLE procedures for geometry calculation for bond angles, wedge angles, Cremer-Pople and Marzec-Day coordinates for five-membered rings, flap angle coordinates for five-membered rings, and bond and wedge angles for four coordinated centers with one strained angle.
- References on Five Membered Rings
- Homework: Facts about SU(2), axis and angle for products of rotations, active and passive rotations, rigid motions, T-matrices as rigid motions
- Homework: Transformations between peptide units poses, peptide helix parameters, 3_10 helix, endocyclic torsion angles for the chair conformation
- XYZ file for Yeast Phenylalanine Transfer RNA, converted from the PDB file: 1TRA
- PDB file for the modified base WYBUTOSINE, appearing in tRNA. View with Rasmol. Add hydrogens.
- XYZ file for Myoglobin plus the Heme group, converted from the PDB file: 1MBO
- XYZ file for Triose Phosphate Isomerase, converted from the PDB file: 1QDS

Graduate course in Biomolecular Simulation (Math 728B, Fall, 2001)

- Course announcement: Numerical Simulation of Biomolecular Systems
- Syllabus
- More on Conical Singularities
- Translational and Rotational Invariance
- Translational and Rotational Invariance II
- Water Molecule I, Vibrations
- Water Molecule II, Rigid Rotations
- Water Molecule III, Rotations and Vibrations combined

Graduate Course: Stochastic Models of Biomolecular Systems (Math 728G, Spring, 2002)