An introduction to the theoretical bases of biophysical concepts and approaches with selected examples of applications of these principles. Topics include: the physics of chemical bonds and molecular architecture, together with the methods for determination of biological structures; elementary quantum mechanics; statistical thermodynamics; energy flow in biological systems; molecular mechanisms of enzyme action; the physics of biological membranes; and the interaction of radiation with biological systems.
Prerequisites: General Physics, Math 115, Chem 330a/332a.
Lectures:
There will be two lectures (MW) and one conference section (F) per week at 930-1020. The core text will be "Biophysics" by Rodney M. J. Cotterill, published by John Wiley & Sons, 2002 (available at Bookhaven). It will be supplemented by class handouts for several topics. Lecture notes and illustrative material such as powerpoint files will be made available on the internet for a limited time after each lecture.
Conferences:
There will be one conference section (F) per week at 930-1020.
Exams and written assignments:
One or two illustrative papers will be provided for the weekly conference sections. Weekly conferences will be moderated by the faculty and Teaching Fellows, but each week, two students will be designated (not in advance) to be the discussion leaders. Thus, all students should come to the conference prepared to lead a discussion of the lecture material for the week as well as a discussion of the assigned paper.
There will be two written exams (a midterm and a final) as well as three take-home written assignments.
Grading:
The course grade will be made up of the grades for the two written exams (total 50%), the grades on the three written assignments (33%) and conference participation (17%).
Syllabus
10/12 Jan (WCS) Chemical Binding (Chapters 1, 2)
Elementary Quantum Mechanics
Ionization Energy, Electron Affinity and Chemical Bonding
14/19 Jan (WCS) Chemical Binding (Chapters 1, 2, Appendix A)
Elementary Quantum Mechanics
Ionization Energy, Electron Affinity and Chemical Bonding
[17 Jan (No Class)]
21 Jan Conference: Review of Wave Mechanics; handout and discussion questions.
24/26 Jan (WCS) Energies, Forces and Bonds (Chapter 3.)
Interatomic Potentials for Strong and Weak Bonds
Bond energies; Spring Constants
28 Jan Conference: K.T. No, et al. A simple functional representation of angular-dependent hydrogen-bonded systems.
J. Phys. Chem. 99(3478-3486) 1995.
31 Jan/2 Feb (VU) Principles of Spectroscopy, UV/VIS, CD, Fluorescence (Notes on classes.yale.edu)
4 Feb Conference; First written assignment due
7/9 Feb (VU) AFM, Light Microscopy, Fluorescence Microscopy, Electron Microscopy (Notes on classes.yale.edu)
11Feb Conference (Papers for discussion on classes.yale.edu)
14 Feb (WCS) Thermodynamics and Statistical Mechanics
16 Feb (WCS) Thermodynamics and Statistical Mechanics; Rates of Reaction (Chapter 4.)
18 Feb Conference: C. Delisi and D. Crothers, Prediction of RNA secondary structure. Proc. Natl. Acad. Sci. 68(2682-2685)1971.
21/23 Feb (VU) Diffraction Methods; Surface Plasmon Resonance
25 Feb MIDTERM
28 Feb/2 Mar (VU) Membrane Biophysics I: Membrane Structure
Membrane Biophysics II: Diffusion, Mobility of Ions, Excitable Membranes
4 Mar Conference; Second written assignment due
SPRING BREAK
21 Mar (WCS) Transport Processes: Sedimentation and Diffusion (Chapter 5)
23 Mar (WCS) Transport Processes: Viscosity and Electrophoresis
25 Mar Conference: W. Keller, "Determination of the number of superhelical turns in simian virus 40 DNA" PNAS 72(4876)1975
31 Mar (WCS) Biological Polymer Conformation Nucleic Acid Conformation; (Chapter 7)
4 Apr (VU) Optical Tweezers
6 Apr (WCS) Biological Polymer Conformation; Protein Folding(Chapter 7)
8 Apr Conference
11 Apr (WCS) Biophysics of radiant energy: production and interaction with matter
13 Apr (WCS) Biological effects of radiation: Target theory; Health Physics and Radiation Safety
15 Apr Conference. James C. Osborne, Jr., Jay H. Miller, and E. S. Kempner "Molecular Mass and Volume in Radiation Target Theory" Biophysical Journal Volume 78 April 2000 1698-1702
18 Apr (WCS) Physical Basis of Life: Origin of Life Theories
20 Apr (WCS) Yale Traditions in MBB. Third written assignment due
25 Apr. NO CLASS
2 May REVIEW SESSION: 7-9 pm... Room 001 WLH
FINAL EXAM: 5 May, 9:00 am, 305 BASS
This page was last up-dated 25 April 2005 .