Molecular Biophysics and Polymer Physics: Physics 621/321. Fall 2003

Instructor: Wayne Reed, Stern 5068, ph. 862-3185, wreed@tulane.edu

Office hours: M,W 3:00-4:00, or by appointment

Reference Text: see below

Class schedule: MWF 11:00-11:50am, Stern 2002

This syllabus, along with the detailed, tentative class notes are available at: http://www.tulane.edu/~wreed/ph621/ph621f00outline.html

  Catalog description of the course

Prerequisites, PHYS 131/132 or equivalent, Math 122 or equivalent. Note the name change from "Molecular Biophysics" to "Molecular Biophysics and Polymer Physics". An introduction to the physics of polymers and the physical bases underlying the biofunctionality of macromolecules in living systems. Polymer reactions, mass distributions, conformations, interactions and hydrodynamics are covered in detail, and applied to proteins, nucleic acids, polysaccharides, and synthetic polymers. Basic notions of molecular self-organization, non-equilibrium processes, and information content are introduced. Equilibrium and non-equilibrium characterization of biomolecules by scattering and other techniques is treated.

Overview for Fall 2003 course

We will first focus Biophysics within its interdisciplinary context as 'Living State Physics', and will address some of the fundamental issues involved. The main orientation of this course, however, is the study of the physical properties of macromolecules. All macromolecules, whether of biological or synthetic origin share many features; chemical bonding mechanisms, conformations, solution properties, ability to associate into supramolecular assemblies, and more. Additionally, the methods of theoretical and experimental study are shared; Molecular dynamics simulations, mean field and density functional theories, Monte Carlo simulations, NMR, scattering, calorimetry, laser spectroscopy, etc. As such, much of the course will treat macromolecules in general, although specific attention will be to biomacromolecules and their relationship to biological function, where appropriate.

Unlike the traditional areas of Physics, such as Electromagnetism, Classical and Quantum Mechanics, for which well established texts and pedagogical paradigms exist, there is no single authoritative text or method of approach to macromolecules. Historically, theories of Relativity and Quantum Mechanics and technologies such as manned flight, mass spectroscopy and particle accelerators were all established well before it was even universally accepted that macromolecules even exist! Now, however, macromolecular science is an essential component in such wide ranging areas as molecular biology, pharmacology, electronics, advanced materials, resins, coatings, adhesives, agroalimentary industries, and more. The worldwide market in macromolecules is estimated to be on the order of one trillion dollars per year. Macromolecular science is inextricably interdisciplinary, and continues to benefit from the contributions of chemists, chemical and materials engineers, physicists, mathematicians, medical and life scientists.

Naturally, this course will concentrate on the physics and quantitative aspects of macromolecules, but some background will be given on relevant chemical and biochemical aspects. Since no authoritative text exists, the selection of an appropriate book has been difficult. I had chosen and ordered "Physical Chemistry of Macromolecules" by Sun as a reference text. As of today, August 22, 2003, I was informed by the publisher that there are no copies of Sun's book left, and a new printing would not be available until January 2004. Hence, as a last minute change of course, I have decided to order Polymer Solutions: An Introduction to Physical Properties. by Ewao Teraoka. John Wiley, 2002. This has very good coverage of much of the polymer physics portion of the course, but does not treat the biophysics portion. I hence urge you to consult one or more of the references listed below as a companion to the biophysics part of the course.

Introductory concepts

Overview of Biophysics; questions involving 'Living State Physics'

Biochemical Overview; proteins, nucleic acids, carbohydrates and lipids. Metabolism.

Electrically charged macromolecules in solution.

Brief introduction to synthesis of macromolecules, including copolymers.

Physics of Macromolecules

Molecular weight distributions

Conformations of macromolecules and chain statistics

Macromolecular Thermodynamics

Interactions between macromolecules; excluded volume theory

Hydrodynamic properties; diffusion, viscosity, electrophoretic mobility

Experimental Approaches to the Study of Macromolecules

Scattering theory and techniques

Chromatography

X-ray crystallography

Other techniques

Theoretical and Computational Approaches to the Study of Macromolecules

Monte Carlo simulations

Perturbation and other approximate theories

Introduction to Cellular Level Biophysics

Transduction processes (light, mobility, etc.)

Membranes

Course grading

(tentatively) 3 semester exams (20% each)

Class participation/possible quizzes (10%)

Research project (30%)

The research project:

Because the area of macromolecules is so vast, and our coverage of any one area is necessarily limited, it is important that each student select a research area to delve into in depth. I will distribute a list of possible research topics, but you should feel free to suggest your own. The idea is that you should choose an area that interests you strongly. A date will be announced by which you should have chosen your topic and written a short proposal/outline; roughly one page that describes the area you have chosen, and the particular aspects you will be researching. A list of texts and articles from the research literature is strongly recommended.

About half way through the semester you will be asked to submit a short progress report (one or two pages), where you describe the progress you have made and identify the sources you are consulting. You must include at least one advanced textbook and two research articles. At the end of the semester each student will give a presentation of about 20 minutes during class, before handing in the final research report.

Click here for research project guidelines and suggestions

Selected reference texts

Molecular Biology of the Cell, 3^rd Ed., Alberts et al., Garland Publishing, 1994

Biochemistry, L. Stryer, Freeman Press

Biophysical Chemistry, Cantor and Schimmel, W.H. Freeman and Co., 1980

Physical Biochemistry, K.E. van Holde, Prentice-Hall, 1985

Physics of Biological Systems, Flyvberg et al. Eds., Springer, 1997

Molecular Biophysics, M.V. Volkenstein, Academic Press, 1977

Foundations of Biophysics, A.L. Stanford, Academic Press, 1975

Prebiotic and biochemical evolution, Kimball and Oró, north-holland, 1971

Biophysical Chemistry; Molecules to Membranes, Bergethon and Simons, Springer, 1990

Molecular and Cell Biophysics, Nossal and Lecar, Addison-Wesley, 1991

Electrical Interactions in Molecular Biophysics, Gabler, Academic Press, 1978

Foundations of Bioenergetics, H.J. Morowitz, Academic Press, 1978

Introductory Biophysics, M. Cerdonio and R. Noble, World Scientific, 1986

The Science of Polymer Molecules, Boyd and Phillips, Cambridge, 1996

Introduction to Macromolecular Science, P. Munk, Wiley Interscience, 1989

Introduction to Polymer Physics, Doi, Oxford Science Pub., 1996

An Introduction to Polymer Science, VCH Pub., 1997

The Theory of Polymer Dynamics, Doi and Edwards, Oxford Science Pub., 1988

Scaling Concepts in Polymer Physics, deGennes, Cornell Uni. Press, 1979

Polymers and Neutron Scattering, Higgins and Benoit, Oxford Science, 1994

Statistical Physics, Landau and Lifshitz, Pergamon Press, 1980

Non-Equilibrium Thermodynamics in Biophysics,Katchalsky and Curran, Harvard U. Press, 1965

Foundations of Synergetics, Mikhailov and Loskutov, Springer, 1991
 

 Class#1 Overview of Physics, Chemistry, Biology and Biophysics

 Class#2   Forces operative in the Living State
 
  Class#3 Fundamental issues in Living State Physics:  Information/entropy, cooperativity, etc.

Class#4, Fall 2003  Biochemical Overview I:  Proteins  and Nucleic acids

Class#5,  Fall 2003  Biochemical Overview II:  Carbohydrates,  Lipids, other molecules  

Class#6, Fall 2003  Biochemical Overview III:  Metabolism, basic cycles, ATP production,     redox reactions, etc.

Class#7, Fall 2003  Electrically charged macromolecules in solutions; ph/pK,  Poisson-Boltzmann     equation, ionic screening

Class#8, Fall 2003  Overview of polymerization reactions.  Ideal free radical  polymerization, chain transfer, inhibition, 'lliving'

 Class#9 Copolymerization reactions, sequence length distributions.  Step growth polymerization

Class#10, Fall 2003    Molecular weight distributions and averages.  Binomial and related distributions.  Examples

Class#11, Fall 2003Conformations of Macromolecules I:  Random coil statistics     

 Class#12    Conformations of Macromolecules II:  Restricted random coils, persistence length, excluded volume

 Class#13   Thermodynamics of multi-component solutions

 Class#14    Excluded volume approach to non-ideal solutions

 Class#15    Molecular transport processes I:  friction factors, viscous flow, Navier-Stokes equation

 Class#16    Molecular transport processes II:  intrinsic viscosity, force-flux relations, diffusion

 Class#17    Light scattering I:  Electromagnetic origin.  Rayleigh scattering from dilute, non-interacting particles

 Class#18    Light scattering II:  Interacting particles, angular dependence of scattered light, Zimm's method

 Class#19    Light scattering Applications I:   characterization of equilibrium properties of polymer solutions

 Class#20   Light scattering Applications II:  monitoring non-equilibrium phenomena in polymer solutions