Schedule of lecture topics
Nov 8 (Tues) - We will discuss the helix-coil transition a little more
and perhaps also some related topics, such as DNA supercoiling. Please
finish reading Chapter 9.
Nov 3 (Thur) - More (gasp) polymers. We'll focus on the cooperative
FJC and the helix-coil transition.
Nov 1 (Tues) - More on polymer models. Please be sure you have
read pages 341-363 of Chapter 9.
Click here to review the in-class assignment.
Recommended Reading:
- Stretch Genes, by Robert H. Austin,
James P. Brody, Edward C. Cox, Thomas Duke and Wayne
Volkmuth. Physics Today Feb 1997, p 32. Part 1 | Part 2
Oct 27 (Thur) - Continue discussion of the wormlike chain model
(Chapter 9). Please continue reading the chapter ...
Click here to review the in-class assignment.
Oct 25 (Tues) - Conclude discussion of Chapter 8, including
amphiphiles, micelle formation, and related phenomena. Begin Chapter
9 (Cooperative transitions in macromolecules). Please begin reading
Chapter 9.
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Oct 20 (Thur) - Continue discussions of Chapter 8, including
aggregation phenomena in macromolecules. Please finish reading the
chapter.
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Oct 18 (Tues) - Begin Chapter 8 (Chemical Forces & Self-Assembly).
Please read pages 294 -308.
Please be prepared to identify the topic for your presentation.
Click here to review the in-class assignment.
Oct 13 (Thur) - Continue discussing entropic forces in solutions, and
especially the properties of electrical fields near macroions in solution
(the Poisson-Boltzmann equation). Please finish reading Chapter 7.
- Suggested reading: DNA-Inspired electrostatics, by
W.Gelbart et al., (Physics Today, 9/2000).
- Please also think seriously about the topic for your presentation.
Look at the Science and Nature websites for some ideas from the current
literature. I would like to have your topics in advance so that (for
example) I can post the titles on the webpage.
Click here to review the in-class assignment.
Oct 11 (Tues) - After a few final comments on Chapter 6, we will
start discussing Chapter 7 (Entropic forces at work). Please read
pages 245-260.
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Oct 6 (Thur) - Further discussion of Chapter 6. Please finish reading
the chapter. This is primarily a review of Statistical Mechanics and
thermal physics, so we won't spend a lot of time on it. If you have
questions about the subject, please bring them to class on Thursday.
Click here to review the in-class assignment.
Oct 4 (Tues) - Finish discussing bacterial flagellar propulsion,
and begin Chapter 6. Please read pages 196-210.
Recommended optional reading:
- A mathematical theory of communication, by Claude Shannon (1948). This doesn't have much to do with biological physics, but it is very
accessible and definitely worth a look.
Click here to review the in-class assignment.
Sep 29 (Thur) - (Almost) conclude discussion of bacterial flagellar
motion. Please read the remainder of Chapter 5 before class.
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Sep 27 (Tues) - Continue discussion of viscosity and its biological applications in Chapter 5.
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Sep 22 (Thur) - We will begin discussing Chapter 5 of Nelson
(i.e. biological physics at low Reynolds number). Please read sections
5.1 - 5.2.3 (pages 158-172) before class.
Click here to review the in-class assignment.
Sep 20 (Tues) - We discussed some statistical mechanics of
polymer chains, including chain models (freely jointed, wormlike,
freely rotating), the Gaussian distribution of end-to-end distances,
entropic elasticity, interaction free energy, the theta condition,
and the coil-globule transition.
Optional reading:
- A.Grosberg, A.Khokhlov, Statistical Physics of Macromolecules, AIP Press, NY (1994)
Sep 15 (Thur) - We continue our discussion of Brownian motion in
Chapter 4 with emphasis on the Einstein relation, Einstein-Stokes, and
Fick's laws of diffusion. Please finish reading the chapter.
Click here to review the in-class assignment.
Sep 13 (Tues) - We may start by discussing radiation damage to
cells, as a supplement to Nelson's brief discussion in Chapter 3.
The main task, however, is to start Chapter 4. This chapter covers
random walks, diffusion, the Einstein relation, and related topics.
Please read sections 4.1 through 4.3.2 of Chapter 4 (pages 108-127)
before class on Tuesday.
Click here to review the in-class assignment.
Sep 8 (Thur) - Conclude discussion of Chapter 3. We discussed
Mendel's laws, chromosome structure, mitosis, and genetic crossover in
some detail.
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Sep 6 (Tues) - Begin discussion of Chapter 3 of Nelson. This
chapter reviews some basic concepts of probability and statistics, which
we will need as we apply statistical mechanics to biological systems.
Please read the chapter before class. Most of the chapter will cover
familiar material, but the discussion of the molecular basis of heredity
(section 3.3) will be less familiar and quite interesting.
Click here to review the in-class assignment.
Sep 1 (Thur) - Conclude discussion of Chapter 2. This means we will review
small organic molecules and discuss their assembly into larger biomacromolecules. We will
especially focus on nucleic acids (DNA and RNA) and proteins.
Aug 30 (Tues) - We will begin discussion of Chapter 2 of Nelson,
emphasizing general properties of cells, their structures & anatomy etc.
Click here to review the in-class assignment.
Aug 25 (Thur) - Review syllabus and discuss Chapter 1 of Nelson.
This chapter is a general review of the concept of free energy and its relevance
to the fact that living organisms can assemble simple small molecules into large
systems of complex, ordered structures.
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