Physics of Living Matter
Rutgers, Spring 2008, Course Number: 16:118:507

Instructor: Alexandre V. Morozov, email: morozov at physics dot rutgers dot edu

Classes will meet on Tuesdays and Fridays 3.00 - 4.20 pm in the BioMaPS seminar room (Hill 260).

Notes on grading:

Textbook:

"Biological Physics: Energy, Information, Life" by Philip Nelson (Chs. 2-11)

Schedule:

  1. Jan.22 - Introductory Lecture: basic vocabulary of cellular and molecular biology (see slides)
  2. Jan.25 - Lecture: introduction to protein structure and function, DNA and RNA structure and chemistry, genetic code (see slides)
  3. Jan.29 - Lecture: discrete and continuous probability distributions, ideal gas law, equipartition theorem
  4. Feb.1 - Lecture: Boltzmann distribution, relaxation to equilibrium, DNA as a physical carrier of genetic information.
    HW#1 assigned: 1) Your Turn 3F and 3L. Hand-drawn graphs are acceptable. 2) Problem 3.2. 3) Problem 3.4. 4) Problem 3.5.
  5. Feb.5 - Lecture
  6. Feb.8 - Lecture
    HW#1 due.
  7. Feb.12 - Lecture
  8. Feb.15 - Lecture
  9. Feb.19 - Lecture
  10. Feb.22 - Lecture
    HW#2 assigned: 1) C.4.16 [p.582] 2) C.4.21a [p.584] 3) 5.3 4) 5.9 [read section 5.3.5 before doing this problem]
  11. Feb.26 - Lecture
  12. Feb.29 - Lecture
    HW#2 due.
  13. Mar.4 - Lecture
  14. Mar.7 - Lecture
  15. Mar.14 - Lecture
  16. Mar.25 - Lecture
    HW#3 assigned: 1) 6.8 2) 7.8 [use Your Turn 6J] 3) C.6.13 [p.587] 4) C.7.17 [p.591; examine Problem 7.7 first]
  17. Mar.28 - Lecture
  18. Apr.1 - Lecture
    HW#3 due.
  19. Apr.4 - Lecture
  20. Apr.8 - Lecture
  21. Apr.11 - Lecture
  22. Apr.15 - Lecture
    HW#4 assigned: 1) C.8.10 [p.592] 2) 9.6 [Hint: use periodic boundary conditions and expand t1(s) + i t2(s) in terms of a complex, discrete Fourier transform] 3) 10.5
  23. Apr.18 - Lecture
  24. Apr.22 - Lecture,
    HW#4 due.
  25. Apr.25 - student presentations
  26. Apr.29 - student presentations
  27. May 2 - student presentations, final exam assigned
  28. May 5 - final exam due by 5 pm in Hill 279

Recommended papers (* marks more difficult ones):

  1. * Marko J.F. & Siggia E.D. "Statistical mechanics of supercoiled DNA", Phys.Rev.E 1995, 52, 2912.
  2. Crick F.H.C. "Linking numbers and nucleosomes", Proc.Nat.Acad.Sci. USA 1976, 73, 2639.
  3. Shimada J. & Yamakawa H. "Ring-closure probabilities for twisted wormlike chains. Application to DNA", Macromolecules 1984, 17, 689.
  4. Slutsky M. et al. "Diffusion in correlated random potentials, with applications to DNA", Phys.Rev.E 2004, 69, 061903.
  5. * Hopfield J.J. "Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity", Proc.Nat.Acad.Sci. USA 1974, 71, 4135.
  6. * Hopfield J.J. "Neural networks and physical systems with emergent collective computational abilities", Proc.Nat.Acad.Sci. USA 1982, 79, 2554.
  7. Wiggins P.A. et al. "High flexibility of DNA on short length scales probed by atomic force microscopy", Nat.Nanotech. 2006, 1, 137.
  8. Gore et al. "DNA overwinds when stretched", Nature 2006, 442, 836.
  9. Olson et al. "DNA sequence-dependent deformability deduced from protein-DNA crystal complexes", Proc.Nat.Acad.Sci. USA 1998, 95, 11163.

Alexandre V. Morozov
Last modified: Tue Apr 15 14:25:52 EDT 2008