Physics of Living Matter
Rutgers, Spring 2010, Course Number: 16:750:567 (Physics) and 16:118:507 (BioMaPS)

• 4 homework assignments (25 points each) - 40% of the grade. NOTE: all problems are from the Updated First Edition of the textbook, unless explicitly indicated otherwise.
• Student presentations of published research papers (see partial list below) - 30% of the grade
• Take-home final exam - 30% of the grade

Textbook:

Schedule:

1. Jan.19 - Introductory Lecture I: basic vocabulary of cellular and molecular biology (see slides)
2. Jan.22 - Introductory Lecture II: protein structure and function, DNA and RNA structure and chemistry, genetic code (see slides)
3. Jan.26 - Lecture: discrete and continuous probability distributions, ideal gas law, equipartition theorem
4. Jan.29 - Lecture: Boltzmann distribution, relaxation to equilibrium, DNA as a physical carrier of genetic information.
   HW#1 assigned: 1) Problem 3.2. 2) Problem 3.4. 3) Problem 3.5. 4) Problem C.3.6.
5. Feb.2 - Lecture
6. Feb.5 - Lecture
   HW#1 due.
7. Feb.9 - Lecture
8. Feb.12 - Lecture
9. Feb.16 - Lecture
   HW#2 assigned: 1) Problem 4.5. 2) Problem C.4.16. 3) Problem C.4.17. 4) Problem 5.5. 5) Problem 5.9.
10. Feb.19 - Lecture
11. Feb.23 - Lecture
    HW#2 due.
12. Feb.26 - Lecture
13. Mar.2 - Lecture
14. Mar.5 - Lecture
15. Mar.9 - No lecture
16. Mar.12 - Lecture
    HW#3 assigned: 1) 6.2 2) C.6.13 [p.587] 3) 7.7 4) 7.8 [use Your Turn 6J] 5) C.7.17 [p.591; follow-up to Problem 7.7]
17. Mar.23 - Lecture
18. Mar.26 - Lecture
    HW#3 due.
19. Mar.30 - Lecture
20. Apr.2 - Lecture
21. Apr.6 - Lecture
22. Apr.9 - Lecture
    HW#4 assigned: 1) C.8.10 2) 9.2 3) C.9.11 4) 10.5 5) C.10.10
23. Apr.13 - Lecture
24. Apr.16 - Lecture
25. Apr.20 - Lecture,
    HW#4 due.
26. Apr.23 - student presentations
27. Apr.27 - student presentations
28. Apr. 30 - student presentations, final exam assigned
29. May 7 - final exam due by 5 pm in Hill 279, or in my mailbox in the Physics Department

Papers recommended for presentations (* 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. Slutsky M. et al. "Diffusion in correlated random potentials, with applications to DNA", Phys.Rev.E 2004, 69, 061903.
4. ^* 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.
5. ^* Hopfield J.J. "Neural networks and physical systems with emergent collective computational abilities", Proc.Nat.Acad.Sci. USA 1982, 79, 2554.
6. Wiggins P.A. et al. "High flexibility of DNA on short length scales probed by atomic force microscopy", Nat.Nanotech. 2006, 1, 137.
7. Gore et al. "DNA overwinds when stretched", Nature 2006, 442, 836.
8. ^* Jarzynski C. "Nonequilibrium equality for free energy differences", Phys.Rev.Lett. 1997, 78, 2690.
9. Elowitz M.B., Levine A.J., Siggia E.D. & Swain P.S. "Stochastic gene expression in a single cell", Science 2002, 297, 1183.
10. Gardner T.S., Cantor C.R. & Collins J.J. "Construction of a genetic toggle switch in E.coli", Nature 2000, 403, 339.
11. Schneidman E., Berry M.J., Segev R. & Bialek W. "Weak pairwise correlations imply strongly correlated network states in a neural population", Nature 2006, 440, 1007.
12. Bialek W. & Setayeshgar S. "Physical limits to biochemical signaling", Proc.Nat.Acad.Sci. USA 2005, 102, 10040.
13. Libby E., Perkins T.J. & Swain P.S. "Noisy information processing through transcriptional regulation", Proc.Nat.Acad.Sci. USA 2007, 104, 7151.
14. Maslov S. & Ispolatov I. "Propagation of large concentration changes in reversible protein-binding networks", Proc.Nat.Acad.Sci. USA 2007, 104, 13655.
15. Deeds E.J., Ashenberg O. & Shaknovich E.I. "A simple physical model for scaling in protein-protein interaction networks", Proc.Nat.Acad.Sci. USA 2006, 103, 311.
16. Deeds E.J., Ashenberg O., Gerardin J. & Shaknovich E.I. "Robust protein-protein interactions in crowded cellular environments", Proc.Nat.Acad.Sci. USA 2007, 104, 14952.