Physics of Living Matter
Rutgers, Spring 2010, Course Number: 16:750:567 (Physics) and 16:118:507 (BioMaPS)
Instructor:
Alexandre V. Morozov,
email:
morozov at physics dot rutgers dot edu
Classes will meet on Tuesdays and Fridays 3.20 - 4.40 pm in Hill 260.
Notes on grading:
- 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:
"Biological Physics: Energy, Information, Life", Updated First Edition by Philip Nelson (Chs. 2-11)
Schedule:
- Jan.19 - Introductory Lecture I: basic vocabulary of cellular and molecular biology (see slides)
- Jan.22 - Introductory Lecture II: protein structure and function, DNA and RNA structure and chemistry, genetic code (see slides)
- Jan.26 - Lecture: discrete and continuous probability distributions, ideal gas law, equipartition theorem
- 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.
- Feb.2 - Lecture
- Feb.5 - Lecture
HW#1 due.
- Feb.9 - Lecture
- Feb.12 - Lecture
- 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.
- Feb.19 - Lecture
- Feb.23 - Lecture
HW#2 due.
- Feb.26 - Lecture
- Mar.2 - Lecture
- Mar.5 - Lecture
- Mar.9 - No lecture
- 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]
- Mar.23 - Lecture
- Mar.26 - Lecture
HW#3 due.
- Mar.30 - Lecture
- Apr.2 - Lecture
- Apr.6 - Lecture
- Apr.9 - Lecture
HW#4 assigned: 1) C.8.10 2) 9.2 3) C.9.11 4) 10.5 5) C.10.10
- Apr.13 - Lecture
- Apr.16 - Lecture
- Apr.20 - Lecture,
HW#4 due.
- Apr.23 - student presentations
- Apr.27 - student presentations
- Apr. 30 - student presentations, final exam assigned
- 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):
- * Marko J.F. & Siggia E.D. "Statistical mechanics of supercoiled DNA", Phys.Rev.E 1995, 52, 2912.
- Crick F.H.C. "Linking numbers and nucleosomes", Proc.Nat.Acad.Sci. USA 1976, 73, 2639.
- Slutsky M. et al. "Diffusion in correlated random potentials, with applications to DNA", Phys.Rev.E 2004, 69, 061903.
- * 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.
- * Hopfield J.J. "Neural networks and physical systems with emergent collective computational abilities", Proc.Nat.Acad.Sci. USA 1982, 79, 2554.
- Wiggins P.A. et al. "High flexibility of DNA on short length scales probed by atomic force microscopy", Nat.Nanotech. 2006, 1, 137.
- Gore et al. "DNA overwinds when stretched", Nature 2006, 442, 836.
- * Jarzynski C. "Nonequilibrium equality for free energy differences", Phys.Rev.Lett. 1997, 78, 2690.
- Elowitz M.B., Levine A.J., Siggia E.D. & Swain P.S. "Stochastic gene expression in a single cell", Science 2002, 297, 1183.
- Gardner T.S., Cantor C.R. & Collins J.J. "Construction of a genetic toggle switch in E.coli", Nature 2000, 403, 339.
- 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.
- Bialek W. & Setayeshgar S. "Physical limits to biochemical signaling", Proc.Nat.Acad.Sci. USA 2005, 102, 10040.
- Libby E., Perkins T.J. & Swain P.S. "Noisy information processing through transcriptional regulation", Proc.Nat.Acad.Sci. USA 2007, 104, 7151.
- Maslov S. & Ispolatov I. "Propagation of large concentration changes in reversible protein-binding networks", Proc.Nat.Acad.Sci. USA 2007, 104, 13655.
- 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.
- 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.
Alexandre V. Morozov
Last modified: Fri Apr 9 12:05:17 EDT 2010