Physics of Living Matter
Alexandre V. Morozov,
morozov at physics dot rutgers dot edu
Rutgers, Spring 2008, Course Number: 16:118:507
Classes will meet on Tuesdays and Fridays 3.00 - 4.20 pm in the
BioMaPS seminar room (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
"Biological Physics: Energy, Information, Life" by Philip Nelson (Chs. 2-11)
- Jan.22 - Introductory Lecture: basic vocabulary of cellular and molecular biology (see slides)
- Jan.25 - Lecture: introduction to protein structure and function, DNA and RNA structure and chemistry, genetic code (see slides)
- Jan.29 - Lecture: discrete and continuous probability distributions, ideal gas law, equipartition theorem
- 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.
- Feb.5 - Lecture
- Feb.8 - Lecture
- Feb.12 - Lecture
- Feb.15 - Lecture
- Feb.19 - Lecture
- 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]
- Feb.26 - Lecture
- Feb.29 - Lecture
- Mar.4 - Lecture
- Mar.7 - Lecture
- Mar.14 - Lecture
- 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]
- Mar.28 - Lecture
- Apr.1 - Lecture
- Apr.4 - Lecture
- Apr.8 - Lecture
- Apr.11 - Lecture
- 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
- Apr.18 - Lecture
- Apr.22 - Lecture,
- Apr.25 - student presentations
- Apr.29 - student presentations
- May 2 - student presentations, final exam assigned
- May 5 - final exam due by 5 pm in Hill 279
Recommended papers (* 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.
- Shimada J. & Yamakawa H. "Ring-closure probabilities for twisted wormlike chains. Application to DNA", Macromolecules 1984, 17, 689.
- 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.
- 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