Physics 446-546: Biological Applications of Physics

Professor: Paul Ginsparg (325 Clark Hall, 5-7371, ginsparg@physics.cornell.edu)

Course Description

Syllabus

Lecture 1 (Tue 25 Jan 05)

Some links mentioned in lecture:

Started covering Part I of course text to develop common terminology and ensure all at same starting point. Chpt 1: elementary overview of key ideas from physics and chemistry: heat, energy, free energy, entropy, energy transduction.

Lecture 2 (Thu 27 Jan 05)

started Chpt 2: cell physiology, molecular parts list (Franklin's "Oil on the Waters")

Lecture 3 (Tue 1 Feb 05)

finished overview of Chpt 2, molecular devices, overall flow of information in cells. (digression on Anastasia; for further background, see DNA interactive, click on "Recovering the Romanovs", then click on "the mystery of Anna Anderson".)

Lecture 4 (Thu 3 Feb 05)

Genetic code, codon, and usage table for different species.
Sections 3.1,3.2: probability distributions, ideal gas law from molecular viewpoint, Boltzmann distribution.

Problem Set 1 (due 15 Feb '05), from course text: 1.3, 1.7, 2.4 (just provide a URL), 3.1, 3.2 , 4.1, 4.2, 4.3, 4.5. See Printable version.

Lecture 5 (Tue 8 Feb 05)

Finish sections 3.2 - 3.3. Begin Chpt 4: Brownian motion and diffusion, random walks
Stirling's formula

Lecture 6 (Thu 10 Feb 05)

finished through section 4.2, derivation of Einstein's relation, more on random walks and diffusion

Lecture 7 (Tue 15 Feb 05)

(Comments on DNA sequencing and gene identification.)
Continued with end Chpt 4 (biological applications of diffusion, Fick's law, diffusion equation).

Lecture 8 (Thu 17 Feb 05)

Finish chpt 4 (relaxation of concentration jump, limit on bacterial metabolism, see also Physical limits to biochemical signaling.)
Start Chpt 6, information content of data streams.
(Who was Claude Shannon, what did he do, and why should you care?)

Problem Set 2 (due 3 Mar 05), from course text: 6.2, 6.3, 6.4, 6.6, 6.7 (and read 6.10), 6.8. See Printable version.

Lecture 9 (Tue 22 Feb 05)

Continue Chpt 6.1-6.3, Information and Entropy.

Lecture 10 (Thu 24 Feb 05)

Further discussion of information and entropy, maximum bitrates per channel.
Discussion of problem 4.2 on HIV mutation rate and viral therapy, including discusion of retroviruses (see also diagram and databases ).
Finished section 6.3, definition of temperature. (measures of disorder, statistical postulate, entropy, ideal gas, and temperature from more formal viewpoint).

Lecture 11 (Tue 1 Mar 05)

Problem Set 3 (unfortunately out of sequence, note corrections to 1c and 3c following class 3 Mar 05)
Parts of section 6.4, 6.5: ideal gas law as consequence of 2nd law, introduction of Helmholtz free energy F, and Boltzmann distribution as consequence of the statistical postulate and two state systems (6.6.1).
(see also Information Flow and Computation in the Maxwell Demon Problem)

Lecture 12 (Thu 3 Mar 05)

Continued 6.5.1,6.5.2: Gibbs free energy G, entropic forces, heat engines, and 6.6.3 (microscopic systems and the partition function).

Lecture 13 (Tue 8 Mar 05)

almost finish chapt 6: 6.5.3 (adiabatic processes), 6.5.4 (biosphere as thermal engine), 6.6.4 (two-state complex systems and free energy, sub-partition functions), 6.7 (RNA folding as two-state system)

Lecture 14 (Thu 10 Mar 05)

Polymers resist stretching with an entropic force and the Freely Jointed Chain model (9.1.3), stretching single macromolecules and the two-state system (9.2).

Lecture 15 (Tue 15 Mar 05)

(brief digression on Rapid nanopore discrimination between single polynucleotide molecules (2000))
Magnetic analog of FJC (worked out problem 6.5, p.240), 3d chain freely jointed chain (eq. 9.35, p.389), Cooperativity (section 9.4.1), including 5 min of Ising history, and introduction of the "transfer matrix"

Lecture 16 (Thu 17 Mar 05)

Cooperativity, transfer matrix, helix coil transition (section 9.4 and beginning 9.5 in the text), some comments on herapathite (search for "brewster kaleidoscope quinine urine").

Problem Set 4 (due 5 Apr '05), from course text: 6.9, "Your turn 9O" (p. 389), 9.4, 9.5, 9.9
See Printable version.

("Spring" Break, 19-27 Mar)

Lecture 17 (Tue 29 Mar 05)

finish sections 9.5,9.6 in text (protein helix/coil transition, DNA cooperative "melting" transition, allostery)

Lecture 18 (Thu 31 Mar 05)

sections 7.5,8.5,8.6 (hydrophic interactions, self-assembly of amphiphiles, self-assembly in cells)
note also animations of various biological activities at the molecular scale.

Lecture 19 (Tue 5 Apr 05)

Molecular devices in cells, some comments on brownian ratchets, mechanical ratchet analogs, Smoluchowski equation (sections 10.1, 10.2 of course text).

Lecture 20 (Thu 7 Apr 05)

Digression on microarrays (see also fig8-62, fig8-63)
Continued discussion of Smoluchowski (10.2) and Fokker-Planck equations, and introduced D-ratchet (10.4).

Possible paper topics

Problem Set 5 (due 19 Apr '05), from course text: 7.6,7.9, (text question on section 8.2.1),10.2,10.3
See Printable version.

Lecture 21 (Tue 12 Apr 05)

some comments on b vs. z dna, and on entropy of multiple distributions. full solution to smoluchowski eqn. continued diffusing ratchet as biased random walk.

Lecture 22 (Thu 14 Apr 05)

finished diffusing ratchet, section 10.4 (identification of physical parameters, section 10.4.4', p.461), enzymes as cyclical motors (10.3.3), started life at low Reynolds number (5.1.3, 5.2.1, 5.3.1), including cilia recovery stroke

Lecture 23 (Tue 19 Apr 05)

Finished discussion of low Reynolds number (5.2, 5.3, and E. M. Purcell, Life at low Reynolds number), bacterial flagellar motor, and including brief discussion of Navier-Stokes equation (and millenium problem)

Lecture 24 (Thu 21 Apr 05)

Digression on info in neural spike trains, and discussion of probability and Bayes' theorem

Lecture 25 (Tue 26 Apr 05)

Continued discussion of Bayes Theorem, mutual information content, maximizing information content of data with application to "designing" the input/output relation for a neuron, model independent approach to info, info content of neural spikes, and info in correlations of neural spikes. See Bialek lecture notes ``Thinking about the brain'' (physics/0205030), pp. 31-47

Problem Set 6 (due 5 May 05), from text 5.4, 5.9, plus a few others on lectures 24,25: printable version

Lecture 26 (Thu 28 Apr 05)

Some comments on discrete subgroups of SO(3), in preparation for Thermodynamics Explains the Symmetry of Spherical Viruses (Physics Today, Dec 2004)

Lecture 27 (Tue 3 May 05)

Continued with Zandi et al., Origin of icosahedral symmetry in viruses (PNAS 101: 15556-15560, Nov 2004)

Answer to problem in class: take a soccer ball and draw a vertex in the middle of each pentagon, and a vertex in the middle of each hexagon. Draw edges connecting the new vertices if their associated faces are adjacent (i.e., draw an edge transverse to each existing edge). The new vertices and edges (the "dual" lattice) are identically the (1,1) icosadeltahedron. See figures.

Lecture 28 (Thu 5 May 05)

Discussion of Markov chain Monte Carlo, Metropolis method, finished icosahedral symmetry of viruses, brief discussion of duality and phase transition in 2 dimensional Ising model.