Physics 446-546: Biological Applications of Physics

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

Syllabus

Lecture 1 (Tue 2 Sep 03)

Some links mentioned in lecture:

Lecture 2 (Thu 4 Sep 03)

Covered most of 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. Chpt 2: cell physiology, molecular parts list, molecular devices, overall flow of information in cells.

Lecture 3 (Tues 9 Sep 03)

finished some comments on info flow in cells, and role of proteins, with some digressions on protein networks, RNAi, and C. Elegans ("It's like discovering the neutrino or something"). Then covered parts of Chpts 3,4 of course text: probability distributions, Boltzman distribution, reaction rates, relaxation equilibrium, Brownian motion, 1D random walk, with digression on analogy between temperature T in partition function and ħ in Euclidean quantum field theory.

Lecture 4 (Thu 11 Sep 03)

Finished through section 4.4.1: derivation of Einstein's relation, more on randum walks and diffusion, and started biological applications. (random digression, mentioned Copied citations create renowned papers?)

Problem Set 1 (due 22 Sep 03), 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 16 Sep 03)

Continued with end Chpt 4 (biological applications of diffusion, Fick's law, diffusion equation, relaxation of concentration jump, limit on bacterial metabolism). Started 6.1 (measures of disorder). Digression from 3.3.3 on on Schrodinger's "What is Life?" and Delbruck's identification of carrier of genetic information. Digression on "Language Trees and Zipping" (see, e.g., cond-mat/0108530 followed by the "raging controversy" cond-mat/0202383, cond-mat/0203275, cond-mat/0205521, cond-mat/0303261).

Lecture 6 (Thu 18 Sep 03)

Inserted the numbers for the limit on bacterial metabolism (course text, p. 138). Described some of the topics at q-bio list as potential topics for 2nd half of course or for papers, then covered roughly sections 6.1 - 6.3 (measures of disorder, statistical postulate, entropy, ideal gas, andd temperature from more formal viewpoint).

Lecture 7 (Tue 23 Sep 03)

Roughly sections 6.4, 6.5: More on ideal gas law as consequence of 2nd law, introduction of Helmholtz free energy F, Gibbs free energy G, entropic forces, heat engines, and biosphere as a thermal engine.

Lecture 8 (Thu 25 Sep 03)

Repaired introduction of F and G, then roughly sections 6.6, 6.7: Boltzmann distribution as a consequence of statistical postulate, two state systems, microscopic systems.

Problem Set 2 (due 7 Oct 03), 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 30 Sep 03)

Recapitulated macroscopic systems in thermal contact, macroscopic system in contact with heat bath, and microscopic system in contact with heat bath [Fire drill]. Two-state complex systems and free energy, sub-partition functions, kinetic interpretation of the Boltzmann distribution, rate constants, and hopping. Motivated by Synthesizing Life, start on Chpt 8 next time.

Lecture 10 (Thu 2 Oct 03)

More comments on self-assembly and the origin of life (RNA life, etc), then Chemical potentials, grand canonical ensemble, equilibria conditions, mass action rule. (Sections 8.1, 8.2 of course text).

Lecture 11 (Tue 7 Oct 03)

Some comments on epigenetics, see 7 Oct article, then self-assembly of amphiphiles (section 8.4 and first part of 8.6 of course txt).

Lecture 12 (Thu 9 Oct 03)

Finished comments on macromolecular folding and aggregation (2nd half of 8.6), then stretching single macromolecules (section 9.2).

Problem Set 3 (due 28 Oct 03), from course text: 7.5, 8.2, 8.4, 8.7, 8.8. See Printable version.

14 Oct: Fall break. 16 Oct: Inauguration

Lecture 13 (Tue 21 Oct 03)

(some comments on electrodes in monkey brains, synopis and article)
Cooperativity, transfer matrix, helix coil transition (section 9.4 and beginning 9.5 in the text).

Lecture 14 (Thu 23 Oct 03)

3d chain freely jointed chain, Heisenberg spin model, more on transfer matrix, and cooperative chain model, protein helix/coil transition (sections 9.5,9.6 in text, and 9.2.2' p.389)

Lecture 15 (Tue 28 Oct 03)

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

Lecture 16 (Thu 30 Oct 03)

more on Smoluchowski equation, more general Fokker-Planck, and energy landscape (finish 10.2 and 10.2.3', p.455)

Problem Set 4 (due 13 Nov 03), from course text: 9.4, 9.5, 9.9, 10.2, 10.3, 10.5. See Printable version.

Lecture 17 (Tue 4 Nov 03)

molecular implementation of mechanical principles (10.3): reaction coordinate, enzymes, random walk on 2d landscape. two-headed kinesin as ratchet (10.4.3), diffusing ratchet (10.4.4).

Lecture 18 (Thu 6 Nov 03)

more on C351 (10.4.4 and 10.4.4' p.461), other molecular motors (10.5)

Lecture 19 (Tue 11 Nov 03)

Some ideas on information theory from section starting on p.29 of Bialek lecture notes ``Thinking about the brain'' (physics/0205030). See also "Biological Sequence Analysis", by Durbin, Eddy, Krogh, Mitchison (ISBN: 0521629713), pp. 6-7.

Lecture 20 (Thu 13 Nov 03)

Continued discussion of Bayes Theorem, mutual information content, and of maximizing information content of data with application to "designing" the input/output relation for a neuron. (Bialek notes, pp. 33-37)

Lecture 21 (Tue 18 Nov 03)

Model independent approach to info, and info in correlations of neural spikes (Bialek notes, pp. 38-42). In preparation for neural networks, 5 min of Ising history, and 15 minute derivation of high-T/low-T duality in the 2D Ising model, (exp(2L)-1)*(exp(2K)-1)=2 .

Problem Set 5 (due 2 Dec 03), printable version.

Lecture 22 (Thu 20 Nov 03)

Intro to neural networks. Used notes from "Introduction to the Theory of Neural Computation" by Hertz, Krogh, Palmer (ISBN: 0201515601), pp. 1-17; and "Brain, neural networks, and computation", by J.J.Hopfield, Rev.Mod.Phys. 71 (1999) S431.

Tue 25 Nov

Discussions with students doing projects for credit.

Lecture 23 (Tue 2 Dec 03)

Continued on the Hopfield model with stochastic noise, mean field theory and phase transitions, analogy to spin systems.

Lecture 24 (Thu 4 Dec 03)

Finished discussion of associative memory models. Introduction to issues in computational biology involving sequence alignment, and the mapping to directed polymers (following cond-mat/9511072 cond-mat/9712081; see also physics/9802023, cond-mat/9811225) with quenched disorder, illustrating use of transfer matrix and scaling laws for finding optimal alignment.