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FALL 2017

Instructor: Prof. Olga Dudko, office: Urey Hall 7234, email: dudko AT physics.ucsd.edu

Lecture Time and Location: Tuesdays and Thursdays 2:00 pm – 3:20 pm, Mayer Hall addition 2623

Office hours: after class or by appointment

Text: Required: Lecture notes.
Recommended: "Physical Biology of the Cell" by Phillips et al. "Biophysics: Searching for Principles" by Bialek. "Biological Physics" by Nelson. "Molecular Biology of the Cell" by Alberts et al.

Course description:
This course teaches how quantitative models derived from statistical physics can be used to build quantitative, intuitive understanding of biological phenomena. This course is different from traditional biology/biophysics courses in that the organizational thread that links various topics of this course is based upon the underlying physics prospective. The idea of two-state variables and the Gibbs distribution will be employed to investigate ion channel gating, phosphorylation, and ligand-receptor binding and cooperativity. Physics of random walks will be used to explore the size of a genome and the geography of chromosomes, DNA looping and gene regulation, and the emergence of entropic elasticity. We will examine diffusion as a transport mechanism in the cell and a mechanism for delivering ligands to receptors. The theory of rate equations will be applied to the dynamics of ion channels, enzyme kinetics, cytoskeletal assembly and cell motility. The propagation of nerve impulses will be discussed as a problem in biological electricity.