WINTER 2010

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

Time and Location: Tuesdays and Thursdays 9:30 am – 10:50 am, York Hall 4050A

Office hours: after class or by appointment

Text: Lecture notes. "Physical Biology of the Cell" by Phillips et al. "Biological Physics" by Nelson. "Molecular Biology of the Cell" by Alberts et al.

Course description: This course is intended to communicate a style of thinking about living matter quantitatively. Tools of statistical mechanics will be developed and applied to a variety of biological problems. Different from how traditional biology courses are organized, the organizational thread that links various topics of this course is based upon the underlying physical prospective. We will repeatedly make use of estimates to develop a feeling for the numbers associated with biological structures and processes. We will explore the range of spatial scales of biological entities and the hierarchy of temporal scales of biological processes, and discuss how organisms manipulate the time scales offered by the intrinsic physical rates of processes. 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, the emergence of entropic elasticity, and protein folding. The theory of elastic rods will be applied to investigate DNA bending during transcriptional regulation, packaging of DNA in viruses and in the eukaryotic nucleus, and the properties of the cytoskeleton. We will examine the microscopic and continuum descriptions of diffusion, the Smoluchowski equation, and discuss diffusion as a transport mechanism and a mechanism for delivering ligands to receptors. We will explore Kramers problem of hopping-over-a-barrier in the context of single-molecule manipulation experiments. The theory of rate equations will be applied to the dynamics of ion channels, enzyme kinetics, cytoskeletal assembly, and the dynamics of molecular motors. The propagation of nerve impulses as a problem in biological electricity will be explored.