Course program, A.Y. 2014-15

Lesson	Date	Topics	Linked slides and useful links
1	March 6th, 2015	introduction to biophysics. Diffusion processes.	Short introduction to cell biology from NIGMS
2	March 13th, 2015	Diffusion processes (ctd.). Discussion of the optimization of cell receptors from diffusion and the electrostatic analogy. Further features of diffusion processes. Reaction-diffusion equations and their applications to morphogenesis.	Slides Movies of a complex reaction-diffusion system, the Belousov-Zhabotinsky (BZ) reaction (1, 2)
3	March 20th, 2015	The physics of water. Hydrogen bonds. Ice. Residual entropy of ice. Proton conduction in water, and the Grotthuss mechanism. Proton currents in action: the bacteriorhodopsin-ATP Synthase mechanism for bacterial photosynthesis.	Slides Bacteriorhodopsin introductory paper
4	March 31th, 2015	Introduction to crystallography and its applications to the structural problems of biology.	Slides Link to the PDB website
5	April 17th, 2015	X-ray crystallography and the discovery of the structure of DNA.	Slides Pauling's triple helix model
6	April 20th, 2015	More on the structure of DNA. The statistical mechanics of DNA. DNA melting.	Slides TED talk by Drew Berry on the visualization of biological processes
7	April 22nd, 2015	DNA melting, helix-to-coil transition.The structure of proteins. Aminoacids. Peptide bonds. Classification of protein structures.	Slides Helicase action PCR
8	April 24th, 2015	Experimental demostration: DNA extraction from plant cells. Protein structure. The protein folding problem and Levinthal's paradox. Homopolymers and the Flory-Huggins theory.	Introductory movie on proteins A primer on protein structure Movies on the RNA-to-protein translation in ribosomes (1, 2)
9	April 27th, 2015	Homopolymers and the Flory-Huggins theory (ctd.). Hydrophobic interactions. Protein folding as a computational problem. The genetic code. The Delbrück-Luria experiment.	Slides TED talk by Ken Dill on protein folding and its technological perspectives
10	May 11th, 2015	The mechanisms of code translation and protein building. Numerical estimates. Mutation rates.	Slides Movie on ribosomes and antibiotics The numbers of cell biology
11	May 15nd, 2015	The hallmarks of cancer. The Nordling and the Armitage-Doll models of carcinogenesis. A simple mathematical model of the age dependence of colorectal cancer. Peto's paradox. Introduction to radiobiology.	Slides Particle tracks in a cloud chamber
12	May 18th 2015	Basics of radiobiology. Stopping Power and Linear Energy Transfer (LET). Dose. Radiolysis of water and the formation of Reactive Oxygen Species (ROS). Oxidative stress. Biological effects of radiation. Survival curves: the linear-quadratic model; the target model. Relative Biological Effectiveness (RBE), Oxygen effect, and other effects that affect the shape of the survival curve.	Slides The Health Risks of Extraterrestrial Environments (NASA)
13	May 22nd 2015	Enzymes. Refresher of chemical thermodynamics. Chemical kinetics. Transition-state Theory (TST). Enzyme action in the context of TST. The Michaelis-Menten equation. The physics of enzymes. The shape of viruses. The Tobacco Mosaic Virus (TMV). Bacteriophage phi X 174. Thermodynamics of viral self-assembly.	Slides Movie on lock-and-key mechanism of enzyme action
14	May 29th 2015	Seminar on computational topics in cellular biophysics by Dr. S. Stella

(gray text means "preliminary program, may change")