Course program, A.Y. 2015-16

Lesson	Date	Topics	Linked slides and useful links
1	March 2nd, 2016	introduction to biophysics. Diffusion processes in biology. The diffusion equation and its solutions.	Slides Short introduction to cell biology from NIGMS
2	March 9th, 2016	The main structural elements in eukaryotic cells. Membranes. Dimensional reduction in the diffusion inside cells. Diffusion and potential theory. Absorbing sphere. Receptors on a spherical cell.	Slides The inner life of the cells (BioVisions @ Harvard University)
3	March 16th, 2016	Reaction-diffusion and morphogenesis. The (bio)physics of water.	Slides Belusov-Zhabotinsky chemical oscillator (video 1, video 2)
4	March 23rd, 2016	The hydrogen bond. Configurational entropy of ice. Dynamics of the hydrogen bond in water: water ions and the Grotthuss mechanism. Proton pumps in membranes, molecular machines and proton pumps.	Slides Short movie on the molecular dynamics of water Short movie on water freezing
5	March 30th, 2016	X-ray crystallography and its applications to the structural problems of biology. The basic ideas of crystallography. The discoveries of von Laue and of the Bragg's. The Laue equations. The data inversion problem. The Patterson function. The Protein Data Bank (PDB).	Slides Link to the PDB
6	March 31st, 2016	The structure of DNA. Griffith's experiment. The experiment of Avery, MacLeod and McCarty. The paper by Timofeev-Ressovsky, Zimmer and Delbrück and its relationship with Schrödinger's "What is life?". The race to uncover the structure of DNA. The contribution of X-ray cristallography. The diffraction pattern due to a helical structure.	Slides
7	April 13th, 2016	The structural elements of DNA: bases, sugars, phosphates. The elements that make up a nucleotide. The hierarchical packaging of DNA in the cell (nucleosomes, chromatin, chromosomes). A glimpse of DNA in present day biophysical research. Graphical representation of the molecular machines in a cell.	Slides Movie on DNA packaging Movie on the history of the discovery of the structure of DNA Movie on the visualization of biophysical processes
8	April 20th, 2016	Exercise: extraction of DNA from bananas and strawberries. The statistical mechanics of DNA. Molecular zipper model of DNA.	Movies on DNA extraction (1, 2)
9	April 21th, 2016	The role of the Gibbs free energy in biophysical contexts. Helix to coil transition in DNA (thermal DNA denaturation). DNA unzipping and helicase dynamics. Polymerase chain reaction (PCR). Proteins. Lysozyme as an example of a small protein. Aminoacids. Peptide bonds. Disulfide bonds. Proteins as polypeptide chains. Geometry of peptide bonds. The Ramachandran plot.	Slides Movie on DNA replication Movie on PCR
10	April 27th, 2016	The secondary structure of proteins, alpha helices and beta sheets. The shape of proteins: the case of hemoglobin and sickle cell anemia. Other generalities on proteins. Ribosomes and proteasomes. The prediction of protein structure from the aminoacid sequence. Levinthal's paradox.	Slides Short movie on proteins Short movie on helices in proteins Movie on protein synthesis Ribosome in action
11	April 28th, 2016	Flory-Huggins theory. Hydrophobic effect. Protein folding. The shape of proteins as a computational challenge. Enzymes. Concentrations and Gibbs free energy. Chemical kinetics. Equilibrium constants. Dissociation reactions, the pK.	Movie on protein folding
12	May 4th 2016	Transition state theory. Arrhenius plots. Enzymes and transition state theory. Michaelis-Menten kinetics. Transition state stabilization. Lock-and-key view of enzyme action. Genetic code. RNA and DNA. Messenger RNA (mRNA) and transfer RNA (tRNA). RNA Polymerase.	Slides Movie on lock-and-key mechanism Movie on DNA transcription
13	May 5th 2016	mRNA splicing. Ribosomes. Ribosomes and antibiotics. Viruses. Bacteriophages. CRISPR. Phages and the Delbrück-Luria experiment.	Slides Movie on RNA splicing Movie on antibiotics targeting the bacterial ribosome The mathematics behind the Delbrück-Luria experiment