Fundamentals of biophysics at the nanoscale
Code 1056I
Credits 6
Learning outcomes
1. Measurements in microscopy and spectroscopy:
Noise in measurements, experimental uncertainties, basics of probability distributions, propagation of uncertainties. Transmission, reflection and epifluorescence microscopy. Magnification and resolution; contrast techniques; spherical and chromatic aberrations; hints on optical filters and dichroics.
Confocal microscopy: set-up, point spread function, hints on deconvolution, comparison with TIRF and 2-photon microscopy. Light-matter interaction: fundamentals (also quantum mechanics) and setups for absorption, fluorescence, Raman, and multiphoton excitation. Jablonski diagrams and properties of fluorescence. Organic dyes: chemical structures and exploitation in fluorescence microscopy.
Hints on fluorescent quantum dots. Fluorescent proteins, GFP family. Diffusion and Brownian motion. Techniques in fluorescence microscopy: colocalization, FRAP-like techniques, FRET, FLIM (fundamentals, instruments, phasors), FCS, super-resolution (RESOLFT, STED, F-PALM, SIM), single molecule spectroscopy and tracking.
2. Basis of molecular and cellular biology:
Introduction to the structure of biological molecule. Fluorescent proteins and their photophysics. Prokaryotes vs eukaryotes. General organization of the eukaryotic cell. Cytoplasm: membrane structure and transport, intracellular compartments, cytoskeleton, cell signalling. The nucleus: chromosomal DNA and its organization, the Nuclear Pore Complex and nucleus-cytoplasmic transport. Cell cycle and cell division. Cell death.
Noise in measurements, experimental uncertainties, basics of probability distributions, propagation of uncertainties. Transmission, reflection and epifluorescence microscopy. Magnification and resolution; contrast techniques; spherical and chromatic aberrations; hints on optical filters and dichroics.
Confocal microscopy: set-up, point spread function, hints on deconvolution, comparison with TIRF and 2-photon microscopy. Light-matter interaction: fundamentals (also quantum mechanics) and setups for absorption, fluorescence, Raman, and multiphoton excitation. Jablonski diagrams and properties of fluorescence. Organic dyes: chemical structures and exploitation in fluorescence microscopy.
Hints on fluorescent quantum dots. Fluorescent proteins, GFP family. Diffusion and Brownian motion. Techniques in fluorescence microscopy: colocalization, FRAP-like techniques, FRET, FLIM (fundamentals, instruments, phasors), FCS, super-resolution (RESOLFT, STED, F-PALM, SIM), single molecule spectroscopy and tracking.
2. Basis of molecular and cellular biology:
Introduction to the structure of biological molecule. Fluorescent proteins and their photophysics. Prokaryotes vs eukaryotes. General organization of the eukaryotic cell. Cytoplasm: membrane structure and transport, intracellular compartments, cytoskeleton, cell signalling. The nucleus: chromosomal DNA and its organization, the Nuclear Pore Complex and nucleus-cytoplasmic transport. Cell cycle and cell division. Cell death.