Fundamentals of Biophysics at the Nanoscale

Period of duration of course
Course info
Number of course hours
Number of hours of lecturers of reference
Number of hours of supplementary teaching

Type of exam

Oral exam


Recommended for PhD students in Nanoscience, suggested for PhD students in Neurosciences, Methods and Models for Molecular Sciences, indicated also for PhD students in Physics.

Prerequisites: basic principles of Optics, of Organic and Inorganic Chemistry, and of Quantum Mechanics.


Measurements in microscopy and spectroscopy [1-4] (40 hours)

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.

Introduction to the structure of biological molecules [6]. Fluorescent proteins and their photophysics. [4]

Basis of molecular and cellular biology [5] (14 hours)

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. Biology laboratory techniques (Methods for cells growth and analysis; purification and analysis of proteins; DNA and RNA: methods for transfection; analysis of genes expression and function; labelling of molecules of interest: strategies and limits)

In-vivo microscopy and electrophysiology (6 hours)

Educational aims

Providing (also theoretical) bases for quantitatively grasping experiments in molecular and cellular Biophysics at the nanoscale; giving a common language in Biophysics to students with different backgrounds.

Bibliographical references

[1] "An Introduction to Error Analysis", J. R. Taylor (Ch. 1-4, 9, 11)
[2] "Microscopy from the very beginning", Dr. H. G. Kapitza, © Carl Zeiss Jena GmbH, 1997, 2nd revised edition, on-line available
[3] "Introduction to Confocal Fluorescence Microscopy", Michiel Müller, edited by SPIE press (WA, USA), second edition (2006)
[4] "Fluorescence Applications in Biotechnology and Life Sciences", edited by Ewa M. Goldys (2009), published by John Wiley & Sons (Hoboken, NJ, USA), Ch. 1-6, 9-11, 16.
[5] "Molecular Biology of the cells", B. Alberts et al. (chosen parts)
[6] "Biophysical Chemistry", Cantor and Schlimmel; Part I