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Fundamentals of Biophysics at the Nanoscale


Monday, 11 November 2019 to Friday, 29 May 2020
Total hours: 60
Hours of lectures: 40
Hours of supplementary teaching: 20

Examination procedure

  • oral exam


Recommended for PhD students in Nanosciences, 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.


The courses is composed by two modules, which can be followed independently.

Measurements in microscopy and spectroscopy [1-4]
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 and dynamics of biological molecules [5]
Molecular forces; bonded and non-bonded interactions; bond energies.
Carbohydrates, lipids and membranes.
Structure and dynamics of proteins: peptidic bond; primary, secondary, tertiary and quaternary structure; folding and stability.
Structure and dynamics of nucleic acids: kinds and functions; primary, secondary and tertiary structure; quaternary structure (nucleosomes and chromatin, ribosomes, nanostructures of nucleic acids).

Basics of MatLab for data analysis.


Educational goals:

MODULE 1: providing (also theoretical) bases for quantitatively grasping experiments in molecular and cellular biophysics; giving a common language in Biophysics to students with different backgrounds.

MODULE 2: learning to implement algorithms (functions, scripts, GUIs) in MatLab.

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] "Biophysical Chemistry", Cantor and Schlimmel; Part I