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Fundamentals of Biophysics at the Nanoscale

Schedule

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

Prerequisites

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.

Syllabus

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).

MODULE 2
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