Educational offer - University of Padova

Information on the course unit

Degree course	Second cycle degree in PHYSICS SC2382, Degree course structure A.Y. 2017/18, A.Y. 2019/20	bring this page with you
Degree course track	PHYSICS OF MATTER [002PD]
Number of ECTS credits allocated	6.0
Type of assessment	Mark
Course unit English denomination	BIOPHOTONICS
Website of the academic structure	http://physics.scienze.unipd.it/2019/laurea_magistrale
Department of reference	Department of Physics and Astronomy
Mandatory attendance	No
Language of instruction	English
Branch	PADOVA
Single Course unit	The Course unit can be attended under the option Single Course unit attendance
Optional Course unit	The Course unit can be chosen as Optional Course unit

Syllabus

Prerequisites:	Biological Physics
Target skills and knowledge:	The course aims to provide in-depth knowledge of Fourier optics, bright field microscopy, contrast generation, conventional and confocal fluorescence microscopy, super-resolution, digital image processing, molecular probes and cell signal detection. The course is specifically designed to provide students with the ability to design optical microscopy experiments for a wide range of potential biological applications.
Examination methods:	Written and an oral exam. The written part concerns topics developed during the course. The oral exam consists in the presentation by the student of one or more original articles related to optical super-resolution techniques.
Assessment criteria:	The evaluation of the student's preparation will be based on the understanding of the topics developed, on the acquisition of the concepts and methodologies proposed and on the ability to apply them in an autonomous and conscious way.
Course unit contents:	Electromagnetic wave propagation: plane waves, spherical waves, phase velocity, irradiance, wave packets, group velocity, coherence length, interference. Scalar diffraction theories: the Kirchhoff formulation, the Rayleigh-Somrnerfeld formulation, the Huygens-Fresnel principle. Geometrical optics: Optical path length, the principle of Fermat, ideal imaging systems, matrix methods in paraxial imaging, cardinal points and planes. Apertures and stops, image-forming instruments, brightness and illumination of images, intensity fluctuations, detection noise. The Debye integral representation of focused fields, irradiance distribution near focus (three-dimensional point spread function). Resolving power: the Rayleigh criterion. Minimum angular separation, visual acuity, phototransduction. Transmitted light microscopy: angular spectrum of plane waves, diffraction gratings, abbe theory and resolution. Phase contrast, dark field, and differential interference contrast microscopy. Fluorescence microscopy: molecular spectra, Jablonski diagram, Stokes' shift, life time and quantum efficiency, saturation of the excited state. Structure of the conventional fluorescence microscope. Confocal microscopy: lateral resolution and axial resolution in the classical limit; optical sectioning and volume reconstruction; physical principles and applications of 2-photon excitation; advantages and disadvantages of different confocal systems. Stimulated emission depletion (STED) nanoscopy and super-resolution. Selected biophotonics applications: optical recording of changes in ion concentration. Optical sensors of Ca2+ ions, protons and other physiologically relevant ionic species. Imaging of Ca2+ at one and two wavelengths; local control of the concentration of Ca2+ and other active molecular species by UV photolysis of caged compounds; FRET, FRAP. Intravital microscopy: biosensors, optochemogenetics, photodynamic therapy of cancer.
Planned learning activities and teaching methods:	Taught lessons
Additional notes about suggested reading:	Lecture notes
Textbooks (and optional supplementary readings)	Born M, Wolf E, Principles of Optics - 7th expanded edition. Cambridge, UK: Cambridge University Press, 1999. ISBN: 9780521642224 Mertz, J, Introduction to Optical Microscopy. Cambridge, UK: Cambridge University Press, 2019. ISBN: 9781108428309 Saleh B, Teich M, Fundamentals of Photonics, 2 Volume Set, 3rd Edition. New York, USA: John Wiley & Sons, Inc., 2019. ISBN: 9781119506874