Optical methods in biophysics

Enrollment into the program.

Optical resonators and laser beams. Laser beam transformations, optical fibers.

Laser sistems: interfaction between light and matter, optical pumping and amplification, laser oscillators, pulsed lasers, overview of laser systems.

Optical detectors: photomultipliers, semiconductor optical sensors, heterodine detection, noise in optical detectors.

Propagation of light in optically inhomogeneous matter, elastic and inelastic scattering, fluorescence, nonlinear optical processes.

Optical microscopy: clasical microscopy, fluorescence microscopy, 3D imaging (confocal, 2 photon), Raman microcsopy, FRET, fluorescence lifetime imaging, deconvolution.

Sub-wavelength resolution microscopy: total internal reflection microscopy (TIRM), stimulated emission depletion microscopy (STED), 4 Pi microscopy, scanning near field optical micriscipy (SNOM).

Optical detection and excitation methods: single molecule techniqeus, evanescent field based sensors, surface plasmon resonance, caged bioactive probes.

B. E. A. Saleh and M. C. Teich: Fundamentals of Photonics, (John Wiley & Sons, 1991)
James B. Pawley ed.: Handbook of Biological Confocal Microscopy, (Plenum Press, NY, 1995, ISBN 0-306-44826-2)

Objectives:
Student gets familiar with up-to-date optical technologies that are used in the biophisics reasearch.

Competences:
Knowledge and understanding of principles of operation of optical methods that are used in biophysics. Knowledge and understanding of experimental planning, performing of measeurements and evaluation of results.

Knowledge and understanding: Understanding of modern optical equipment and metodologies used in biophysics that enables it’s further development and adaptation to specific requiremnents.

Application: Knowing, understanding and application of physics methods and optical techniques in biophysics, biology and medicine.

Reflection: Application of physics methods in research and diagnostics of complex biological systems.

Transferable skills:
Ascociation of basic physics principles and theoretical concepts with modern experimental approaches in biophysicsm biology and medicine.

Lectures, exercises, homework, consultations

Written exam
Oral exam
grading: 5 (fail), 6-10 (pass) (according to the Statute of UL)

MUR, Jaka, KAVČIČ, Blaž, POBERAJ, Igor. Fast and precise Laguerre-Gaussian beam steering with acousto-optic deflectors. Applied optics, ISSN 1559-128X. Tiskana izd., 2013, vol. 52, iss. 26, str. 6506-6511. http://www.opticsinfobase.org/ao/abstract.cfm?uri=ao-52-26-6506, doi:10.1364/AO.52.006506. [COBISS-SI-ID 2608228]

VILFAN, Andrej, BABIČ, Dušan, KAVČIČ, Blaž, KOKOT, Gašper, OSTERMAN, Natan, POBERAJ, Igor, VILFAN, Mojca. Measurement of fluid flow generated by artificial cilia. V: TOONDER, Jaap M. J. de (ur.), ONCK, Patrick R. (ur.). Artificial cilia, (RSC nanoscience & nanotechnology, ISSN 1757-7136). Cambridge: The Royal Society of Chemistry, 2013, str. 244-258. http://pubs.rsc.org/en/content/chapter/bk9781849735971-00244/978-1-84973-597-1. [COBISS-SI-ID 26814759]

KOKOT, Gašper, VILFAN, Mojca, OSTERMAN, Natan, VILFAN, Andrej, KAVČIČ, Blaž, POBERAJ, Igor, BABIČ, Dušan. Measurement of fluid flow generated by artificial cilia. Biomicrofluidics, ISSN 1932-1058, 2011, vol. 5, no. 3, str. 034103-1-034103-9, doi: 10.1063/1.3608139. [COBISS-SI-ID24932135]

OSTERMAN, Natan, POBERAJ, Igor, DOBNIKAR, Jure, FRENKEL, Daan, ZIHERL, Primož, BABIČ, Dušan. Field-induced self-assembly of suspended colloidal membranes. Physical review letters, ISSN 0031-9007. [Print ed.], 2009, vol. 103, str. 228301-1-228301-4, doi:10.1103/PhysRevLett.103.228301. [COBISS-SI-ID 2204516]

KAVČIČ, Blaž, BABIČ, Dušan, OSTERMAN, Natan, PODOBNIK, Boštjan, POBERAJ, Igor. Magnetically actuated microrotors with individual pumping speed and direction control. Applied physics letters, ISSN 0003-6951, 2009, vol. 95, str. 023504-1-023504-3, doi: 10.1063/1.3176969. [COBISS-SI-ID 2184036]