Studium

Overview of topics of university theses:

Diploma theses

FIB: a manufacturing tool for nanostructures

FIB SIMS is a modern physical tool for the creation of nanometer sized objects using a focused ion beam. Those nanoobjects can be formed either by the sputtering effect of the ion beam, which we call the nanomachining, or by locally inducing the decomposition of a properly chosen gas adsorbed on the sample surface, which is used for the growth of nanoobjects.
The goal of the thesis is a controlled creation of two- and three-dimensional nanostructures for photonic and sensor applications.  
The available facility is a new multifunctional instrument based on a scanning electron microscope, FIB-type ion gun producing Ga+ ions, and a computer controlled gas injection system.

Qualifications: students of physics, chemistry, materials science and related disciplines.

Supervisors: Jan Grym, Ph.D.; Jan Vaniš, Ph.D.

Preparation and Characterization of Semiconductor Nanostructures

Low dimensional semiconductor structures have been intensively studied for prospective electronic and photonic applications. Diploma or Ph.D. thesis will focus on the preparation of one-dimensional ZnO structures, investigation of their structural, electrical, and optical properties and description of the phenomena occurring when these nanostructures interact with gas molecules and electromagnetic radiation.

Infrastructure:

• Laboratories for the preparation of ZnO nanostructures by hydrothermal growth, electrochemical deposition, chemical vapour deposition, and electrophoretic deposition.
• Clean rooms.
• Multifunctional apparatus based on an electron microscope SEM equipped with focused ion beam FIB of Ga+ ions, computer controlled gas injection system GIS, and nanomanipulator. This apparatus allows for the observation, analysis, milling, and preparation of contacts to the nanostructures.
• Laboratories for the electrical and optical characterization of the materials and structures

(I-V and C-V measurements in a wide range of temperatures, DLTS, conductive AFM, STM, Raman and optical spectroscopy, Low temperature photoluminescence, cathodoluminescence).

Qualifications: students of physics, chemistry, materials science and related disciplines.

Supervisors: Roman Yatskiv, Ph.D.; Jan Grym, Ph.D.; Jan Vaniš, Ph.D.

Dissertations

Super-resolution microscopy with scattering labels

Supervisor: Marek Piliarik, Ph.D.

Molekulární značky umožňují v přirozeném prostředí sledovat chování a pohyb jednotlivých molekul, například proteinů. Použití fluorescenčních značek je limitováno stabilitou a saturací fluorescenčního signálu. Alternativou jsou takzvané rozptylové značky, jakými jsou například kovové nanočástice, které vykazují silný rezonanční rozptyl. Nevýhodou rozptylových značek je jejich obvyklá velikost v řádu 20 až 50 nm, která významně přesahuje velikost sledovaných molekul a ovlivňuje jejich pohyb a interakce. 

Cílem tohoto projektu je výzkum vlastností nové generace extrémně malých rozptylových molekulárních značek, jejichž velikost bude menší než velikost označené molekuly (např. 1.4 nm Au55 klastr). Takové nanočástice pak budou využity jako značky různých vazebných míst jediné molekuly (např. proteinu) a mohou posunout limity rozlišení „super-resolution“ optických mikroskopů až na na sub-molekulární úroveň.

Optical imaging of protein nano-dynamics

Supervisor: Marek Piliarik, Ph.D.

Pochopení dynamiky vnitřního uspořádání makromolekul, zejména proteinů, v jejich přirozeném prostředí je kritickým krokem k poznání jejich biologické funkce. Experimentální metody však v této oblasti narážejí na řadu fundamentálních překážek, ať už to je prostorové rozlišení optických soustav, rychlost snímání fluorescenčních signálů, nebo průměrování přes heterogenní soubor molekul. 

Náplň disertační práce využívá nejnovější metodu optického zobrazování jednotlivých molekul bez použití fluorescenčních značek, která je prvním krokem k jejich další analýze. Cílem projektu je vyvinout optické metody, které umožní na základě změn rozptylu světla na jednotlivých molekulách popsat změny prostorového uspořádání makromolekul v reálném čase. 

Spectroscopic characterization of rare-earth-doped optical fibers for fiber lasers 

Supervisor: Pavel Peterka, Ph.D.

The aim of the work will be research of novel types of fiber lasers based on silica-fibers doped with thulium or with thulium in combination with holmium. Attention will be focused on investigation of energy transfer processes and determination of coefficients characterizing these processes and their application in numerical models of fiber lasers. The rare-earth-doped fiber samples will be prepared in the team of Fiber lasers and nonlinear optics of the Institute of Photonics and Electronics of the CAS. The samples will be also obtained thanks to the existing cooperation within the European Action COST MP1401 "Advanced fibre laser and coherent source as tools for society, manufacturing and lifescience". Experimental demonstrations of selected applications of the developed rare-earth-doped fibers in fiber lasers around wavelengths of 2000 nm are expected.

Investigation of fiber laser instabilities

Supervisor: Pavel Peterka, Ph.D.

Instability of fiber lasers are currently highly relevant field of research, particularly with regard to increasing output power and new wavelengths of these types of lasers and with the perspective of rapidly growing impact of fiber lasers to the society. The thesis will be aimed at research on physical origins of spontaneous self-pulsations of fiber lasers in several configurations of the laser cavity, e.g., for Fabry-Perot and a ring resonator. The theoretical and experimental research is focused on the role of the recently discovered phenomenon of self-sweeping of the laser wavelength as the trigger mechanism of the laser self-Q-switching and the role of stimulated Brillouin scattering.

Thulium-doped fiber lasers

Supervisor: Pavel Peterka, Ph.D.

Teoretický a experimentální výzkum nových typů laserů s křemennými optických vlákny dopovanými thuliem, případně thuliem a yterbiem. Sestavení spektrálně, časově a prostorově rozlišeného numerického modelu vlákna. Teoretická optimalizace parametrů thuliem dopovaných optických vláken a dvouplášťových optických vláken dopovaných kromě thulia i yterbiem. Charakterizace vláken připravených v laboratoři optických vláken Ústavu fotoniky a elektroniky AV ČR nebo na spolupracujícím pracovišti na Univerzitě v Nice ve Francii. Spektroskopická charakterizace připravených vláken s použitím teoretického modelu. Experimentální ověření vybraných aplikací thuliem dopovaných křemenných optických vláken v laserech a zesilovačích v pásmech v okolí vlnových délek 800, 1470 nm a 2000 nm.

Effect of intense short electric pulses on protein nanostructures

Supervisor: Michal Cifra, Ph.D.

The work will be focused on research of an effect of intense short electric pulses on natural protein nanostructures. Results of this thesis will contribute to understanding of mechanisms of electric fields effects at a molecular level and open new technological possibilities in biomedicine and bionanotechnology. Candidate is expected to have a knowledge at the level of master degree in the field of biophysics or chemical physics or equivalent. Fluency in English is necessary.

List of bibliography:

1. Hekstra, Doeke R., K. Ian White, Michael A. Socolich, Robert W. Henning, Vukica Šrajer, and Rama Ranganathan. “Electric-Field-Stimulated Protein Mechanics.” Nature 540, no. 7633 (December 7, 2016): 400–405. https://doi.org/10.1038/nature20571.
2. Chafai, Djamel Eddine, Vadym Sulimenko, Daniel Havelka, Lucie Kubínová, Pavel Dráber, and Michal Cifra. “Reversible and Irreversible Modulation of Tubulin Self‐Assembly by Intense Nanosecond Pulsed Electric Fields.” Advanced Materials 31, no. 39 (August 13, 2019): 1903636. https://doi.org/10.1002/adma.201903636.
3. Havelka, Daniel, Djamel Eddine Chafai, Ondrej Krivosudský, Anastasiya Klebanovych, František Vostárek, Lucie Kubínová, Pavel Dráber, and Michal Cifra. “Nanosecond Pulsed Electric Field Lab-on-Chip Integrated in Super-Resolution Microscope for Cytoskeleton Imaging.” Advanced Materials Technologies 0, no. 0 (2019): 1900669. https://doi.org/10.1002/admt.201900669.

Molecular simulations of the effect of intense short electric pulses on protein nanostructures

Supervisor: Michal Cifra, Ph.D.

The work will be focused on research of an effect of intense short electric pulses on natural protein nanostructures employing computational methods based on molecular dynamics simulations. Results of this thesis will contribute to understanding of mechanisms of electromagnetic fields effects at a molecular level and open new technological possibilities in biomedicine and bionanotechnology. Candidate is expected to have a knowledge at the level of master degree in the field of biophysics or chemical physics or similar. Affinity towards computer work is required. Fluency in English is necessary.

List of bibliography:

1. Hekstra, Doeke R., K. Ian White, Michael A. Socolich, Robert W. Henning, Vukica Šrajer, and Rama Ranganathan. “Electric-Field-Stimulated Protein Mechanics.” Nature 540, no. 7633 (December 7, 2016): 400–405. https://doi.org/10.1038/nature20571.
2. Marracino, Paolo, Francesca Apollonio, Micaela Liberti, Guglielmo d’Inzeo, and Andrea Amadei. “Effect of High Exogenous Electric Pulses on Protein Conformation: Myoglobin as a Case Study.” The Journal of Physical Chemistry B 117, no. 8 (February 28, 2013): 2273–79. https://doi.org/10.1021/jp309857b.
3. Carr, Lynn, Sylvia M. Bardet, Ryan C. Burke, Delia Arnaud-Cormos, Philippe Leveque, and Rodney P. O’Connor. “Calcium-Independent Disruption of Microtubule Dynamics by Nanosecond Pulsed Electric Fields in U87 Human Glioblastoma Cells.” Scientific Reports 7 (January 24, 2017): 41267. https://doi.org/10.1038/srep41267.

Electromagnetic chips for analysis and function modulation of molecular nanostructures

Supervisor: Michal Cifra, Ph.D.

The work will be focused on the theoretical design and fabrication of electromagnetic microstructured chips compatible with super-resolution microscopy for analysis and function modulation of natural protein nanostructures, mainly components of the cytoskeleton. The results of this thesis will contribute to the understanding of electromagnetic properties of organisms at a molecular level and open new technological possibilities in biomedicine and bionanotechnology. The candidate is expected to have knowledge at the level of a master's degree in the field of applied physics or similar. Fluency in English is necessary..

List of bibliography:

1. Havelka, Daniel, Ondrej Krivosudsky, Jiri Prusa, and Michal Cifra. “Rational Design of Sensor for Broadband Dielectric Spectroscopy of Biomolecules.” Sensors and Actuators B: Chemical 273C (May 2018): 62–69. https://doi.org/10.1016/j.snb.2018.05.124.
2. Havelka, Daniel, Djamel Eddine Chafai, Ondrej Krivosudský, Anastasiya Klebanovych, František Vostárek, Lucie Kubínová, Pavel Dráber, and Michal Cifra. “Nanosecond Pulsed Electric Field Lab-on-Chip Integrated in Super-Resolution Microscope for Cytoskeleton Imaging.” Advanced Materials Technologies (2019): 1900669. https://doi.org/10.1002/admt.201900669.