Doctoral studies

Doctoral Study Programmes

Standard Ph.D. study programmes last four years. Students are required to take courses and examinations, present seminars, annual progress reports, pursue research and publish their data in scientific journals according to their individual study plans governed by respective supervisors. Results of the research are compiled in Ph.D. thesis. Students prepare for the State Doctoral Examination, which tests the range and quality of the student's abilities in respective field of study and the potential to acquire and creatively implement the knowledge. After successful defense of the doctoral thesis and passing the State Doctoral Examination, the student will be awarded the degree Ph.D.

Ph.D. study application guide

  1. Choose your field of study and thesis topic.
  2. Contact your potential supervisor and get the endorsement for your application. Only then you can apply for your study programme!
  3. Include the necessary documents with your application.
  4. Complete the electronic application. Choose only fields of study with English titles.
  5. In order to complete the e-application, you have to pay the processing fee 690 CZK (approximately 27 EUR) by credit card. Without the payment, the application will not be considered.
  6. Entrance examinations are usually oral (e.g. via Skype) and take place in June (date should by specified by your supervisor).
  7. Be aware that tution fee up to 4000 EUR per academic year is required.
  8. A limited number of scholarships is available each year.

Fields of Study

Biology, Ecology and Environmental Sciences

  • Botany - NOT OPEN
  • Ecology
  • Experimental Biology (full-time, part-time)
  • Molecular and Cell Biology (part-time)
  • Zoology (full-time, part-time)

Chemistry

Computer Science

Earth Sciences

Mathematics

Physics

Thesis topics

Thesis topics for the academic year 2020/2021

Topics will be updated continuously.

Biology, Ecology and Environmental Sciences

Field of Study Botany
Field of Study Ecology

Population ecology and conservation of the common hamster
Supervisor: prof. MVDr. Emil Tkadlec, CSc.

Population dynamics in small rodents
Supervisor: prof. MVDr. Emil Tkadlec, CSc.

Personality in soil invertebrates
Supervisor: doc. RNDr. Ivan H. Tuf, Ph.D.

CO2 and CH4 emissions from small floodplain pools
Supervisor: doc. RNDr. Martin Rulík, Ph.D.

Soil quality indicators in agroecosystems
Supervisor: prof. Dr. Ing. Bořivoj Šarapatka, CSc.

Phylogeny and taxonomy of Curculigo (Hypoxidaceae) in Borneo
Supervisor: RNDr. Martin Dančák, Ph.D.

Field of Study Experimental Biology

All topics for Fischer stipend

The role of blue light photoreceptors in plant tolerance to abiotic stress
Supervisor: prof.  Martin Fellner, PhD.

Characterization of the mode of action of biostimulants
Supervisor: Nuria de Diego Sanchez Ph.D.

Field of Study Zoology

Chemistry

Field of Study Analytical Chemistry

Identification of binders in historical artworks
Supervisor: prof. RNDr. Karel Lemr, Ph.D.

Analysis of biologically active compounds by capillary electrophoresis and mass spektrometry
Supervisor: doc. RNDr. Jan Petr, Ph.D.

Field of Study Inorganic Chemistry

Quantitative relationships between structure and luminescence properties of platinum metals complexes with material applications potential: Experimentally-theoretical study.
Supervisor: doc. RNDr. Michal Čajan, Ph.D.

Transition metal complexes with macrocyclic ligand exploitable in the field of molecular magnetism
Supervisor: RNDr. Bohuslav Drahoš, Ph.D.

Photomagnetically active molecular magnets
Supervisor: doc. Ing. Radovan Herchel, Ph.D.

Coordination compounds of f-elements with radical ligands
Supervisor: doc. Ing. Radovan Herchel, Ph.D.

Lanthanide compounds as probes for biological systems
Supervisor: doc. Ing. Radovan Herchel, Ph.D.

Preparation of benzimidazoles and their complexes with the elements of the first transition series
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.

Low dimensional magnetic materials for the study of the magnetocaloric effect based on Copper(II) and Manganese(II)
Supervisor: doc. RNDr. Juraj Kuchár, Ph.D.

Magnetically bistable molecular materials with toroidal magnetic moment
Supervisor: Ing. Ivan Nemec, Ph.D.

Biologically active mono- and heterobimetallic coordination compounds of 4d and 5d metals
Supervisor: Ing. Ivan Nemec, Ph.D.

Coordination compounds showing the magnetic bi- or multistability – materials for new generation of memory devices
Supervisor: doc. Ing. Ivan Šalitroš, PhD.

Field of Study Nanomaterial Chemistry

Synthesis, characterization and applications of new graphene derivatives
Supervisor: prof. RNDr. Michal Otyepka, Ph.D.

Topic for Fischer stipend

Hybrid MOF Materials for Energy Applications
Supervisor: prof. RNDr. Michal Otyepka, Ph.D.

Nanomaterials for catalytic application
Supervisor: prof. RNDr. Radek Zbořil, Ph.D.

Hybrid nanostructures for photoelectrochemical water splitting
Supervisor: prof. RNDr. Radek Zbořil, Ph.D.

Catalytic activity of metal nanoparticles and their composites for applications in energy production
Supervisor: doc. RNDr. Libor Kvítek, CSc.

Theoretical study of charge transport in nanostructures
Supervisor: doc. Ing. Pavel Jelínek, Ph.D.

Chemical and physical properties of molecular nanostructures on surfaces investigated by means of scanning probe microscopy
Supervisor: doc. Ing. Pavel Jelínek, Ph.D.

Theoretical studies of material properties of molecular nanostructures on solid surfaces
Supervisor: doc. Ing. Pavel Jelínek, Ph.D.

Design of novel hybrid functional Graphene@Metal-Organic hybrid porous Materials for energy and environmental applications
Supervisor: Kolleboyina Jaya Ramulu  Ph.D.

Self-organized biopolymer layers and coatings with mineral fillers for special application
Supervisor: Prof. Ing. L. Lapčík, Ph.D.

Nanomaterials for biological applications
Supervisor: doc. Ing. Pavel Jelínek, Ph.D.

Advanced Nanomaterials: Synthesis and Applications in Catalysis, Organic Transformations, Photo (electro) catalysis
Supervisor: doc. Manoj B. Gawande, Ph.D.

Field of Study Organic Chemistry

Design, synthesis and evaluation of selected heterocyclic compounds with potential biological activity
Supervisor: doc. RNDr. Miroslav Soural Ph.D.
Aim of the thesis will be the preparation of novel heterocyclic derivatives designed as ligands of selected biological targets (e.g. specific protein kinases, phosphodiesterases, receptors localized in the CNS etc.). Structural design will be performed on a basis of conventional methods (such as scaffold hopping, molecular modelling) with use of known literature information. Design will be followed by development and optimization of synthetic method, evaluation of biological properties of prepared compounds and structure-activity relationship studies.

Design and synthesis of novel heterocyclic compounds with potent antimicrobial activity
Supervisor: RNDr. Lucie Brulíková, Ph.D.
The aim of this work is design and synthesis of novel heterocyclic compounds with potent biological activity, antimicrobial in particular. Set of compounds will be synthesized employing of solution phase and/or solid phase synthetic approach. Final compounds will be further modified according to biological activity testing. Alternatively, new pharmacophore will be investigated.

Nitrogen-Containing Heterocyclic Compounds: Synthesis, Method Development, Study of Physical-Chemical Properties and Reactivity
Supervisor: doc. RNDr. Petr Cankař, Ph.D.
The PhD thesis will be focused on the synthesis of nitrogen-containing heterocyclic compounds with the potential biological relevance or the development of novel synthetic methods. The prepared compounds will be studied with regard to physical-chemical properties, reactivity, and potential biological activity.

Study of new fluorescent systems for applications in molecular electronics and chemical biology
Supervisor: prof. RNDr. Jan Hlaváč, Ph.D.
Molecular electronics is the field of study focused on research of chemical compounds able to substitute various electronic components.  The main motivation in this research is miniaturization of electronic devices. Although number of chemical compounds has been already described as part of molecular gates operated by change of chemical surrounding and their combination resulted in more complicated circuits, practical applications are very limited from many reasons. One of the most developed application areas is chemical biology, where one of the main aims is the precise detection of significant markers typical for relevant metabolic changes or visualization of targeted drug delivery and releasing.
This topic will be focused on development of quite new molecular electronic components or significant improvement of the already described ones. Application of these molecular electronic devices will be oriented to chemical biology with aim to detect more various analytes (markers) with use of one system. Multianalytical systems will be studied also without a necessity of their molecular electronics nature.

Asymmetric synthesis via Brønsted acid catalysis
Supervisor: RNDr. Jiří Pospíšil, Ph.D.
Over the past two decades, organic synthesis underwent to a significant transformation. Indeed, attempts to find an alternative transformation to well established enantioselective transition metal catalyzed reactions led to generation of new field in organic synthesis – organocatalysis. In this field, organic transformations are catalyzed with small chiral organic molecules. This type of catalysis underwent tremendous development over the past 20 years and has become an integral part of the organic catalytic transformations that are now commonly performed in the laboratories of synthetic and medicinal chemists. Many of these reactions are catalyzed by Brønsted acids. In terms of the pKa, acids generally employed in organocatalytic reactions can be divided into two main groups: weakly acidic (pKa => 10), also called hydrogen bonding catalysts, and stronger Brønsted acids (typically pKa = <3). Surprisingly, the acid catalyzed transformations using acids with pKa ranging from 3 to 10 were till recently completely ignored. Interestingly, such pKa window covers all carboxylic acids. In the past 5 years, however, the use of chiral carboxylic acids to catalyze organic transformation started to flourish. However, with results far beyond expectation. We believe that the reason for disappointing results is due to somewhat more difficult spatial control (and the associated enantioselectivity of the reactions) connected with the carboxylic acid hydrogen. The goal of this project is to develop novel chiral Brønsted acids that bear hydrogen atom with pKa like carboxylic acid, but do not have carboxylic group. The second goal is to develop organocatalytic reactions that would be catalyzed by such acids.

Development of new synthetic methods based on the chemistry of heterocyclic sulfides, sulfoxides and sulfones
Supervisor: RNDr. Jiří Pospíšil, Ph.D.
The search for new biologically active substances that would serve as molecular probes to study the biological processes, is one of the main topics of chemical biology. But to find such a molecular probe - a small organic molecule - that would allow us to understand the studied biological processes, it is very difficult and it turns out to be a real challenge even at the onset of 21st century. Seemingly, this search reminds a well-known "search for a needle in a haystack". One of the answers chemists and biologists to this challenge is the preparation of structurally diverse chemical libraries of organic molecules. Thus, simple, short and stereo and regioselective synthesis of structurally diverse molecules that would start from ideally one commercially available organic molecule belongs to one of the top priorities of modern synthetic chemistry. The aim of this PhD topic is to develop sulfide, sulfoxide and sulfone-based synthetic methods and procedures that would allow us to constitute large chemical libraries containing structurally diverse molecules in selective and rapid (2 to 4 steps) manner.

Field of Study Physical Chemistry

Topic for Fischer stipend

Graphene and Graphene Derivatives
Supervisor: prof. RNDr. Michal Otyepka, Ph.D.

Topic for Fischer stipend

Advanced nanomaterials for heterogeneous catalysis, photocatalysis and electrocatalysis
Supervisor: prof. RNDr. Radek Zbořil, Ph.D.

Topic for Fischer stipend

Hybrid nanostructures for photoelectrochemical water splitting
Supervisor: prof. RNDr. Radek Zbořil, Ph.D.

Molecular Simulations of Biomembrane Systems
Supervisor: doc. RNDr. Karel Berka, Ph.D.

Theoretical study of charge transport in nanostructures
Supervisor: doc. Ing. Pavel Jelínek, Ph.D.

Chemical and physical properties of molecular nanostructures on surfaces investigated by means of scanning probe microscopy
Supervisor: doc. Ing. Pavel Jelínek, Ph.D.

Topic for Fischer stipend

Structure and Dynamics of RNA
Supervisor: prof. RNDr. Jiří Šponer, DrSc.

Topic for Fischer stipend

Origin of Life Theory – Studies of Prebiotic Chemical Reactions
Supervisor: prof. RNDr. Jiří Šponer, DrSc.

Multiscale Modeling of Nucleic Acid
Supervisor: prof. RNDr. Jiří Šponer, DrSc.

Computer Science

Field of Study Computer Science

Relational data analysis
Supervisor: prof. RNDr. Radim Bělohlávek, DSc.
The goal is to develop new methods and algorithms for relational data analysis, particularly for discovery of clusters a concepts in data, dependencies in data, factorization and dimensionality reduction of data. This also involves exploration of time complexity of selected problems and proposed algorithms, and testing of the methods and algorithms on data.

Verification problems: algorithms, complexity, experiments
Školitel: doc. RNDr. Petr Jančar, CSc.
In the area of automated verification of behavioural properties of (software and hardware) systems there are various problems whose computational complexity has not been sufficiently clarified so far. The aim of proposing this topic is to attract a student to this area, possibly within a running project of the Czech Grant Agency; the research effort can be directed at a theoretical and/or an experimental part.

Earth Sciences

Field of Study Geoinformatics and Cartography

Managing diverse data sources for complex visualization of urban areas
Supervisor: Prof. RNDr. Vít Voženílek, CSc.
The thesis aim is to identify all data sources of the selected urban area, to integrate its data in the most suitable environment for remote data management and to prepare them for all-embracing visualization. The thesis will result in innovative knowledge about data management for comprehensive cartographic production. The main outputs will consist of analysis of data sources, data model, templates for cartographic visualization and map outputs in printed and digital form.

Spatial evaluation of walkability
Supervisor: Doc. Ing. Zdena Dobešová, Ph.D. 
The structure and layout of the urban environment significantly affects the walkability of the population. The automatic processing of spatial data in GIS enables the assessment of the level of walkability. Different views and possibilities of automatic spatial data processing will be the aim of the dissertation research.

Visual programming for spatial data processing
Supervisor: Doc. Ing. Zdena Dobešová, Ph.D. 
Visual programming in GIS is a straightforward method of designing spatial data processing workflows in a graphical form.  The aim of work is a research of cognition and functional aspects of visual languages. Improvements in graphical notation and functionality of visual languages have the potential for wider usability of workflows in GIS.

Urban Simulation Models and their Applications in Spatial Planning
Supervisor: Doc. RNDr. Jaroslav Burian, Ph.D.
The aim of this thesis is to explore the possibilities of application of selected urban simulation models in spatial planning. The work will focus mainly on selected microsimulation model(s) enabling to predict selected aspects of urban systems (e.g. land prices, jobs, household distribution or population movement). Significant part of the work will be devoted to the preparation of suitable datasets that are difficult to obtain in many countries or are available at insufficient detail. Advanced possibilities of spatial data collection and processing including aggregation and disaggregation procedures will be used for this purpose. With respect to the selected model(s) and the selected area, several case studies will be conducted to elaborate possibilities of application of micro-simulation modeling in spatial planning.

Spatial continuity of statistical data in cross-border areas
Supervisor: Doc. RNDr. Jaroslav Burian, Ph.D.
The aim of this thesis is to focus on spatial continuity of selected social and economic phenomena in cross-border areas. The work will focus mainly on the identification and analysis of spatial patterns using advanced statistical and geoinformation methods. For this purpose, a tool (e.g. script, model, extension) will be created to allow for automatic evaluation of continuity, clusters, differences and spatial patterns. An important part of the work will be the selection and processing of appropriate datasets, which vary from country to country in detail, timeliness, method of processing and their availability. The work will be solved with an emphasis on the Czech borderland with the potential of transfer of acquired knowledge and all cross-border areas in Europe.

Field of Study Geological Sciences

Topic for Fischer stipend

Sequence-stratigraphic framework and hydrocarbon potential of stylolite distribution in Upper Cretaceous Kometan Formation, western Zagros, Iraqi Kurdistan
Supervisor: Prof. Mgr. Ondřej Bábek Dr.
Co-supervisor: prof. Howri Mansurbeg, Soran, Kurdistan Region of Iraq
The Kometan Formation (Turonian – Campanian), which is a prospective carbonate reservoir for oil and gas of northern Iraq, is composed of fractured, fine-grained, foraminifer-rich carbonate sediments deposited in shallow-water shelf and open marine to pelagic settings. Depositional facies of the formation are arranged into three stratigraphic units with variable lithology and siliciclastic admixture as indicated by gamma-ray logs. Porosity and permeability are controlled mainly by fracture distribution and modified by pressure dissolution features, particularly stylolites, which may represent potential conduits for hydrocarbon migration. The content of detrital minerals in the carbonate successions is largely controlled by the extent of terrestrial input into marine realm versus biologic carbonate production, both being strongly affected by relative sea-level fluctuations and climate. Pressure dissolution may show preferential occurrence at sequence-stratigraphic surfaces with high- or contrasting detrital contents, such as the maximum flooding surface, maximum regression surface or basal surface of forced regression. Thus, primary signals including sea-level changes may affect the reservoir quality. The aim of this project is to: (i) map the distribution of stylolites in outcrop sections of the Kometan Formation in the High-Folded Zone of western Zagros, Iraqi Kurdistan (Dokan and Sulaimani areas); (ii) link the distribution of stylolites to the sequence stratigraphic framework based on facies and microfacies analysis, outcrop gamma-ray- and magnetic susceptibility logging; (iii) correlate the outcrop data with wire-line logging data (gamma-ray, caliper, neutron, density, image log, ...) from the Taq Taq, Kikruk and related oil-fields of the Low-Folded Zone; and (iv) assess the potential role of stylolites as hydrocarbon conduits based on a detailed petrologic study of thin sections. The project will combine outcrop data collection with microscopic techniques, bulk elements geochemistry, petrophysics a microchemistry (electron microprobe). The project will be based on instrumental equipment and facilities of the Department of Geology, UP Olomouc (gamma-ray spectrometer, laboratory kappa-bridge, optical, CL- and fluorescence microscopes, energy-dispersive and wave-dispersive XRF analysis of bulk sediment samples, and electron microprobe analyses of key diagenetic phases with EDX, WDX analysis).

Topic for Fischer stipend

Dam reservoirs and ponds as archives of historical anthropogenic contamination in Upper Silesia urban agglomeration (Czechia, Poland)
Supervisor: Prof. Mgr. Ondřej Bábek Dr.
Sedimentary infills of dammed reservoirs represent an important environmental and economic issue due to the limited life time of reservoirs, costs related to dredging and further management of contaminated reservoir sediments. Simple prediction models of reservoir infill are difficult to achieve due to a high number of factors that influence the sediment accumulation rates. Site-specific data such as erosion rates in the river catchment, grain size characteristics of the sediment load and the bottom morphology are usually needed in such an effort while, in general, little is known about the depositional architecture of reservoir lakes sediments.
Dam reservoirs and historical ponds in the urban agglomeration of Ostrava and surrounding cities in Upper Silesia in the Odra River catchment offer a unique case to study the long-term effects of pollutant accumulation in a highly industrial landscape subject to long-term anthropogenic pollution. This project will focus on quantitative stratigraphic analysis and inorganic and organic geochemistry of sediment cores from water reservoirs along the Odra River in Czechia (Bezruč, Kukla, Heřmanický r., Vrbické j., Kališovo j.) and Poland (Roszków, Staw Syrinski, Babiczak). The project´s aim will be deciphering history of anthropogenic contamination, separating of background geochemical signals from anthropogenic signals and deciphering the spatial dispersal of pollutants in the lakes and on the catchment scale.
The project will rely on bathymetric mapping of reservoir bottom, geophysical imaging of sediment architecture using ground penetrating radar (GPR) a sub-bottom profiler, drilling of sediment cores and analysis of sediment grain size, inorganic and organic geochemistry and analysis of sediment accumulation rates using 137Cs dating. Results will be published in peer-reviewed journals (WoS)

Tracing of Medieval and modern iron smelting based on magnetic contamination of the Moravian Karst environment
Supervisor: doc. RNDr. Jaroslav Kadlec, Dr., Geofyzikální ústav AV CR
Co-supervisor: doc. RNDr. Eduard Petrovský, CSc., Geofyzikální ústav AV CR
Research is focused on detailed assessment of pollution related to the iron ore smelting at the Moravian Karst between 8th and 19th centuries. Both surface (soils) and subsurface (clastics and speleothems) sedimentary archives accumulate pollution particles including specific microspherules formed during the smelting processes. The pollution record will be examined in detail using spectrum of analytical approaches namely mineral magnetic techniques combined with geochemical, mineralogical, and sedimentological methods. Results will yield a new insight how the pollution record preserved in soil archives are vulnerable due to post-depositional changes in comparison with calm cave environment. Except of temporal and spatial pollution reconstruction of different contamination rates a new model of the near surface wind directions will be proposed based on distribution of the magnetic particles. The study will also improve our knowledge about negative human impacts to the local environmental history thru e.g. forest clearance (triggering soil erosion) closely related to the iron smelting. Results will be disseminated in scientific journals (two IF papers at least) and on meetings.

Origin and evolution of anastomosis of the Morava River: geophysical and geomorphologic analysis
Supervisor: Prof. Mgr. Ondřej Bábek Dr.

Side stepping the Andesite density-viscosity trap
Supervisor: Dr. Graham Hill, Institute of Geophysics CAS
Andesite, with a silica content between basalt and rhyolite, is the dominant volcanic rock type found in subduction zones globally and represents the average composition of continental crust. As such, the generation of andesite assumes great importance in relation to volcanic hazard and the formation of andesite-hosted economic minerals. Thus it is of more than academic interest how, when, and where andesite volcanoes form. Andesites have been interpreted as resulting from crystal fractionation, a mixing origin between end member compositions (basalt and rhyolite), or direct melting of the mantle or subducting slab (i.e. unconnected to either basalt or rhyolite). Recently, the debate has focussed on two mechanisms for andesite formation production: the prior crystal-liquid segregation of mantle derived basalt melt over large time periods; or that andesitic magmas are formed only days before eruption by mixing a deep originating basaltic magma with a rhyolitic magma resident at crustal depths.
If andesite and dacite melts are produced via liquid crystal segregation, large volumes of mafic parental melts must be accommodated likely via significant crustal under-plating or as crustal cumulates. In this mechanism for generation of andesite melt, the difficulty is how to extract a viscous liquid from the fluid crystal mush zone. While the mixing generation model for andesite implies that liquids of andesitic composition are not common in crustal magma reservoirs, the two parental magmas (basalt and rhyolite) are rarely found as eruptive products in association with andesite volcanoes. In this model it is argued that the parent magmas are prevented from erupting by their contrasting densities and viscosities; the higher-density, low-viscosity basaltic magma is trapped beneath a blanket of low-density high-viscosity rhyolitic magma that is too viscous to erupt.
How can this model be reconciled with the need for thorough, but rapid mixing? The geometry of the magmatic system is the missing factor needed to complete the model. Magnetotellurics (MT) is the method with the strongest chance of providing the missing geometry and structure. A new MT data set will be obtained for the Katmai Group in Alaska a system known to have recently extruded both the parental magmas and andesite eruptive products. The MT data will be co-located with existing passive-seismic data. The co-located data sets will enable direct comparison of highly complementary physical properties, allowing identification of both lithological boundaries and the presence of thermally elevated fluid/melt zones.
The end member geometries will be tested by constructing 3D images from the magnetotelluric survey (resistivity model) that can be compared to ongoing seismic monitoring efforts and petrological/geochemical work. The Katmai group is unique in having recent concurrent andesitic and rhyolitic volcanism occur in close proximity: the largest rhyolitic (ignimbrite forming) eruption of the 20th century occurred in 1912 from the Novarupta vent at the centre of the Katmai group of Andesitic cone volcanoes.

Mathematics

Field of Study Algebra and Geometry

Aggregation operators on lattices and posets
Supervisor: Prof. Mgr. Radomír Halaš Dr.

Special diffeomorphisms of differentiable manifolds
Supervisor: Prof. RNDr. Josef Mikeš DrSc.

Residuated structures
Supervisor: Doc. Mgr. Michal Botur Ph.D.

Divisible residuated po-monoids and their subreducts
Supervisor: Doc. RNDr. Jan Kühr Ph.D.

Field of Study Applied Mathematics

Regression models with complex structure
Školitel: Doc. RNDr. Eva Fišerová, Ph.D.
Regression models are typically used to understand better the relationships between different dependent (target) and explanatory variables. The aim of the dissertation is the development of suitable statistical methods and algorithms mainly focused on statistical modelling when the variables are interrelated by complex functional relationships and have a complex variation structure. The emphasis will be given both on theoretical aspects concerning estimation, uncertainty and statistical inference, as well as practical implementation and computational feasibility.

Functional data analysis using Bayes spaces
Školitel: Doc. RNDr. Karel Hron, Ph.D.
Functional data analysis of probability density functions needs to reflect specific properties of these objects carrying relative information. For this purpose the Bayes space methodology was developed which provides a flexible framework for statistical processing of densities. Aim of the dissertation is to develop methods for a comprehensive statistical analysis of density functions as well as to generalize the related concepts.

Compositional data analysis in the era of Data Science
Školitel: Doc. RNDr. Karel Hron, Ph.D.
The Data Science era assumes dealing with complex data sets composed of various types of objects which should be processed by respecting their specific nature wrt. domain and scale, i.e., discrete and continuous variables with multivariate of functional character carrying essentially either absolute or relative information. For processing of relative data a general framework is provided by the Bayes space methodology which includes also the logratio approach to compositional data analysis. Aim of the dissertation will be to develop original methods using up-to-date approaches of statistical learning for processing of complex data sets containing objects (variables) carrying relative information.

Field of Study Mathematical Analysis

Physics

Field of Study Applied Physics

Analysis of cosmic ray events at the highest energy
Supervisor: prof. Miroslav Hrabovský, DrSc.
Consultants: RNDr. Petr Trávníček, Ph.D., Ing. Jakub Vícha
Pierre Auger Observatory is the largest experimental apparatus in the field of astroparticle physics. Particles with energies larger than that of the LHC beams are detected by the array covering 3000 square kilometres in the Argentinian pampa. These cosmic particles originate in yet unknown sources in the Universe. The Aim of the Observatory is to measure the energy spectrum, direction of the incoming particles and answer the question about  their chemical composition.
New analysis techniques at the Observatory will be developed by the student as well as new emerging detection techniques of cosmic rays will be investigated.

Optical detecting systems for cosmic radiation – selected questions 
Supervisor: prof. Miroslav Hrabovský, DrSc.
The topic is concentrated on the study of current optical detectors of cosmic radiation, participation in some of current international scientific projects of cosmic-ray research and participation at the research of new particular types of optical detectors of cosmic radiation, including participation in the scientific part of a related international collaboration.

Analysis of characteristics of parametric down-conversion 
Supervisors: doc. RNDr. Ondřej Haderka, Ph.D., doc. RNDr. Jan Peřina, Ph.D.
Simulation and testing of spontaneous parametric down-conversion, correlation measurement using photon-counting techniques as well as by classical intensity measurement.

Photocount statistics and its measurement in nonlinear optical processes
Supervisor: doc. RNDr. Jan Peřina, Ph.D.
Theoretical models of photocount statistics arising in different nonlinear optical processes will be studied. Special attention will be paid to parametric processes. Characteristics of the obtained fields will be discussed with respect to measurement.

Photon-pair generation in metal-dielectric photonic structures
Supervisor: doc. RNDr. Jan Peřina, Ph.D.
Properties of photon pairs in metal-dielectric layers will be studied, especially spectral and timing characteristics and quantum correlations of the photons in a pair. Special attention will be devoted to intense generation of pairs in metal layers.

Characteristics of parametric processes in nonlinear periodically-poled media
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Space beam properties. Study of efficiency of various processes. Optimization of generation of frequency down-conversion.

Quantum information processing with correlated photon pairs
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Arrangement, processing and detection of special light states of single photon level. An interference of the second and fourth order is utilized in the experiments

Testing modern materials using optical spectroscopic methods
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Measurement of absorbance, fluorescent and time-resolved fluorescent spectra of carbon, metal and metal-oxide nanostructures. Development of appropriate methods.

Analysis of cosmic gamma ray events in the CTA experiment
Supervisor: RNDr. Karel Černý, Ph.D.
The Cherenkov Telescope Array Observatory (CTAO or CTA) is going to be the largest and technically most advanced ground-based  facility for detection of high-energy cosmic gamma rays. CTA will be located at both the southern and norther hemisphere. Both locations will be equipped with three types of telescopes covering three ranges of energies of the incoming gamma photons. The ultimate sensitivity will span energies from 20 GeV to 100 TeV. The detection principle is based on detection of Cherenkov light in the telescopes generated by charged particles traversing a medium with a speed greater than the actual speed of light in the given medium, i.e. in atmosphere. The charged particles are created in cascades of interactions whose onset is the primary interaction of the incoming gamma photon with atoms in the atmosphere. The envisaged work is supposed to cover the tasks of analysis and interpretation of the measured data. The primary task of CTA is to measure the energy spectrum and distribution sources of the gamma photons.

The fluorescence telescope for future FAST telescope array.
Supervisor: Mgr. Dušan Mandát, Ph.D.
Consultants: Mgr. Miroslav Pech, Ph.D., Dr. Toshihiro Fujii
The Fluorescence detector Array of Single-pixel Telescopes (FAST) is an R&D project devoted to the development of a low-cost fluorescence detector telescope, which could provide inexpensive hybrid coverage for existing experiments, such as the Pierre Auger Observatory and Telescope Array experiment, and serve as a proof-of-concept for future large-scale Ultra-High Energy Cosmic Ray (UHECR) observations. The aim of this work will be focused on the analysis of data from the current FAST prototypes, optical simulations, and future giant array optimization.

Complete characterization of strip silicon detectors developed for the ATLAS Inner Tracker by using testbeams and computer simulations
Supervisor: RNDr. Karel Černý, Ph.D.
The Large Hadron Collider accelerator at CERN will be upgraded to the High-Luminosity Large Hadron Collider (HL-LHC) machine between 2024 and 2027. The instantaneous luminosity of the HL-LHC will reach 7×1034 cm-2s-1, corresponding to an average of 200 inelastic proton-proton collisions per bunch crossing, and the total integrated luminosity delivered to the ATLAS experiment will be higher than 4000 fb-1. Parameters of the HL-LHC accelerator thus imply high requirements on radiation hardness, granularity, as well as the speed of data transfer and data processing of the inner tracking detector. The current inner detector of the ATLAS experiment will be replaced by the completely new all-silicon Inner Tracker (ITk), which will consist of pixel and strip silicon detectors. The main topic of this doctoral thesis is a detailed characterization of detection properties of strip silicon detectors developed by the ATLAS ITk collaboration. This characterization will be performed by using testbeams of ultrarelativistic electrons and hadrons at DESY II and CERN SPS synchrotrons using the EUDET beam Telescope built from several pixel silicon detectors located in front of and behind of the tested sample. The recorded experimental data will be compared to outputs of computer simulations prepared in Allpix Squared and Athena simulation frameworks which provide libraries to simulate a complete testbeam experiment, starting from the calculation of energy deposited by a charged particle passing through the silicon sensor to the signal digitization in individual readout channels.

Field of Study Biophysics

All topics for Fischer stipend

Ultra-weak photon emission in plant and animal cells
Supervisor: doc. RNDr. Pavel Pospíšil, Ph.D.
Ultra-weak photon emission originates from oxidative metabolic processes in microbial, plant and animal cells. Electronically excited species (triplet excited carbonyls and singlet oxygen) formed during the oxidative metabolic processes are responsible for the ultra-weak photon emission. Role of reactive oxygen species in oxidation of lipids and proteins will be studied in plant and animal cells.

Noble metal nanoclusters for dual imaging
Supervisor: doc. RNDr. Karolína Machalová Šišková, Ph.D.
Composite nanomaterials consisting of a biocompatible organic component and a functional inorganic component are frequently investigated and in several cases already employed in praxis, e.g. in catalysis and/or imaging. Nanoclusters containing tens to hundreds of noble metal atoms are sort of a size interconnection between atoms and nanoparticles; their properties are considered as molecule-like. The aim of this PhD thesis is the experimental preparation of new bimetallic and trimetallic nanoclusters, their characterization and testing of their interactions with cells (the latter in collaboration with Institute of Clinical and Experimental Medicine in Prague).

Investigation of mastitis in bovines using an electrochemical method
Supervisor:  Ankush Prasad, M.Sc., Ph.D.
Currently, the somatic cell count (SCC) is widely used as a method for monitoring of mastitis. When the number of somatic cells in bovine milk reach a threshold, it is believed to be an indicator of mastitis. Dairy farmers need to send bovine milk to laboratories to perform this inspection because the SCC device is large and expensive. Therefore, it is time-consuming and at the same time does not provide the real-time measurement. In the current program, we plan the development of a detection method using an electrochemical method, which is projected to be small and cost-effective. The device will be based on evaluation of respiration activity reflected by oxygen reduction current of somatic cells in bovine milk.

Characterization of reactive oxygen species (ROS) generation in human cells
Supervisor:  Ankush Prasad, M.Sc., Ph.D.
Immune cells in our body undergoes phagocytosis as a response to invasion by foreign body. During this, monocyte and neutrophil are known to produce reactive oxygen species (ROS). The ROS generated in animal cells are known to be involved in several diseases and ailments, when generated in excess. Thus, if the ROS generated can be measured and analysed precisely, it can be utilized in immune function evaluation and detection of diseases. The current project is aimed to perform localization of various ROS such as superoxide anion radical, hydrogen peroxide, hydroxyl radical and singlet oxygen formed in human cells spontaneously and during stress using confocal laser scanning microscopy. The results will be validated using another method.

Field of Study Optics and Optoelectronics

All Topics for Fischer stipend

Advanced manipulation and detection of optical beams
Supervisor: prof. Mgr. Jaroslav Řeháček, Ph.D.
Spatial degrees of freedom of light will be mastered for the purpose of metrology and  information processing. Mode sorters will be designed and realized experimentally based on spatial light modulation principles with the idea of implementing efficient projective measurements on the spatial modes of light on demand. Mode sorters will be utilized in optical processing of information, preparation of special states of light, and super-resolution imaging.

Quantum detection and estimation in optical metrology
Supervisor: prof. Mgr. Jaroslav Řeháček, Ph.D.
Fundamental limits of imaging and metrology will be investigated. Inspired by quantum theory of detection and estimation, novel theoretical and experimental protocols and estimation techniques will be proposed for achieving the ultimate resolution limits compatible with the laws of physics. Potential applications are in observational astronomy, spectroscopy, microscopy, calibration of photo-lithography systems operating in DUV and improved wafer inspection.

Optimization of the UV Raman spectrometer with excitation wavelength in the range 206.5 – 250 nm
Supervisor: RNDr. Josef Kapitán, Ph. D.
Resonance enhancement is one way to increase sensitivity of Raman spectroscopy as an analytical technique used in many applications, one of which is the study of the structure of peptides and proteins. A very active and open topic in recent years is also the study of the properties of chiral molecules using resonance Raman optical activity. The dissertation thesis will focus on the optimization of the Raman spectrometer with excitation wavelengths in the range of 207-250 nm, especially with regard to the expansion of the spectrometer for precise polarization measurements. The developed equipment will become the basis for experiments in the field of Raman spectroscopy and Raman optical activity, both in applied (study of conformational and dynamic behavior of biomolecules in solution) and fundamental research (study of electron and vibrational molecular structure).

Quantum tomography in phase space
Supervisor: prof. RNDr. Zdeněk Hradil, CSc.
The objective of the proposed research is to analyse non-traditional regimes of phase sensitive  optical methods allowing to determine  full quantum state.  The associated research may focus either on analytical issues or on the  possible experimental realizations of feasible optical schemes.  Theory part  is closely intertwined with the quantum theory of detection related to approximate simultaneous detection of non-commuting variables.

Control of nonclassical light emission from trapped ion strings
Supervisor: Mgr. Lukáš Slodička, Ph.D.
All practical applications of trapped ions as nonclassical light sources are strongly challenged by the effectively small collection and absorption efficiencies of light from single trapped ions in free space. The thesis will focus on the development of the nonclassical light sources which will attempt to overcome this limitation by combining several unique properties of trapped ions, in particular the purity of the single photon emission, the possibility of the deterministic control of their collective internal states, and the sub-wavelength localization. It will include the realization of novel ion trapping apparatus which will allow for exploitation of the deterministic control of internal states of trapped ions for the efficient control of the direction and collection efficiency of emitted fluorescence. The proposed experimental setup would represent a feasible and broadly applicable architecture for controlling the light emission from atoms in free space applicable for construction of quantum communication networks and fundamental tests of light-atom interaction.

Field of Study Nanotechnology

Structural changes of materials induced by swift heavy ions irradiation
Supervisor: doc. RNDr. Jiří Pechoušek, Ph.D.

Analysis of characteristics of parametric down-conversion 
Supervisors: doc. RNDr. Ondřej Haderka, Ph.D., doc. RNDr. Jan Peřina, Ph.D.
Simulation and testing of spontaneous parametric down-conversion, correlation measurement using photon-counting techniques as well as by classical intensity measurement.

Photocount statistics and its measurement in nonlinear optical processes
Supervisor: doc. RNDr. Jan Peřina, Ph.D.
Theoretical models of photocount statistics arising in different nonlinear optical processes will be studied. Special attention will be paid to parametric processes. Characteristics of the obtained fields will be discussed with respect to measurement.

Photon-pair generation in metal-dielectric photonic structures
Supervisor: doc. RNDr. Jan Peřina, Ph.D.
Properties of photon pairs in metal-dielectric layers will be studied, especially spectral and timing characteristics and quantum correlations of the photons in a pair. Special attention will be devoted to intense generation of pairs in metal layers.

Characteristics of parametric processes in nonlinear periodically-poled media
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Space beam properties. Study of efficiency of various processes. Optimization of generation of frequency down-conversion.

Quantum information processing with correlated photon pairs
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Arrangement, processing and detection of special light states of single photon level. An interference of the second and fourth order is utilized in the experiments

Testing modern materials using optical spectroscopic methods
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Measurement of absorbance, fluorescent and time-resolved fluorescent spectra of carbon, metal and metal-oxide nanostructures. Development of appropriate methods.

Contacts

Faculty of Science, Palacký University Olomouc
Student Affairs Office
17. listopadu 1192/12
779 00 Olomouc
+420 585 634 010-14
+420 585 225 737
studijni.prf@upol.cz

 

Contact person for foreign students:

Dana Gronychová
dana.gronychova@upol.cz
+420 585 634 058
Room no. 1.005, ground floor next to the reception. Please, respect the office hours!