Framework thesis topics for the academic year 2024/2025

Important note: You can already register in the online application and fill out your personal data. However, submitting the application is possible only by choosing and applying for a particular thesis topic upon which you have previously agreed with the topic's supervisor.

The topics will be continuously updated in the electronic application. Ask about that your potential supervisor. When your chosen topic, confirmed by the supervisor, appears in the application, you can apply for it and submit your application.

Biology, Ecology and Environmental Sciences

Study programme Botany

Mechanisms of the evolutionary adaptations of cyanobacteria
Supervisor: doc. Mgr. Petr Dvořák, Ph.D.
Cyanobacteria belong to the most important primary producers thriving in all environments with sufficient light intensity for billions of years. They inhabit extreme environments such as desert soils, therefore, they are adapted to broad temperature fluctuation, high UV radiation, and drought stress. With climate change, the drylands are expanding, and the importance of cyanobacteria rise. The PhD project will be focused on the investigation of the transcriptome and epigenome response to these stresses (e.g. drought stress) in several species of cyanobacteria. The transcriptome of the strains will be sequenced by short reads using Illumina. Furthermore, the PhD student will use third-generation sequencing (PacBio or Oxford Nanopore) to reconstruct epigenomic profiles in several related species of cyanobacteria. The epigenomic profiles will be investigated at the population and species levels. The expression profiles will be connected with phenotype, epigenome, and genome diversity. Altogether, the result will provide evidence for the role of adaptation, selection, and environment in the speciation of cyanobacteria.

The evolution of cyanobacterial genome and epigenome
Supervisor: doc. Mgr. Petr Dvořák, Ph.D.
Cyanobacteria belong to the most important primary producers thriving in all environments with sufficient light intensity around the globe. They inhabit extreme environments such as desert soils, therefore, they are adapted to broad temperature fluctuation, high UV radiation, and drought stress. With climate change, the drylands are expanding, and the importance of cyanobacteria rise. The PhD student will use third-generation sequencing (PacBio or Oxford Nanopore) to reconstruct epigenomic profiles in several related species of cyanobacteria. The epigenomic profiles will be investigated at the population and species levels. They will be connected with expression profiles, phenotype, stress response, and environmental conditions. Together, all these approaches will provide evidence for the role of epigenetic modification in the speciation and adaptation of cyanobacteria.

Study programme Ecology

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

Predicting the tick-borne disease risk using rodent host abundances and large-scale climate variability
Supervisor: prof. MVDr. Emil Tkadlec, CSc.

Landscape epidemiology of tick-borne pathogens
Supervisor: doc. RNDr. Tomáš Václavík, Ph.D.

Field size and farmland biodiversity in high-intensity agricultural landscapes
Supervisor: doc. RNDr. Tomáš Václavík, Ph.D.

Soil invertebrates invading buildings - protection against them
Supervisor: doc. RNDr. Mgr. Ivan Hadrián Tuf, Ph.D.

Terrestrial isopods outside soil environment - their activity on walls and trees
Supervisor: doc. RNDr. Mgr. Ivan Hadrián Tuf, Ph.D.

Indicators of soil quality in connection with its degradation, especially by erosion processes
Supervisor: prof. Dr. Ing. Bořivoj Šarapatka, CSc.

Land use optimization from the point of view of erosion and biodiversity of the landscape
Supervisor: prof. Dr. Ing. Bořivoj Šarapatka, CSc.

Life cycle of mosquitoes in floodplain forest pools
Supervisor: doc. RNDr. Martin Rulík, Ph.D.

Population dynamics of amphibians in urban environments
Supervisor: doc. RNDr. Martin Rulík, Ph.D.

Study programme Experimental Biology

Multi-phytohormone analysis in different Ri plants
Supervisor: prof. Mgr. Ondřej Novák, PhD.

TOPICS FOR FISCHER STIPEND

Cancer Chemopreventive Potential of Edible Fruits
Supervisor: Dr. Lutfun Nahar PhD. MRSC. FHEA

Cancer Chemopreventive Potential of Common Vegetables
Supervisor: Dr. Lutfun Nahar PhD. MRSC. FHEA

Mass spectrometry Imaging-based hormonomics analysis for plant stress  studies
Supervisor: Mgr. Karel Doležal, Dr., DSc.

Developing mass spectrometry imaging-based hormonomics methods for  plant tissue imaging
Supervisor: Mgr. Karel Doležal, Dr., DSc.

Non-canonical regulation of cytokinin signaling pathway in Arabidopsis
Supervisor: Mgr. David Zalabák, PhD.

Study of methionine metabolism and related compounds in plants
Supervisor: Mgr. Michal Karady, PhD.

Study programme Zoology

Systematics and phylogeny of selected groups of Central American herpetofauna
Supervisor: Doc. RNDr. Mlan Veselý, Ph.D.

Ecological and evolutionary relationships of tropical insects
Supervisor: Mgr. Milan Janda, Ph.D.

Physics

Study programme Applied Physics

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 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.

Damage of materials induced by nanosecond particle bunches
Supervisor: prof. Jan Řídký, DrSc.
Laser-driven particle-acceleration experiments produce high luminosity particle bunches of nanosecond lengths. The aim of the thesis is to inspect mechanisms of damage induced in materials due to the interaction with such a short-time bunched particles.

Exclusive processes as a road to New Physics
Supervisor: Mgr. Marek Taševský, PhD. DSc.
Consultant: RNDr. Karel Černý, Ph.D.
Standard model is extremely successful in describing interactions of elementary particles, nevertheless there are areas that it is not able to explain, that's what we call New Physics. Signals of New Physics are also seen in the so-called exclusive processes. They occur scarcely nevertheless background to them is well under control. The student will get familiar with forward and diffraction physics at large experiments on large colliders of particles, and also with detection techniques and generating artificial (Monte Carlo) events. Emphasis on the former or latter will be decided upon with the supervisor. Stays at CERN are foreseen.

Experimental physics, thin film deposition
Supervisor: RNDr. Zdeněk Hubička, Ph.D.
The content of the topic is the study of physical processes in plasma using various selected experimental physical methods. These measurements will be performed in reactive low-temperature plasma, which is intended for the deposition process of various selected types of thin films with defined physical properties. As the main diagnostic systems for measuring plasma parameters, systems that are not affected by being covered with a thin semiconductor or electrically insulating thin film will be chosen. Also, the studied reactive plasma will not be time constant, but will be time variable or pulsed. Therefore, high-frequency measurement methods with time resolution will mostly be used. The aim will be to understand the physical processes in the plasma using the mentioned experimental methods and their influence on the parameters of the resulting deposited thin films.

Analysis of characteristics of parametric down-conversion 
Supervisor: prof. RNDr. Ondřej Haderka, Ph.D.. / prof. 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: prof. 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.

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.

Quantum correlations in multi-mode optical fields generated in the process of spontaneous parametric down-conversion
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Quantum correlations in photon numbers of multi-mode optical fields originating in the process of spontaneous parametric down-conversion, that generates photons in pairs, and prepared by further manipulations (e.g. postselection) will be studied. Quantification of the quantumness of such correlations, striking features of these correlations as they exhibit in physically interesting quantities and their application potential will be addressed. Theoretical models appropriate for these fields will be developed and compared witht he experimental data, This will allow us  to determie the practical potential of these  fields in various applications including metrology. The topic may be extended to include the experimental part.

Noclassical properties of simple PT-symmetric quantum systems described using methods of quantum statistical physics
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Simple quantum PT-symmetric and generalized systems like two- and more-level atoms and multi-mode optical bosonic systems will be studied from the point of view of their nonclassical properties. The analyzed systems will be described by Liouvillians and attention will be paid to their asymptotic behavior. Exceptional points are the striking features of PT-symmetric systems. At these points, the system behavior qualitatively changes, which may be used, e.g., for increasing sensitivity of quantum measurements. We will identify the exceptional points of analyzed systems including their degeneracies and study the behavior of system nonclassicality close to these points. We will look for suitable applications that expoint the striking properties  of the analyzed systems.

Study programme Biophysics

Detection of voice disorders from clinical high-speed videokymographic videos and electroglottographic signals with the help of machine learning
Supervisor: prof. RNDr. Jan Švec, Ph.D. et Ph.D.
The work will be devoted to the analysis and classification of clinical records of patients with voice disorders using machine learning. It will explore a database of more than 1,000 records including diagnostic information along with synchronized videokymographic and electroglottographic recordings of vocal fold oscillations and sound. It will aim at relating different types of vocal fold oscillation disorders to different types of voice disorders. Within the analysis, there will be the need of separating the parts of the recordings where phonation and respiration occur, recognizing the location of the kymographic line recording the vocal fold vibrations, identifying whether the images are properly focused, and classifying the type of vibration disorder. The work is conceived as a basis for automatic functional diagnosis of voice disorders.

Studies of voice production using physical, mathematical and biological models
Supervisor: prof. RNDr. Jan Švec, Ph.D. et Ph.D.
Physical, mathematical and biological models provide the most detailed insight into voice production mechanisms. This work will involve studies of biological models of excised larynges, where the oscillatory movements of the vocal folds and of the mucosal waves will be investigated. These movements will then be parameterized and simulated within the framework of artificial silicone and mathematical models of vocal folds, so that they correspond to the characteristics of the vibration of real vocal folds as closely as possible.
Reactive oxygen species in plant cell
Supervisor: Prof. RNDr. Pavel Pospíšil, Ph.D.
Reactive oxygen species (ROS) formed in photosystem II (PSII) under various types of abiotic and biotic stresses are known to oxidatively modify lipids and proteins. Lipid peroxidation involves oxidative modification of polyunsaturated fatty acids, leading to the formation of reactive aldehyde. Protein oxidation comprises an oxidation of specific amino acid side chains in proteins, resulting in the formation of carbonyl groups on the protein molecules. The thesis is focused on the characterization of oxidation products of lipids and proteins in plants formed under environmental stresses.

Ultra-weak photon emission in living organisms
Supervisor: Prof. RNDr. Pavel Pospíšil, Ph.D.
Living organisms such as microorganisms, plants, and animals, including human beings, form spontaneously electronically excited species through oxidative metabolic processes. The thesis will aim to study the mechanisms of ultra-weak photon emission. Bringing a detailed understanding of the mechanisms of the formation of electronically excited species permits the use of ultra-weak photon emission as a diagnostic tool in basic and clinical research

Study programme Nanotechnology

Nanocomposites for biomedical applications
Supervisor: doc. RNDr. Karolína Šišková Ph.D.
Nanocomposites in general are perspective materials in many domains, including tissue engineering, drug-delivery, bio-imaging etc. Due to their sizes, nanocomposites possess unique properties that cannot be achieved by molecules and/or macroscopic materials. Therefore, the experimental PhD thesis will be devoted to the development of nanocomposites with improved properties in comparison to the currently available analoques.

Experimental physics, thin film deposition
Supervisor: RNDr. Zdeněk Hubička, Ph.D.
The content of the topic is the study of physical processes in plasma using various selected experimental physical methods. These measurements will be performed in reactive low-temperature plasma, which is intended for the deposition process of various selected types of thin films with defined physical properties. As the main diagnostic systems for measuring plasma parameters, systems that are not affected by being covered with a thin semiconductor or electrically insulating thin film will be chosen. Also, the studied reactive plasma will not be time constant, but will be time variable or pulsed. Therefore, high-frequency measurement methods with time resolution will mostly be used. The aim will be to understand the physical processes in the plasma using the mentioned experimental methods and their influence on the parameters of the resulting deposited thin films.

Analysis of characteristics of parametric down-conversion 
Supervisor: prof. RNDr. Ondřej Haderka, Ph.D.. / prof. 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: prof. 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.

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.

Quantum correlations in multi-mode optical fields generated in the process of spontaneous parametric down-conversion
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Quantum correlations in photon numbers of multi-mode optical fields originating in the process of spontaneous parametric down-conversion, that generates photons in pairs, and prepared by further manipulations (e.g. postselection) will be studied. Quantification of the quantumness of such correlations, striking features of these correlations as they exhibit in physically interesting quantities and their application potential will be addressed. Theoretical models appropriate for these fields will be developed and compared witht he experimental data, This will allow us  to determie the practical potential of these  fields in various applications including metrology. The topic may be extended to include the experimental part.

Noclassical properties of simple PT-symmetric quantum systems described using methods of quantum statistical physics
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Simple quantum PT-symmetric and generalized systems like two- and more-level atoms and multi-mode optical bosonic systems will be studied from the point of view of their nonclassical properties. The analyzed systems will be described by Liouvillians and attention will be paid to their asymptotic behavior. Exceptional points are the striking features of PT-symmetric systems. At these points, the system behavior qualitatively changes, which may be used, e.g., for increasing sensitivity of quantum measurements. We will identify the exceptional points of analyzed systems including their degeneracies and study the behavior of system nonclassicality close to these points. We will look for suitable applications that expoint the striking properties  of the analyzed systems.

Study programme Optics and Optoelectronics

Optimization of the UV Raman spectrometer with excitation wavelength in the range 207 – 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).

Nonlinear interactions between microwave cavity modes
Supervisor: Mgr. Ondřej Černotík, Ph.D.
Superconducting quantum devices exhibit strong nonlinearity enabled by the Josephson effect, allowing a range of applications in quantum technologies. Particularly interesting is the possibility of full quantum control of a linear microwave mode controlled using a nonlinear superconducting circuit.

Quantum non-Gaussianity and Correlations from Fundamental Forces
Supervisor: prof. Mgr. Radim Filip, Ph.D.
Assistant: Darren Moore, Ph.D.
As part of the dissertation, the doctoral student will investigate the principles and use of fundamental electric, magnetic, dipole and also gravitational interactions currently achievable in experiments with trapped and cold ions, atomic ensembles, molecules and nanoparticles for the preparation, manipulation and detection of quantum non-Gaussian states, quantum correlations and their applications. The goal of the work will be to propose new theoretical methods and concepts of the first suitable experimental tests and subsequently contribute to the analysis of data from the experiments. This new direction will thoroughly combine the theoretical and experimental knowledge of research teams at Palacky University in Olomouc and foreign partners.

Quantum non-Gaussian emission of atoms
Supervisor: prof. Mgr. Radim Filip, Ph.D.
Assistant: Mgr. Lukáš Lachman, Ph.D.
As part of the dissertation, the doctoral student will investigate the principle use of highly nonlinear quantum interactions currently achievable in nonlinear optics and quantum electrodynamics with atoms and similar systems, both in free space and in optical resonators and waveguides. The thesis will aim to propose a methodology for generating quantum non-Gaussian states and their first suitable experimental tests. This new direction will thoroughly combine the theoretical and experimental knowledge of research teams at Palacky University in Olomouc and foreign partners.

Hybrid quantum technology
Supervisor: prof. Mgr. Radim Filip, Ph.D.
Assistant: Andrey Rakhubovskiy, Ph.D.
As part of the dissertation, the doctoral student will investigate the principle and use of hybrid quantum interactions currently achievable when connecting atomic, molecular, nanoscopic and superconducting systems to construct new robust methods in quantum sensing, quantum communications, simulations and quantum computing using optical and microwave channels. The work will aim to propose a methodology for constructing hybrid circuits and their first suitable experimental tests. This new direction will thoroughly combine the theoretical and experimental knowledge of research teams at Palacky University in Olomouc and foreign partners.

Quantum non-Gaussian spin-mechanics of ions
Supervisor: Kimin Park, Ph.D.
Assistant: prof. Mgr. Radim Filip, Ph.D.
As part of the dissertation, the PhD student will investigate the principle exploration of highly nonlinear quantum interactions currently achievable in experiments with trapped and cold ions and similar systems to prepare, manipulate and detect quantum non-Gaussian states and their applications. The thesis will propose new theoretical methods and concepts of the first suitable experimental tests and contribute to subsequent experimental data analysis. This new direction will thoroughly combine the theoretical and experimental knowledge of research teams at Palacky University in Olomouc and foreign partners.

Highly nonlinear quantum technology
Supervisor: Darren Moore, Ph.D.
Assistant: prof. Mgr. Radim Filip, Ph.D.
As part of the dissertation, the doctoral student will investigate the principle use of highly nonlinear quantum interactions currently achievable in superconducting and atomic systems to construct new robust methods in quantum sensing, quantum simulations and quantum computing with linear and nonlinear measurements. The thesis will aim to propose a methodology for building highly nonlinear circuits and their first suitable experimental tests. This new direction will thoroughly combine the theoretical and experimental knowledge of research teams at Palacky University in Olomouc and foreign partners.

Quantum nonlinear optomechanics
Supervisor: Andrey Rakhubovskiy, Ph.D.
Assistant: prof. Mgr. Radim Filip, Ph.D.
Quantum high-order nonlinearity is a long-sought operation in quantum information processing as it is the missing link to achieve universal quantum computation with continuous variables. Nanomechanical oscillators such as levitated nanoparticles and other systems can quickly achieve such nonlinearity via a feasible application of a nonlinear potential of mechanical motion. This work aims to research the generation, application, and verification of the nonlinear potentials for levitated nanoparticles. Different potentials will be studied: higher-order polynomial, double-well, and a combination thereof. Verification of nonlinear states from polynomial nonlinearities can be performed via observation of noise suppression in a specific nonlinear combination of quadratures of mechanical oscillators. Criteria will be optimised to adjust the requirements to certain potentials and the experimental conditions. Interaction with Prof. Zemánek's lab at ISI CAS Brno and Prof. M. Aspelmeyer's experimental group in Vienna will help to test and verify theoretical findings

Open system dynamics generating quantum coherence
Školitel: Mgr. Michal Kolář, Ph.D.
Assistant: prof. Mgr. Radim Filip, Ph.D.
The aim is to numerically model and analyze dynamics of open quantum multi-level systems to obtain transient and stationary states with quantum coherences for applications in quantum technology. Such analysis will be further used to propose a feasible thermodynamic engine producing quantum coherence of multi-level systems. Such engines will be, as well, analyzed from the point of view of their thermodynamic properties. Experimental tests with atoms, molecules and solid-state systems will be proposed.

Chemistry

Study programme Analytical Chemistry

Development of microanalytical techniques for the analysis of archaeological samples
Supervisor: RNDr. Lukáš Kučera, Ph.D.

A multimodal approach to assessing environmental burdens in human history
Supervisor: RNDr. Lukáš Kučera, Ph.D.

Central Nervous System diagnostics
Supervisor: prof. Ing. Vladimír Havlíček, Dr.
Central nervous system infections cause acute changes in mental and physical brain functions, leading to chronic impairment of cognitive, memory, and motor abilities. These changes are related to alterations in brain neuronal signaling in susceptible brain regions. This Ph.D. topic aims to utilize matrix-assisted laser desorption/ionization-mass spectrometry imaging and highly multiplex immunohistochemistry-based mass spectrometry imaging to analyze and quantify molecular interactions between host and pathogen in cases of neuroaspergillosis caused by Aspergillus fumigatus and pneumococcal meningitis caused by Streptococcus pneumoniae. The Ph.D. project will determine the optimal transport mechanism for microbial secondary metabolites, such as toxins and quorum sensing molecules, across the blood-brain barrier. The study will analyze the impact of microbial metabolites on neurotransmitter signaling, specifically through the dopaminergic and glutamatergic pathways, in critically affected brain regions. The candidate biomarkers will successfully diagnose CNS infections in human cerebrospinal fluid samples based on the host-pathogen molecular fingerprint. This study will provide new insights into the molecular interplay between pathogens and hosts in fungal and bacterial central nervous system infections, and offers more accurate alternatives to the current unspecific diagnostic methods.

Host and microbe: tug-of-war for nutrients
Supervisor: prof. Ing. Vladimír Havlíček, Dr.

Molecular Mechanisms of host pathogen interaction in Lyme disease and Post-treatment Lyme disease syndrome
Supervisor: prof. Ing. Vladimír Havlíček, Dr.

Brain neurochemistry in bacterial central nervous system infections
Supervisor: prof. Ing. Vladimír Havlíček, Dr.

Ion mobility of isomeric biologically active substances
Supervisor: prof. RNDr. Karel Lemr, Ph.D.

Changes in ions' internal energy during ion mobility separation
Supervisor: prof. RNDr. Karel Lemr, Ph.D.

Identification of components of art paintings by desorption ionization and mass spectrometry with ion mobility
Supervisor: prof. RNDr. Karel Lemr, Ph.D.

Mechanism of desorption and ionization in desorption nanoelectrospray
Supervisor: prof. RNDr. Karel Lemr, Ph.D.

Metrological aspects of microplastics analysis
Supervisor: doc. Ing. David Milde, Ph.D.

Analysis of biologically active compounds by capillary electrophoresis
Supervisor: doc. RNDr. Jan Petr, Ph.D.
Capillary electrophoresis, as a separation technique based on differences in the speed of substances in an electric field, enables the analysis of a wide range of substances, from small inorganic ions to large molecules such as proteins or DNA fragments. Within this dissertation, the attention will be devoted to the development of new methods for analyzing selected biologically active substances. The research will also focus on studying the possibilities of influencing the selectivity of separation, particularly in the case of optical isomers, using chiral solvents or chiral nano- and micro-objects. Additionally, the potential of combining capillary electrophoresis with mass spectrometry, or the utilization of other detectors such as conductivity or amperometric, will be investigated. The work will lead to publication outputs.

New procedures for microanalysis of plant material
Supervisor: doc. RNDr. Petr Bednář, Ph.D.
Modern analytical chemistry faces a number of challenges. One challenege is the reduction of sample size available for analysis. The preparation of a plant sample is then difficult and requires the development of new procedures including its defined micropreparation from the material, physical or chemical treatment, transfer of the sample for microanalysis, often under microscopic control. The analytical technique used must have sufficient sensitivity and selectivity. The topic of the dissertation is focused on the development of new complex procedures for the analysis of plant material at the microscopic level, from sample collection and treatment, through its processing, measurement using mass spectrometry techniques, Raman and infrared microscopy, to data processing. The developed procedures will be applied to the metabolomic analysis of different types of plant material.

Modern chemical microanalysis in material research of tangible cultural heritage
Supervisor: doc. RNDr. Petr Bednář, Ph.D.
In the last decade, the chemical analysis of archaeological findings and objects of material cultural heritage has become an integral part of comprehensive historical research and preservation of monuments. In many cases, non-invasive analysis is required. If this does not provide sufficient information, it is necessary to proceed with the micro-sampling of the sample with full respect to the value of the investigated object. In both cases, there is a great demand for new analytical procedures allowing chemical exploration at the microscale. This topic is focused on the development and application of these procedures in archeology and monument care. Methodologically, the focus will be on chemical microanalysis using mass spectrometry, Raman and infrared microscopy, and the possibilities of integrating the obtained data into the broader context of archeology and heritage preservation.

Ion chromatography in the study of plant metabolism
Supervisor: doc. RNDr. Petr Bednář, Ph.D.
Ion chromatography is a suitable technique for the sensitive analysis of a mixture of inorganic and organic ions in a wide range of research areas as well as control practice. The topic of the dissertation deals with the development of new analytical procedures for the study of the composition of plant material from sampling, through sample treatment, analysis of the present metabolites using modern ion chromatography and the integration of the obtained data into a broader investigation of plant metabolism. The possibilities of influencing the selectivity of the separation, the sensitivity of conductivity detection and the possibility of connection with mass spectrometry will be monitored, and the potential of ion chromatography will be compared with selected other techniques using the principles of separation in liquid phase.

Study programme Inorganic Chemistry

Lanthanide complexes with large magnetic anisotropy and slow relaxation of magnetization
Supervisor: RNDr. Bohuslav Drahoš, Ph.D.

Transition metal and lanthanide complexes with macrocyclic ligands as important building blocks in preparation of single-molecule magnets
Supervisor: RNDr. Bohuslav Drahoš, Ph.D.

Complexes of macrocyclic ligands applicable in the field of theranostics
Supervisor: RNDr. Bohuslav Drahoš, Ph.D.

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

Preparation of biologically active benzimidazoles and benzazoles and their complexes with ruthenium
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.

Antibacterial properties of gold and silver complexes and nanoparticles
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.

Nanotransporters of potential drugs based on coordination compounds
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.

Development of hybrid plasmonic photocatalysts for the conversion of carbon dioxide into value added chemicals
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Development of chemically functionalized graphene based single atom catalysts for hydrogen production from water electrolysis
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Multicomponent coordination compounds of platinum metals for biological applications
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.

Liposomal formulation of bioactive coordination compounds for polypharmacology
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.

Platinum metal complexes for medicinal chemistry and catalysis
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.

Anticancer heterometallic coordination compounds
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.

Study programme Physical Chemistry

Chemical databases
Supervisor: doc. RNDr. Karel Berka, Ph.D.
In today's age of information technology, technologies for managing and mining available chemical data are also coming into their own. Within the group, we have already developed several databases (MolMeDB, ChannelsDB or Pokusnice) that store specific chemical data and allow basic manipulation and mining. The aim of the work is to extend the databases, automate their execution, increase their interoperability (e.g. by linking to Wikidata), improve the existing data management, and, above all, use their outputs to address research questions. Knowledge of programming language (active HTML, Python, etc.) and working with databases (SQL, SPARQL) welcome.

Theoretical study of biomembrane systems
Supervisor: doc. RNDr. Karel Berka, Ph.D.
The aim of this research topic is to understand the behaviour and nature of the interaction of small molecules and biomacromolecules with biological membranes. A combination of simulation techniques (e.g. molecular dynamics simulations or quantum chemical calculations) and bioinformatic and cheminformatic approaches - e.g. identification of compounds suitable for encapsulation in liposomes (e.g. bioRxiv, 05(11), 087742, 2020. ) and storing this information in a publicly available database (e.g. molmedb.upol.cz Database, 2019, baz078, 2019.); the mode of action of membrane-bound proteins together with the development of the necessary structural bioinformatics tools (e.g. mole.upol.cz - Nucleic Acids Res, 46(W1), W368-W373, 2018. or SecStrAnnotator - bioRxiv, 04(15), 042531, 2020.) We expect close collaboration with colleagues from the European bioinformatics infrastructure ELIXIR, Masaryk University, Brno, CZ; Université de Limoges, FR; Uppsala Universitet, SE and University of Chemical Technology, Prague, CZ.

Intermolecular interactions in biomolecules
Supervisor: doc. RNDr. Petr Jurečka, Ph.D.
While the structure of ribosomal RNA is relatively well known, the interactions that determine and stabilize it are less well understood. With the rapid development of computers, quantum chemical and molecular dynamics calculations are becoming increasingly popular methods for analyzing intermolecular interactions in biomolecules. In our work, we focus on interactions in biomolecules such as ribosomal RNA or protein-DNA complexes and try to find important structural stabilizers of these unique molecular architectures.

Development of empirical potentials for modelling biomolecules
Supervisor: doc. RNDr. Petr Jurečka, Ph.D.
The development of empirical potentials for molecular dynamics is a necessary condition for the development of the whole field of molecular modelling. At the Department of Physical Chemistry, UP Olomouc, several years ago we developed a promising method for obtaining high-quality empirical parameters. The newly developed parameters are mainly intended for modelling biomolecules such as RNA and DNA and under the acronym "OL" (Olomouc) are nowadays used worldwide in the most popular simulation package AMBER. We will apply and test our method on dozens of biologically interesting systems such as DNA structures, protein-DNA complexes and ribosomal RNA fragments.

Study of natural antioxidants for therapeutic applications
Supervisor: prof. Ing. Lubomír Lapčík, Ph.D.
Natural antioxidants play an important role in protecting the body against cancer. This is particularly the use of their antioxidant properties in the human body. The aim of this work will be to compare antioxidants obtained from selected types of natural plant products, especially with regard to their ability as radical scavengers. The basic kinetic parameters of the quenching of these radicals by antioxidants, their identification and thermal or chemical stability in different environments will be determined.
Candidate requirements: Graduate of a university degree in science or engineering in chemistry, physical chemistry, materials chemistry and technology.

Nanomaterials for biological applications
Supervisor: doc. RNDr. Aleš Panáček, Ph.D.
Nanostructured materials are unique due to their specific physicochemical properties, which are also reflected in their specific interaction with living organisms, making nanomaterials exhibit unique biological properties. The useful properties of nanomaterials with biological properties are broad and can be used, e.g. in medicine for the treatment or diagnosis of diseases; biologically active nanomaterials can be applied in industrial sectors or in environmental applications to remove undesirable biological, especially microbial, contaminations. A typical example is silver nanoparticles that exhibit high antimicrobial activity, which can be used in the treatment of microbial infections, including those caused by highly resistant bacterial strains for which treatment with conventional antibiotics has failed. On the other hand, consideration must be given to the potential adverse biological effects of nanomaterials when interacting with biological systems, which may occur precisely because of their unique and unusual biological properties. Thus, the study of the mechanism of interaction of nanomaterials with biological systems at different cellular levels and their use for biological and medical applications represents a very interesting and diverse area of scientific research.

Preparation of nanoparticles and nanocomposites for catalytic applications
Supervisor: doc. RNDr. Robert Prucek, Ph.D.
Current developments in the field of nanotechnology are moving from the preparation and use of isolated nanoparticles to systems where they are fixed on a suitable substrate (colloidal particles, microparticles or macrosystems). Such composites exhibit unique physicochemical properties, distinct from the nanoparticles themselves. In addition to the increased aggregate stability of the nanoparticles, there is often a synergistic effect of improved physicochemical properties of the materials in question (e.g. catalytic activity, optical properties, separation, aggregate stability, etc.). The aim of this work will be research and development in the field of preparation, characterization and application of nanoparticles of noble metals (copper, silver, gold, platinum, palladium, etc.) or their compounds. The area of preparation will be focused on the development and optimization of methods for the preparation of nanoparticles and nanocomposites based on these metals and their compounds (in the form of aqueous dispersions, self-organized layers or immobilized particles on supports such as SiO2, Al2O3, ZrO2, FexOy, glass, quartz, etc.), including their characterization (size, morphology, stability, etc.). These materials will then be studied and tested for their efficiency for heterogeneous catalysis or spectroscopic applications (surface-enhanced Raman spectroscopy).
In the field of catalysis, micro or nanoparticles or nanocomposites are used on a very large scale in the field of organic synthesis (Ullmann synthesis, Fischer-Tropsch synthesis, ammonia preparation (Haber-Bosch reaction), hydrogenation or dehydrogenation reactions, Suzuki reactions, etc. ), as well as in very intensively developing fields such as fuel cells, photovoltaics, photocatalysis, photochemical water splitting, catalysts in cars for the oxidation of unburned hydrocarbons, carbon monoxide and the reduction of nitrogen oxides. Another important application of these materials is their use in advanced oxidation processes used for remediation technologies used for the treatment of wastewater and old environmental loads. A common and frequently occurring requirement underlying industrial applications is their ability to degrade toxic and often persistent organic pollutants that defy or directly deactivate the traditionally used biological stage that is an integral part of most wastewater treatment plants.

Preparation of nanoparticles and nanocomposites for spectroscopic applications
Supervisor: doc. RNDr. Robert Prucek, Ph.D.
Surface-enhanced Raman spectroscopy is one of the modern analytical techniques allowing the detection of very low concentrations of substances. The continuous development of Raman spectrometers has resulted in these instruments becoming more affordable and, as a consequence, the number of these instruments is increasing not only in scientific workplaces, but especially in commercial laboratories. A very important area where these instruments can be found, whether in the form of classical or especially mobile versions, are selected police, fire brigade or army units, where these instruments are used for the identification of flammables, drugs, explosives, etc. Since surface-enhanced Raman spectroscopy has a very significant potential, which predestines it for future expansion into many areas of human activity (rapid and sensitive detection of explosives, drugs, or markers for disease detection, toxicology, forensic analysis, etc.), the goal of the problem will be the reproducible preparation of efficient, reliable, and easy-to-use substrates based on silver and gold.

Study programme Organic and Bioorganic Chemistry

Synthesis and study of nitrogenous heterocycles as ligands for various biological targets
Supervisor: doc. RNDr. Miroslav Soural Ph.D.
Nitrogenous heterocycles represent a very important group of organic compounds. They form a common structural motif in a number of natural or synthetic, biologically active substances. Approximately 60% of drugs that have been approved for clinical use to date contain a nitrogen heterocycle in their structure. For this reason, nitrogenous heterocycles are an attractive chemotype in the field of medicinal chemistry. A number of heterocyclic derivatives have been prepared that exhibit a variety of biological effects, such as antibiotic, antibacterial, antifungal, antitumor, antiviral, analgesic, etc. If the biological target is known, a rational design of new analogues is possible to find analogues more advantageous pharmacological properties, e.g. higher activity, selectivity and metabolic stability. The aim of the dissertation is to search for new heterocyclic drugs based on standard procedures: 1) biological target selection and structural design of potential ligand (typically using scaffold hopping approach or molecular docking), 2) development and optimization of synthetic method to prepare target scaffold , 3) preparation of a series of substituted derivatives to study the structure-activity relationships, 4) primary testing and evaluation of SAR, 5) further rational structure modifications using the information obtained, leading to advanced derivatives and their pharmacological evaluation. The specific structural motives will be determined on the basis of the current results of the research group. At present, attention is paid mainly to cytotoxic compounds acting against tumor cells and derivatives oriented to biological targets located in the central nervous system. The biological evaluation is carried out in cooperation with the Department of Experimental Biology, the Institute of Molecular and Translational Medicine and the Jagiellonian University in Krakow.

Tunable non-covalent interaction-based catalysts for stereoselective reactions of iminium and oxonium intermediates
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.
Anion-binding catalysis is a fast-growing but very challenging field of organic asymmetric synthesis. The principle of such transformation is fairly simple: the chiral catalyst scavenge/recognizes the anion (generally the chloride anion) and then exerts precise geometric control on the prochiral reaction site. However, the selectivity of the transformation does not rely on interactions with the variable substituents on the substrate. Criteria seem simple, but are not easy to fulfil, and so it is not surprising that only a few so-called 'privileged' molecular scaffolds can meet them. In our proposal, we introduce the novel molecular scaffold for asymmetric catalysis that has not been evaluated before, 1,2-diazetidin-3-one (DAZDO), as a new privileged molecular scaffold for asymmetric catalysis. To prove our concept, we developed DAZDO catalysts that are able to generate oxonium and iminium intermediates in situ and allow them to react with various C-nucleophiles with high stereoselection. Our concept and catalysts will be applied to the total synthesis of selected natural products. Aims of the project: (1) to develop a new generation of anion-binding organocatalysts based on the diazetidinone molecular skeleton (DAZDO); (2) to demonstrate the use of DAZDO catalysts in the context of natural product synthesis (stereoselective addition of C-nucleophiles to iminium and oxonium cyclic intermediates).

Dynamic "lego-like" approach for in situ preparation of (organo)catalysts
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.
Organocatalysis belongs to the well-established fields of organic asymmetric synthesis. Over the past 25 years, it has undergone fast development, and the basic principles of it are well established. However, as with any of the field of asymmetric catalysis, the design of catalytical systems is strongly substrate and reaction mechanism dependent and therefore when a specific transformation is required to proceed in high stereoselectivity, it often required long and tedious catalyst system development. Our project aims to overcome such difficulties by generating a catalyst in situ starting from well-defined ligands containing organocatalytic motives. The ligands will be preorganized into the catalytical pocket with the help of a selected metal. Such a “organocatalysis in disguise” approach should allow us to design quickly and straightforward various organocatalytic systems that would allow us to combine the nucleophilic and H-bonding activation system (aim 1) or anion-binding catalysis with nucleophilic catalysis (aim 2).

Modification of pentacyclic triterpenoid molecules in the E and A ring region and study of their anticancer and neuroprotective aktivity
Supervisor: doc. RNDr. Milan Urban, Ph.D.
Triterpenoids are natural compounds with a number of biological activities, at our research group we are mainly concerned with compounds with cytotoxic and related anticancer activity. The most active derivatives have IC50 values in the low micromolar to submicromolar range which, in the context of low toxicity, would predispose these molecules to become anticancer therapeutics. Lupane derivatives in particular are highly cytotoxic (Fig. 1) and have therefore received particular attention. A second area of interest is triterpenes with neuroprotective activity, which show significant protective effects in cellular models of Parkinson's and Alzheimer's disease.The main problem with active triterpenes is their high lipophilicity, low water solubility and associated lack of bioavailability when administered orally. For some neuroprotective compounds, the downside is their excessive cytotoxicity. One possibility to modify these undesirable properties is the preparation of prodrugs. Despite great efforts to find optimal prodrugs, the results of this research have so far been rather partial.
In the framework of this work, new compounds will be prepared mainly by a series of different oxidation reactions, halogenations, cross-couplings, cycloaddition reactions, etc. with the main aim to find molecules with better selective cytotoxic activity or neuroprotective activity than previously prepared derivatives.  For all new derivatives, the values of both biological activities will be measured and based on the results, suitable candidates will be selected for further development in one or the other activity category from which further derivatives will be synthesized with respect to pharmacological parameters, especially solubility, toxicity and bioavailability. For this purpose, previously developed procedures for the preparation of prodrugs will be used, but new alternatives will also be sought. It is anticipated that several series of derivatives will be prepared in the course of the work and will be fully characterised and tested for their biological activities. The results should show the effect of the different modifications and prodrug groups on activity and pharmacological properties, especially bioavailability and metabolism. The work should lead to the formulation of structure-activity relationships. All syntheses will go hand in hand with biological screening and feedback from this testing will guide the direction of syntheses towards optimised molecules suitable for anticancer drug development.

Design and synthesis of novel heterocyclic compounds with potent antimicrobial aktivity
Supervisor: Doc. RNDr. Lucie Brulíková, Ph.D.
The increasing prevalence of microbial infections and the emergence of resistance to the currently available antimicrobial drugs requires the development of new chemical entities with an alternative mechanism of action to existing therapeutics directed toward unknown targets. The main goal of the thesis will be the design, synthesis and biological activity studies of novel antibacterial and antiparasitic agents. This work will cover the novel compounds design based on the molecular docking studies, their synthesis and optimisation of reaction sequences. Further, this project deals with biological testing. Moreover, these studies will be complemented with enzymatic assays. Final compounds will be further modified according to biological activity testing. Alternatively, a new pharmacophore will be investigated.

Axially Chiral Heterocyclic Compounds with Potential Application in the Area of Organocatalysis, Chiral Derivatization Agents, and Inhibition of Protein Kinases
Supervisor: doc. RNDr. Petr Cankař, Ph.D.
Axial chirality of organic compounds is often described for the ortho-substituted biaryl compounds, where is a single bond joining both aryls with restricted rotation. This bond lies on the chiral axis. In case, the energy barrier of restricted rotation is sufficiently high, it is possible to synthesize and isolate atropisomers for a variety of practical applications. Initially, the attention to atropisomerism was inadequate, since the first isolated atropisomers were not sufficiently stable for practical use. In the recent 20 years, there is a renaissance of the use of axial chirality for organic compounds; especially in organocatalysis and also medicinal chemistry in the last decade. The main reasons are novel opportunities in the spatial arrangement of molecules.
The goal of the Ph.D. thesis will be the synthesis and study of axially chiral heterocyclic compounds, which allow novel various spatial interactions by functional groups and heterocyclic systems for stereoselective organocatalysis or inhibition of protein kinases. Alternatively, another research area can be the use of axially chiral compounds as derivatizing agents for the analysis of stereoisomers and their mixtures.

Study programme Nanomaterial Chemistry

Catalytic activity of metal nanoparticles and their composites for energy applications
Supervisor: prof. RNDr. Libor Kvítek, CSc.
Nanomaterials based on metals and their compounds have a number of unique properties from the point of view of many natural sciences. From the point of view of chemistry, these include in particular their catalytic activity, which is primarily associated with a high ratio between the atoms or molecules on the surface of the particle compared to its volume. Current developments in nanotechnology for energy applications are related to this high catalytic activity of nanomaterials. In addition to research aimed at the development of new energy harvesting systems, either by chemical means (electrochemical cells) or by solar energy conversion, the focus of many research teams is also on energy storage in energy-rich compounds. One such reaction that allows the conservation of the energy obtained for later use and at the same time eliminates part of the adverse carbon dioxide emissions is the reduction of this product of fossil fuel combustion to form a range of organic compounds for reuse in the energy sector, but also with further applicability to the chemical industry or transport. It is the reaction of the reduction of carbon dioxide by hydrogen to form a range of hydrocarbons and other organic compounds, typically methanol. This reaction, similar to the Fischer-Tropsch synthesis of hydrocarbons from carbon monoxide, is carried out efficiently only with the aid of catalytic systems based on metals or their compounds (usually oxides). Long-term experience in the field of research on the catalytic activity of metal nanomaterials at the Faculty of Science of the University of Applied Sciences has recently led to the development of an efficient composite nanocatalyst for this reaction based on copper nanoparticles bonded to nanostructured iron oxide. Initial tests of this catalyst in collaboration with the catalytic group of Dr. Vajda from Argonne National Laboratory (Chicago, USA) have shown the high activity of this catalyst with respect to hydrocarbon production. Further research will be carried out using a PID microreactor to study heterogeneous catalysis in gaseous reaction systems with interfacing to a GC/MS based analytical system. The main objective of this thematic focus of the PhD thesis will be the research and development of a catalytic system based on noble metal nanoparticles combined with iron oxide nanoparticles with high catalytic activity for low-temperature (up to about 300 °C) hydrogenation of carbon dioxide to form further usable compounds not only for energy but also for other areas of human activity.

Nanomaterials for biological applications
Supervisor: doc. RNDr. Aleš Panáček, Ph.D.
Nanostructured materials are unique due to their specific physicochemical properties, which are also reflected in their specific interaction with living organisms, making nanomaterials exhibit unique biological properties. The useful properties of nanomaterials with biological properties are broad and can be used e.g. in medicine for the treatment or diagnosis of diseases, biologically active nanomaterials can be applied in industrial sectors or in environmental applications to remove undesirable biological, especially microbial, contaminations. A typical example is silver nanoparticles that exhibit high antimicrobial activity, which can be used in the treatment of microbial infections, including those caused by highly resistant bacterial strains for which treatment with conventional antibiotics has failed. On the other hand, consideration must be given to the potential adverse biological effects of nanomaterials when interacting with biological systems, which may occur precisely because of their unique and unusual biological properties. Thus, the study of the mechanism of interaction of nanomaterials with biological systems at different cellular levels and their use for biological and medical applications represents a very interesting and diverse scientific research area.

Preparation of nanoparticles and nanocomposites for catalytic applications
Supervisor: doc. RNDr. Robert Prucek, Ph.D.
Current developments in the field of nanotechnology are moving from the preparation and use of isolated nanoparticles to systems where they are fixed on a suitable substrate (colloidal particles, microparticles or macrosystems). Such composites exhibit unique physicochemical properties, distinct from the nanoparticles themselves. In addition to the increased aggregate stability of the nanoparticles, there is often a synergistic effect of improved physicochemical properties of the materials in question (e.g. catalytic activity, optical properties, separation, aggregate stability, etc.).
The aim of this work will be research and development in the field of preparation, characterization and application of nanoparticles of noble metals (copper, silver, gold, platinum, palladium, etc.) or their compounds. The area of preparation will be focused on the development and optimization of methods for the preparation of nanoparticles and nanocomposites based on these metals and their compounds (in the form of aqueous dispersions, self-organized layers or immobilized particles on supports such as SiO2, Al2O3, ZrO2, FexOy, glass, quartz, etc.), including their characterization (size, morphology, stability, etc.). These materials will then be studied and tested for their efficiency for heterogeneous catalysis or spectroscopic applications (surface-enhanced Raman spectroscopy).
In the field of catalysis, micro or nanoparticles or nanocomposites are used on a very large scale in the field of organic synthesis (Ullmann synthesis, Fischer-Tropsch synthesis, ammonia preparation (Haber-Bosch reaction), hydrogenation or dehydrogenation reactions, Suzuki reactions, etc. ), as well as in very intensively developing fields such as fuel cells, photovoltaics, photocatalysis, photochemical water splitting, catalysts in cars for the oxidation of unburned hydrocarbons, carbon monoxide and the reduction of nitrogen oxides. Another important application of these materials is their use in advanced oxidation processes used for remediation technologies used for the treatment of wastewater and old environmental loads. A common and frequently occurring requirement underlying industrial applications is their ability to degrade toxic and often persistent organic pollutants that defy or directly deactivate the traditionally used biological stage that is an integral part of most wastewater treatment plants.

Preparation of nanoparticles and nanocomposites for spectroscopic applications
Supervisor: doc. RNDr. Robert Prucek, Ph.D.
Surface-enhanced Raman spectroscopy is one of the modern analytical techniques allowing the detection of very low concentrations of substances. The continuous development of Raman spectrometers has resulted in these instruments becoming more affordable and, as a consequence, the number of these instruments is increasing not only in scientific workplaces, but especially in commercial laboratories. A very important area where these instruments can be found, whether in the form of classical or especially mobile versions, are selected police, fire brigade or army units, where these instruments are used for the identification of flammables, drugs, explosives, etc. Since surface-enhanced Raman spectroscopy has a very significant potential, which predestines it for future expansion into many areas of human activity (rapid and sensitive detection of explosives, drugs, or markers for disease detection, toxicology, forensic analysis, etc.), the goal of the problem will be the reproducible preparation of efficient, reliable, and easy-to-use substrates based on silver and gold.

Nanocatalysis for oxidative and non-oxidative hydrogenation of alkanes
Supervisor: RNDr. Štefan Vajda, CSc., Dr.habil.
Catalysts are prepared in several ways from (i) subnanometric clusters of precise atomic size and composition supported on metal oxide or carbon-based supports deposited by molecular beam in vacuum and (ii) nanoparticle catalysts prepared by conventional chemical methods from solution. The performance of the catalysts is tested on an experimental reactor using a mass spectrometer and gas chromatography for product analysis. The catalysts are characterized using electron microscopy and other solid phase study techniques. More information on research activities can be found at www.heyrovsky-chair.eu

Nanocatalysis of carbon oxides
Supervisor: RNDr. Štefan Vajda, CSc., Dr.habil.
Catalysts are prepared in several ways from (i) subnanometric clusters of precise atomic size and composition supported on metal oxide or carbon-based supports deposited by molecular beam in vacuum and (ii) nanoparticle catalysts prepared by conventional chemical methods from solution. The performance of the catalysts is tested on an experimental reactor using a mass spectrometer and gas chromatography for product analysis. The catalysts are characterized using electron microscopy and other solid phase study techniques. More information on research activities can be found at www.heyrovsky-chair.eu

Theoretical study of charge transfer in nanostructures
Supervisor: doc. Ing. Pavel Jelínek, Ph.D.
The ability to actively control charge transfer at the atomic level in nanostructures opens up new possibilities in the field of nanoelectronics. A deeper understanding of the processes involved in charge transfer at the atomic level requires new approaches in theoretical simulations. The aim of this work is to learn the density functional theory and its application to selected problems of charge transfer in nanostructures. Theoretical calculations will be performed in close cooperation with experimental measurements. Further development of computer simulations is foreseen in the framework of the PhD study. Expected knowledge: Basic knowledge of quantum mechanics and solid state theory, or quantum chemistry, Knowledge of programming language (Fortran, C, etc.) welcome.

Chemical and physical properties of molecular nanostructures on surfaces studied with scanning electron microscopes
Supervisor: doc. Ing. Pavel Jelínek, Ph.D.
The current development of scanning electron microscopes operating in ultra-high vacuum allows high-resolution measurements of atomic forces and tunnelling currents on individual atoms or molecules on the surface of a solid. The ability to simultaneously measure atomic forces and tunnelling currents opens up entirely new possibilities for the characterization of single molecules or molecular nanostructures on the surface of solids. The aim of this thesis is to learn how to use an atomic force microscope and a scanning tunnelling microscope operating in a high vacuum. The study will include high-resolution measurements of the atomic and electronic structure of selected molecular complexes on the surface of solids. The main objective of the work is to study selected chemical and physical properties of molecular systems. Assumed knowledge: Basic knowledge of quantum mechanics and solid state theory, Knowledge of the basic principles of scanning electron microscopes welcome.

Mathematics

Study programme Applied Mathematics

Functional regression models with complex structure
Supervisor: doc. RNDr. Eva Fišerová Ph.D.
Functional data analysis is a set of methodologies suitable for the analysis of high-dimensional measurements, such as curves or surfaces, which consider data not as a sequence of single measurements taken one after another, but as whole functional entities. Regression models are considered to be functional if the explanatory variable, the dependent variable, or both the explanatory and dependent variables can be treated as functions. The aim of the dissertation is the development of suitable statistical methods and algorithms mainly focused on statistical modelling when the random variables have a complex variation and correlation structure, there are restrictions on regression parameters, or observations are incomplete. The emphasis will be given both on theoretical aspects concerning estimation, uncertainty and statistical inference, as well as practical implementation and computational feasibility.

Analyzing probability density functions using Bayes spaces
Supervisor: Doc. RNDr. Karel Hron, Ph.D.
The analysis of probability density functions needs to reflect specific properties of these objects that carry relative information. For this purpose, the Bayes space methodology has been developed, which provides a flexible framework for the statistical processing of densities. Moreover, in the multivariate case, there is an orthogonal decomposition of densities into their independent and interaction parts, which allows a deeper insight into the dependence structure of variables. The aim of the dissertation is to develop methods for analysing univariate and multivariate density functions, with a particular interest in dependence analysis.

Models for survival analysis and challenges of their use
Supervisor: Mgr. Ondřej Vencálek Ph.D.
In the framework of medical research, there is a need to analyze the survival time from the diagnosis of a certain disease and the dependence of this time on various socio-demographic and biological characteristics of the patient. A specific feature of the analysis of the distribution of survival time is the presence of so-called censoring, i.e. only partial information about the value of the studied variable in some individuals. The most commonly used regression models for this type of data include the Cox model, also known as the proportional hazards model, or the accelerated time failure model, in some applications competing risk models are needed. The analysis of survival time can bring some problems that lead to difficulties with the interpretation of the model, but also with the estimation of its parameters. The first challenge is the skewness of the distribution of biological characteristics with the occasional occurrence of zero values. Another challenge is presence of more measured characteristics than number of observations. The third challenge is the non-trivial (hierarchical) structure of these measured characteristics. The aim of the work is to find a solution to these problems and to apply these solutions in a practical analysis regarding the survival prognosis of patients with head and neck cancer.

Study programme Mathematical Analysis

Analysis of equilibria
Školitel: Prof. RNDr. dr hab. Jan Andres CSC.,DSc.
Nonlinear and multivalued analysis of equilibria will be considered to dynamical systems and differential inclusions. Standard well known equilibria are, for instance those of Nash in the frame of the game theory. Using the fractional and topological methods (degree arguments, or so), the existence, localization, multiplicity and stability results will be of an interest.

Multivalued boundary value problems
Školitel: Prof. RNDr. dr hab. Jan Andres CSC.,DSc.
Boundary value problems for the second-order differential inclusions with Neumann boundary conditions will be under consideration. The applied technique will be based on a combination of topological (e.g. degree) arguments and Lyapunov-type bounding functions. The existence, localization and multiplicity results will be of an interest.

Almost-periodic sequences
Školitel: Prof. RNDr. dr hab. Jan Andres CSC.,DSc.
The hierarchy of almost-periodic sequences will be investigated in various metrics. The existence of almost-periodic solutions will be then considered. In the particular case of limit-periodic solutions, the difference equations will be preferably explored in the absence of global lipschitzianity imposed on the right-hand sides.

Earth Sciences

Study programme Geoinformatics and Cartography

Real-time Interactive Atlas in Dashboard Concept for Online Geovisualization of Dynamic Phenomena
Supervisor: Prof. RNDr. Vít Voženílek, CSc.
The aim of this thesis is to design, develop, implement and validate the concept of a dashboard for compilation of interactive atlases. The student will focus on the geovisualization of a selected group of dynamic phenomena and develop the theoretical background and practical guidelines for the effective making and using a new type of web-based thematic atlases. For this purpose, the student will necessarily establish cooperation with selected entities, generating a time series of geodata. Student will focus on visualization and analytical tools for the atlases.

Study programme Geological Sciences

Eligible for Fischer scholarship

Modern techniques of carbon dioxide and hydrogen geo-storage in response to climate change
Supervisor: Jagar Ali, Ph.D.
The world faces a dual challenge of diminishing fossil fuel reserves and escalating energy demand due to changing lifestyles. Fossil fuel usage, primarily emitting carbon dioxide (CO2), raises environmental concerns, making CO2 reduction a critical research focus. Various methods, including renewable energy and geoengineering, have been employed, but the focus has shifted to deep ocean and geological sequestrations for carbon capture and storage (CCS). Geological storage techniques involve evaluating diverse trapping mechanisms to prevent CO2 from rising to the surface. Structural and residual trapping, influenced by CO2 wettability in rock minerals, play crucial roles. However, complex wetting behavior in real reservoir conditions lacks sufficient literature coverage. Recent studies reveal the presence of water-soluble organic components in geological formations, affecting rock wettability. Chemical modifications and nanofluid treatments show promise in enhancing CO2 storage capacities. Silica nanoparticles, in particular, exhibit favorable wetting behavior, making them suitable for CO2 geo-sequestration. Despite progress, further research is needed on the effects of organic acids and nanoparticles in high salinity, high temperature and high-pressure conditions. Additionally, hydrogen (H2) is explored as a cleaner fuel alternative, with potential storage in geological formations to mitigate CO2 emissions.
The project focuses on the promising applications of nanofluids, particularly silica nanoparticles, in subsurface operations such as enhanced oil recovery, chemical flooding, and CO2 storage. It highlights the potential of nanofluid treatment for wettability reversal in CO2-brine-mineral systems, particularly in high-pressure and high-temperature reservoir conditions. Additionally, the study explores the cleaner fuel alternative, hydrogen (H2), and its potential for geological storage. The research aims to provide a comprehensive review of current technologies, proposing new materials and methods for improved absorption, and assessing economic and environmental feasibility. The investigation includes the effects of nanomaterials and chemicals on rock wettability and their impact on CO2 and H2 storage capacities under various conditions. The study also addresses the influence of organic matter on CO2 storage potential and explores the application of machine learning models to predict CO2 storage capacity. Results will be published in peer-reviewed journals (WoS).
Suitable candidates typically have a MSc. degree in petroleum engineering with excellent results and previous experience with work in the field. Good written and spoken English is required. Previous experience with scientific publishing is an advantage.

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).
Suitable candidates typically have a MSc. degree in geology / physical geography with excellent results and previous experience with work in the field (Bc., MSc. thesis in sedimentary geology or geomorphology). Good written and spoken English is required. Previous experience with scientific publishing is an advantage.

 

Study programme Environmental and Development Studies

Analysis of sustainable development metrics used at national and global scales
Supervisor: doc. Mgr. Miroslav Syrovátka Ph.D.
The topic responds to the Sustainable Development Goals’ target “to develop measurements of progress on sustainable development that complement gross domestic product”. The dissertation will analyze and evaluate selected aspects of sustainable development metrics and their institutionalization (van den Bergh, 2022) and develop new approaches or improve metrics. The conceptual framework includes the Sustainable Development Goals (see, e.g., van Vuuren et al., 2022; Hametner, 2022), the Safe and Just Space (see, e.g., Fanning et al., 2022; Aleissa & Bakshi, 2023), and their relationship with Earth System Justice (see, e.g., Gupta et al., 2023; Ryberg et al., 2020). The methodology includes quantitative analysis of metrics and other methods, given the interdisciplinary nature of the topic. After consultation with the potential supervisor, the candidates prepare a research draft with specific research questions and methods within this framework. The dissertation shall consist of at least three academic papers linked by a commentary.

Analyzing the Relationships between Social Progress, Pro-poor Growth, and the Environment as Key Dimensions of Sustainable Development
Supervisor: doc. Ing. Mgr. Jaromír Harmáček Ph.D.

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