Diversity and Structural Variation in Genomes of Terrestrial Cyanobacteria
Supervisor: doc. Mgr. Petr Dvořák, Ph.D.
Consultant: Mgr. Svatopluk Skoupý, Ph.D.
Understanding the genomic mechanisms that drive microbial adaptation and diversification in extreme environments remains a fundamental challenge in evolutionary biology. This dissertation will investigate genomic diversity and structural variation in terrestrial cyanobacteria, focusing on the filamentous genus Microcoleus, an ecologically important crust-forming cyanobacterium that inhabits hot and cold drylands. The research will employ comprehensive sampling strategies to establish a collection of unialgal strains from diverse geographical locations including hot and cold deserts. The strains will be sequenced using Illumina and Oxford Nanopore technologies. The study will examine patterns of structural variation across populations and environmental gradients, including analysis of pangenome architecture, while phylogenomic approaches will reconstruct population structure and evolutionary relationships. This will improve our understanding of the influence of environmental variables such as temperature, UV radiation, and precipitation on genomic diversity, addressing fundamental questions about how environmental pressures shape genome architecture in prokaryotes.
Place: Cyanobacterial Evolution Research Lab, Department of Botany, Palacký University Olomouc. The laboratory is focused on the evolution and taxonomy of cyanobacteria and algae. We established a wide network of collaborations in Europe and the USA (University of North Florida, USA; University of Florida, USA; Stockholm University, Sweden; Natural  History Museum London, UK etc.).

Population dynamics in small rodents in a dynamical landscape
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.

They live with us – synanthropic myriapods and isopods    
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.
Consultant: Ing. Marek Bednář, Ph.D

Impact of Heavy Machinery on Fluvial Ecosystems: Restoration Measures for Degraded Habitats of Rheophilic Fish in Trout Zones
Supervisor: doc. RNDr. Martin Rulík, Ph.D.

Importance of water bodies in the landscape methane Exchange
Supervisor: doc. RNDr. Martin Rulík, Ph.D.

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.

Hormopriming as a potential tool for regulating plant stress responses
Školitel: RNDr. Ondřej Plíhal, PhD.

Protein-protein interactions as target for pharmacological modulation of aryl hydrocarbon receptor AhR signaling pathway
Supervisor: prof. RNDr. Zdeněk Dvořák DrSc., Ph.D.

Function of plant RAD60 in SUMO-dependent genome stability signaling
Supervisor: Mgr. Eva Dvořák Tomaštíková, Ph.D.

Genetic and developmental consequences of ploidy transitions in barley seeds
Supervisor: Ing. Anna Katarzyna Nowicka, Ph.D.

Systematics and diversity of selected groups of Elateroidea (Coleoptera)
Školitel: Doc. RNDr. Robin Kundrata, Ph.D.

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

Anticipating freshwater biota responses to climate-driven habitat shifts based on the evolutionary history of lotic and lentic odonates
Supervisor: Mgr. Hana Šigutová, Ph.D.

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
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: prof.. RNDr. Jan Soubusta, Ph.D.
Space beam properties. Study of efficiency of various processes. Optimization of generation of frequency down-conversion.
Testing modern materials using optical spectroscopic methods
Supervisor: prof.. 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.

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.

Quantum correlations in multi-mode optical fields generated in the process of spontaneous parametric down-conversion
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Consultant: prof. RNDr. Ondřej Haderka, 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.

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.

Collective measurements for quantum communications
Supervisor: doc. Mgr. Karel Lemr, Ph.D.
Collective measurements are quantum measurements carried out simultaneously on multiple copies of the quantum state under investigation. They have been shown to be an invaluable tool for efficiently detecting and quantifying several key properties of quantum states, such as different entanglement measures or stronger quantum correlations. At the same time, collective measurements can be easily implemented in quantum communications networks, making them a key tool for the operation of prospective large-scale quantum networks connecting multiple users. Thus, the study of collective measurements promises interesting fundamental insights as well as results applicable to practical quantum communications.

Fisher information in classical and quantum optics
Supervisor: doc. RNDr. Pavel Pavlíček, Ph.D.
Fisher information is a quantity that allows the calculation of the uncertainty with which the value of a parameter can be determined. In classical and quantum optics, it is used to calculate the uncertainty with which the value of the phase in a Mach-Zehnder interferometer can be determined. Calculations of measurement uncertainty for different types of light will be performed. The results obtained using classical and quantum methods will be compared with each other.

Open quantum systems with spectral singularities and memory effects
Supervisor: Mgr. Ievgen Arkhipov, Ph.D.
This PhD project will explore non-Markovian quantum dynamics in open quantum systems, with a particular focus on the interplay between memory effects and spectral singularities (so-called exceptional points) in non-Hermitian systems. The research will investigate few-mode quantum optical systems interacting with structured, non-Markovian environments, where time-dependent dissipation and information backflow play a crucial role. Using numerical simulations based on time-dependent Lindblad master equation and non-Markovian stochastic differential equations, the project aims to understand how spectral singularities (exceptional points) and memory effects jointly affect system dynamics and how they can be harnessed for quantum sensing applications.

Production of Strange Particles and Neutral Mesons in Reactions with Heavy Ion Beams
Supervisor: Mgr. Luboš Krupa Ph.D.
Revealing the properties of strongly interacting matter at non-zero temperatures and densities is one of the key goals of nuclear collision experiments. Gravitational waves, electromagnetic radiation, and the abundant production of dielectrons and strangeness of produced particles are promising probes of the equation of state of dense matter produced at the intersection of relativistic heavy ion collisions and binary neutron star fusion. In the region of high temperatures and/or densities, strongly interacting matter, produced in heavy ion collisions, undergoes a phase transition between hadron gas and quark gluon plasma. The HADES dielectron spectrometer operating at the SIS18 synchrotron, FAIR/GSI Darmstadt, Germany, provides information on electron pair production and strangeness from nucleus-nucleus collisions, as well as from elementary reactions, allowing the measurement of photons and thus the study of the production of strange particles and neutral mesons through their two-photon decay. The aim of the work is to identify the properties of strongly interacting matter (hadron gas, quark-gluon plasma), similar to the matter in the core of neutron stars, by studying strange particles and neutral mesons produced in heavy ion collisions with a kinetic energy of the beam of 0.2–1.0A GeV using the HADES experiment.

Experimental study of the properties of neutrinos and antineutrinos
Supervisor: Mgr. Luboš Krupa Ph.D.
Experimental study of the properties of neutrinos and antineutrinos within the framework of the European project KM3NeT (located at the bottom of the Mediterranean Sea). The aim of the projects is to search for neutrinos from distant astrophysical sources, such as supernova remnants, gamma-ray bursts, supernovae or stellar collisions and to investigate the properties of neutrinos from the sun, especially oscillations and mass. The dissertation will also deal with the most advanced topics in modern astrophysics, cosmology and machine learning. The research will focus on the applications of machine learning tools for dark matter, indirect search, gamma-ray telescopes, black holes, gravitational waves, stellar physics and cosmology. The work also includes short-term and long-term stays (2-3 months) in France and Italy.

Electromagnetic radiation and catastrophe theory
Supervisor: Mgr. Luboš Krupa Ph.D.
Study and application of mathematical ideas and methods of “Catastrophe theory” in physics. The aim of the project is to research the manifestations of given catastrophes (fold, cusp, tip, butterfly, swallowtail, wigwam, star and so on) in physics, especially in the field of electromagnetic radiation. The main aim of this work is to study cuspoid and Cherenkov radiation emitted by a charge during its arbitrary movement in anisotropic and inhomogeneous environments (metamaterials, materials with a negative charge index, photonic crystals, hyperbolic materials, materials with a gradient charge index, plasmonic metasurfaces, uniaxial and biaxial crystals, etc.). Its possible application in high-energy physics, neutrino physics, in the synthesis of superheavy elements and everywhere where Cherenkov radiation is used will also be investigated. Monte Carlo simulation will be used to propose the optimal use of cuspoid and Cherenkov radiation for particle identification in high-energy physics and neutrino physics.

Oxidative modification of proteins and lipids in tumor cells
Supervisor: Prof. RNDr. Pavel Pospíšil, Ph.D.

Ultra-weak photon emission in animal cells
Supervisor: Prof. RNDr. Pavel Pospíšil, Ph.D.

Molecular mechanisms of oxidative stress-induced skin aging and barrier dysfunction
Supervisor: doc. Ankush Prasad, Ph.D.

Bioactive compounds as modulators of oxidative stress and inflammatory signaling in human skin cells
Supervisor: doc. Ankush Prasad, Ph.D.

Detection of voice disorders from clinical high-speed videokymographic videos and electroglottographic signals
Supervisor: prof. RNDr. Jan Švec, Ph.D. et Ph.D.

Studies of voice production using biological models
Supervisor: prof. RNDr. Jan Švec, Ph.D. et Ph.D.

Investigation of voice production using mathematical and physical modeling
Supervisor: prof. RNDr. Jan Švec, Ph.D. et Ph.D.

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: prof.. RNDr. Jan Soubusta, Ph.D.
Space beam properties. Study of efficiency of various processes. Optimization of generation of frequency down-conversion.
Testing modern materials using optical spectroscopic methods
Supervisor: prof.. 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.
Consultant: prof. RNDr. Ondřej Haderka, 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.

Collective measurements for quantum communications
Supervisor: doc. Mgr. Karel Lemr, Ph.D.
Collective measurements are quantum measurements carried out simultaneously on multiple copies of the quantum state under investigation. They have been shown to be an invaluable tool for efficiently detecting and quantifying several key properties of quantum states, such as different entanglement measures or stronger quantum correlations. At the same time, collective measurements can be easily implemented in quantum communications networks, making them a key tool for the operation of prospective large-scale quantum networks connecting multiple users. Thus, the study of collective measurements promises interesting fundamental insights as well as results applicable to practical quantum communications.

Fisher information in classical and quantum optics
Supervisor: doc. RNDr. Pavel Pavlíček, Ph.D.
Fisher information is a quantity that allows the calculation of the uncertainty with which the value of a parameter can be determined. In classical and quantum optics, it is used to calculate the uncertainty with which the value of the phase in a Mach-Zehnder interferometer can be determined. Calculations of measurement uncertainty for different types of light will be performed. The results obtained using classical and quantum methods will be compared with each other.

Open quantum systems with spectral singularities and memory effects
Supervisor: Mgr. Ievgen Arkhipov, Ph.D.
This PhD project will explore non-Markovian quantum dynamics in open quantum systems, with a particular focus on the interplay between memory effects and spectral singularities (so-called exceptional points) in non-Hermitian systems. The research will investigate few-mode quantum optical systems interacting with structured, non-Markovian environments, where time-dependent dissipation and information backflow play a crucial role. Using numerical simulations based on time-dependent Lindblad master equation and non-Markovian stochastic differential equations, the project aims to understand how spectral singularities (exceptional points) and memory effects jointly affect system dynamics and how they can be harnessed for quantum sensing applications.

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.

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).

Quantum Connections of Hybrid Systems
Supervisor: prof. Mgr. Radim Filip, Ph.D.
The doctoral student will explore elementary quantum connections in hybrid systems currently accessible in atomic, solid-state, and superconducting circuits, using optical and microwave resonators and waveguides. The project aims to develop a methodology for quantum interconnections via converters and measurements, assemble a set of quantum gates and combined operations, and propose initial experimental tests of these complex hybrid systems. These efforts will have applications in quantum communications and possibly in distributed quantum computing. The research will build on the extensive theoretical and experimental expertise of teams at Palacký University in Olomouc, the Institute of Quantum Physics at the Czech Academy of Sciences in Brno, and international partners such as TU Delft, KIT Karlsruhe, and Aalto University. This dissertation is a vital part of the upcoming EU project SUPERSPIN (2026-2029) and the national project QUEENTEC (2024-2028).

Counterdiabatic driving on quantum computing algorithms
Supervisor: prof. RNDr. Tomáš Opatrný, Dr.
The goal is to systematically investigate the role of counterdiabatic driving in quantum computing algorithms, both from a theoretical and an algorithmic perspective, with a particular emphasis on gate-based quantum processors. The thesis will analyze how counterdiabatic terms can be derived, approximated, and implemented for algorithmically relevant Hamiltonians, including those arising in adiabatic state preparation, quantum phase estimation, variational quantum algorithms, and quantum optimization protocols. Special attention will be paid to the trade-off between algorithmic speed-up and implementation cost, such as circuit depth, control complexity, and robustness against noise.

Simulation of quantum thermodynamic processes on quantum computers
Supervisor: prof. RNDr. Tomáš Opatrný, Dr.
The objective is to investigate the simulation of quantum thermodynamic processes using gate-based quantum computers, with a focus on nonequilibrium dynamics, work statistics, and entropy production in finite quantum systems. The thesis will analyze how fundamental thermodynamic protocols—such as quantum quenches, driven Hamiltonian evolution, thermalization processes, and quantum heat-engine cycles—can be encoded into quantum circuits and implemented on realistic quantum hardware. Particular emphasis will be placed on the formulation of thermodynamic quantities in terms of measurable quantum observables and on the comparison between idealized theoretical models and experimentally accessible implementations.

Non-Gaussian operations utilizing nonlinear feed-forward
Supervisor: prof. Mgr. Petr Marek Ph.D.

Feasible generation of non-Gaussian states for quantum information processing
Supervisor: prof. Mgr. Petr Marek Ph.D.

Characterization of non-Gaussian states suitable for quantum information processing
Supervisor: prof. Mgr. Petr Marek Ph.D.

Analysis of nanoobjects by capillary electrophoresis
Supervisor: doc. RNDr. Jan Petr, Ph.D.

Ion mobilty-mass spectrometry in disease diagnostics
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.

Development and Optmization of Electrochemical Detection Systems for Liquid Chromatography)
Supervisor: doc. RNDr. David Jirovský, Ph.D.

Development, Preparation and Characterization  of Functional Materials for Electrochemical Sensors
Supervisor: doc. RNDr. David Jirovský, Ph.D.

New applications of ion chromatography
Supervisor: doc. RNDr. Petr Bednář, Ph.D.

Microanalytical procedures in metabolomics
Supervisor: doc. RNDr. Petr Bednář, Ph.D.

New methods for chemical analysis in archeology and cultural heritage research
Supervisor: doc. RNDr. Petr Bednář, Ph.D.

Analytical chemistry of Polymicrobial Infections
Supervisor: prof. Ing. Vladimír Havlíček, Dr.

Central Nervous System diagnostics
Supervisor: prof. Ing. Vladimír Havlíček, Dr.

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

Specific Extractions of active subsatnces and products of their transformations
Supervisor: doc. RNDr. Petr Barták, Ph.D.

More effective single-molecule magnets based on lanthanide complexes with macrocyclic ligands
Supervisor: Doc. RNDr. Bohuslav Drahoš Ph.D.

Theranostics based on complexes with macrocyclic ligands
Supervisor: Doc. RNDr. Bohuslav Drahoš Ph.D.

Continuous flow chemistry – a tool for efficient synthesis of macrocyclic ligands and their metal complexes suitable for molecular magnetism
Supervisor: Doc. RNDr. Bohuslav Drahoš Ph.D.

Flow reactor assisted continuous conversion of biomass into value-added products: Process design and scale-up
Supervisor: Doc. RNDr. Bohuslav Drahoš Ph.D.
Consultant: Subodh Kumar, Ph.D.

Rational Synthesis of Chiral Spin Crossover Complexes via Ligand Design for Tuneable Dielectric and Magnetoelectric Properties
Supervisor: prof. Ing. Radovan Herchel, Ph.D.
Consultant: Dr. Sriram Sundaresan

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

Chiral molecular nanomagnets for magneto-optical phenomena
Supervisor: prof. Ing. Radovan Herchel, Ph.D.
Consultant: Mgr. Kamil Kotrle, Ph.D.

Photoactive magnetic molecular switches
Supervisor: prof. Ing. Radovan Herchel, Ph.D.

Functional MOF materials
Supervisor: prof. Ing. Radovan Herchel, Ph.D.
Consultant: Mgr. Ondřej Bárta, Ph.D.

The design, synthesis, and characterization of complexes incorporating derivatives of quercetin and the study of antiproliferative aktivity
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.

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

Antibacterial and anti-inflammatory 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.

Design and synthesis of nanocatalysts for biomass transformation into value added chemicals
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Passivation of black phosphorous with single-molecule magnets
Supervisor: doc. Ing. Ivan Nemec, Ph.D.

Semi-coordination in single-molecule magnets
Supervisor: doc. Ing. Ivan Nemec, Ph.D.

Multicomponent coordination compounds 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.
Consultant: Mgr. Ondřej Bárta, Ph.D.

Heterogenization of the Metal Complexes for the Conversion of CO2 into Industrially Important Chemicals
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Development of visible light active 2D nanocomposites for the photocatalytic water reduction to produce hydrogen
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Coordination compounds with polydentate β-carboline derivatives for medicinal applications
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.
Consultant: Mgr. Radka Křikavová, Ph.D.
Consultant: Mgr. Kamila Petrželová, Ph.D.

Efficient electroluminescent devices via triplet-to-singlet conversion in organic emitters
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.
Consultant: Sohrab Nasiri, PhD

Development of high-performance light-emitting electrochemical cells using novel wide-bandgap semiconductors
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.
Consultant: Sohrab Nasiri, PhD

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.

Interactions of Guanine Quadruplexes with Proteins
Supervisor: Mgr. Petr Stadlbauer, Ph.D. (BFÚ AV ČR)
G-quadruplexes represent a unique four-stranded conformational motif of nucleic acids that forms in guanine-rich sequences. These structures have been identified not only in DNA but also in RNA and are associated with important biological processes, such as the regulation of gene expression, DNA replication, and telomere maintenance.

Proteins capable of recognizing and binding to G-quadruplexes are involved in a wide range of cellular processes, and their dysfunction can lead to the development of various diseases, including cancer and neurodegenerative disorders. The study of these interactions offers an opportunity to understand the molecular mechanisms that regulate the biological functions of G-quadruplexes. The insights gained can contribute to the development of new therapeutic strategies, such as targeted drugs.

The subject of this dissertation focuses on a detailed examination of the interactions between G-quadruplexes and proteins, employing theoretical approaches such as molecular modeling and, in particular, molecular dynamics simulations. These methods will enable a detailed analysis of the structure and dynamics of the complexes, thereby contributing to a deeper understanding of their biological functions and roles in cellular processes.

Study of Folding of Non-Canonical Nucleic Acid Motifs
Supervisor: Mgr. Petr Stadlbauer, Ph.D. (BFÚ AV ČR)
Non-canonical structures of nucleic acids, such as guanine quadruplexes, i-motifs, and other less common conformational motifs, play a crucial role in many biological processes. These structures are characterized by unique stability and dynamics, which are key to their function. The folding of these non-canonical structures involves complex transient ensembles and intermediates, whose existence is essential for understanding the mechanism of the native structure formation.
The aim of this work is a detailed analysis of the folding mechanisms of selected non-canonical nucleic acid structures using computational modeling methods, particularly standard and advanced molecular dynamics simulations. The research will focus on identifying and characterizing the key steps in the formation of these structures. The results obtained will contribute to a better understanding of the folding dynamics of these structures and their roles in biological processes.

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.

Pauli Repulsion Lowering HBD Organocatalysis for Spiroacetalization: Anomer Switching, Diversity Oriented Synthesis, and Anthelmintic Applications
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.
This project develops tunable hydrogen bond donor (HBD) organocatalysts (thiourea, urea, squaramide; including confined HBD pockets) that activate spiroacetal precursors via Pauli repulsion lowering—polarizing occupied π orbitals away from the forming bonds to diminish two orbital/four electron Pauli repulsion in the transition state, thereby enabling selective access to either anomer. The strategy applies to intra  and intermolecular variants and is designed to suppress external substrate chirality, achieving high ee/er from achiral/homochiral/racemic precursors. From unified starting materials we will generate a diversity oriented library of spiroacetals and evaluate anthelmintic activity with anomer resolved SAR. ASM/EDA/NOCV analyses will guide catalyst selection and fine tuning by correlating ΔEPauli with experimental selectivity and rate.

Polyketides & Macrolides as AmB Alternatives: DOS‑ Synthesis and Synergy with Polypeptides
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.
This project, supervised by Assoc. Prof. Jiří Pospíšil, PhD, aims to identify new alternatives to amphotericin B (AmB) through polyketide and macrolide chemotypes, leveraging diversity oriented synthesis (DOS) for rapid structural diversification. Priority scaffolds include enigmazole macrolides (new congeners and fully synthetic accessible variants), phytohabitols A–C (δ lactone polyketides with demonstrated antitrypanosomal activity), and polyketide motifs derived from fumagillin/fumagillol (targeting MetAP1/2). A central component of the project is the systematic evaluation of synergy between these small molecules and polypeptides (AMPs/peptidomimetics), given their expected membrane permeabilizing and immunomodulatory enhancement and especially the potential for marked dose reduction compared to monotherapy; synergy will be quantified using Chou–Talalay CI, Bliss, and Loewe models. Extensive literature on AMPs confirms their synergistic interactions with antimicrobial small molecules, and peptide fragments such as lactofungin are known to potentiate AmB—an effect highly relevant to trypanosomatid pathogens. The project’s objectives therefore include (i) DOS enabled chemistry and (semi)synthesis, establishing modular synthetic routes for enigmazoles and phytohabitols as well as designing less reactive, more selective fumagillol analogues; and (ii) a systematic synergy screening program, preparing libraries of peptides/peptidomimetics, testing combination matrices (CI, isobolograms, time kill), and identifying dose sparing, low toxicity synergistic pairs.

Synthesis and study of novel low-molecular-weight compounds with potent antimicrobial aktivity
Supervisor: Doc. RNDr. Lucie Brulíková, Ph.D.
The growing resistance of microorganisms to existing antimicrobial agents is a major global issue and underscores the urgent need to develop new, effective compounds with innovative structures and mechanisms of action. This doctoral dissertation will focus on the design, synthesis, and thorough study of new organic compounds with potential antimicrobial activity. The main goal is to create rationally designed libraries of low-molecular-weight compounds based on promising structural motifs, perform chemical characterization, and systematically evaluate their biological activity against selected strains, including clinically relevant resistant isolates. The project will also explore structure–activity relationships (SAR), optimize structures for better efficacy and selectivity, and investigate the mechanisms of action of the most active compounds. The findings are expected to deepen understanding of the structural features necessary for antimicrobial activity and could serve as a foundation for developing new antimicrobial drug candidates.
Thanks to a longstanding collaboration with a partner institution in Antwerp, Belgium, there is an opportunity to obtain a Joint PhD degree.

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
Školitel: 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.

Hydrogenation reactions by multi-metallic size-selected cluster catalysts   
Supervisor: RNDr. Štefan Vajda, CSc., Dr.habil.
Global warming is a critical issue, largely driven by CO2 emissions. Tackling this challenge effectively requires innovative solutions, such as catalytic CO2 hydrogenation. This process not only removes CO2 but also transforms it into valuable energy-related products. Among the most promising methods, size-selected cluster-based catalysts have shown remarkable performance in this reaction. Clusters are aggregates of matter consisting of just a few atoms, with chemical and physical properties that vary non-linearly with their size and composition. By precisely controlling the number of atoms in these clusters, it is possible to optimize their activity and selectivity toward desired products. Furthermore, combining different metals within the clusters and leveraging interactions between clusters and their supports unlocks additional degrees of freedom, enabling the design of highly efficient multi-metallic sub-nanometer catalysts.
This PhD research will focus on exploring the catalytic performance of these advanced materials, primarily, but not exclusively, in CO2 hydrogenation. The scope may also extend to other industrially significant hydrogenation reactions. The work will be conducted in the state-of-the-art laboratories of the Department of Nanocatalysis, where size-selected clusters are synthesized, deposited on technologically relevant supports, and tested in custom-built reactor systems. Additionally, the department's extensive network of international collaborations will provide access to cutting-edge facilities worldwide for further characterization of these catalysts.

Cluster-based nanocatalysts for hydrogenation and dehydrogenation reactions
Supervisor: RNDr. Štefan Vajda, CSc., Dr.habil.
Nanocatalysts composed of metal clusters have gained considerable attention due to their high activity and selectivity in various chemical reactions, owing to the unique properties exhibited by materials at the nanoscale. Metal clusters, typically consisting of only a few atoms, possess distinctive catalytic behaviors that arise from their small size and high surface area. These clusters are often more active and selective compared to bulk metals, due to the increased number of unsaturated coordination sites, which can be tailored for specific reactions. The versatility of metal clusters is further enhanced when they are combined into bimetallic systems, where the interaction between two distinct metals can lead to synergistic effects that boost catalytic performance. The interaction between the clusters and their supports is also a critical factor influencing the catalytic efficiency, stability, and reactivity of the system. The use of such supported clusters, especially in the context of hydrogenation and dehydrogenation reactions, is particularly promising for energy applications, such as hydrogen storage, the development of sustainable fuels, and the chemical industry, where nanocatalysts can facilitate the activation of reactants or the transformation of complex molecules with high efficiency.
The objective of this PhD research is to develop and study transition metal clusters, with a particular focus on size-selected clusters, ensuring precise control over the number of atoms within each cluster. Both monometallic and bimetallic clusters will be synthesized, with an emphasis on substituting noble metals with more cost-effective alternatives, which could make these catalysts more economically viable. The interaction of these clusters with various oxide supports, such as ZrO2, Al2O3, and CeO2, will be explored to understand the role of the support in stabilizing the clusters and modulating their catalytic activity. This research will involve exploring various cluster configurations, investigating the role of metal-support interactions, and assessing the performance of both single and bimetallic nanocatalysts. Extensive research using temperature-programmed reactions will be conducted in the context of key reactions for energy applications, including hydrogenation (e.g., CO2 to methanol) and dehydrogenation (e.g., cyclohexane to benzene), where these catalysts could potentially provide more efficient, sustainable, and cost-effective solutions. In addition, comprehensive characterization of the catalysts' morphology, chemical composition evolution, and other factors using in-situ and operando techniques will be conducted within the framework of existing international collaborations to fully understand the reaction mechanisms.

Size and composition effect of trimetallic cluster-based nanocatalysts
Supervisor: RNDr. Štefan Vajda, CSc., Dr.habil.
Size-selected clusters, atomic aggregates composed of only a few atoms, exhibit remarkable properties that differ significantly from those of bulk materials, nanoparticles, or individual atoms. Intriguingly, the addition or removal of a single atom can drastically alter their physical and chemical behavior. This unique feature is particularly valuable in catalysis, where precise control over cluster size enables fine-tuning of catalytic activity and selectivity. Recent technological advancements have not only facilitated control over the size of these clusters but also enabled the manipulation of their chemical composition. Bimetallic size-selected clusters, for instance, have demonstrated synergistic effects between two metals. This synergy allows for the substitution of expensive precious metals, such as platinum, with more affordable and abundant alternatives, like silver, while maintaining or even enhancing catalytic performance.
Building upon this foundation, the primary goal of this PhD thesis is to take the next step by exploring trimetallic size-selected clusters. These advanced systems offer even greater potential for catalytic innovation. Synthesis of these clusters is achievable using state-of-the-art cluster sources at the Department of Nanocatalysis. These sources enable the deposition of clusters onto support oxides, followed by testing in a diverse range of reactions—from model reactions such as CO oxidation to more challenging and critical processes like dry methane reforming and ammonia synthesis. The research will involve a comprehensive approach that includes synthesis, characterization, and testing of trimetallic cluster-based catalysts. Furthermore, the project will leverage a robust international network of collaborators, providing access to cutting-edge laboratories, advanced facilities, and computational methods to model and understand these systems.

Catalytic transformation of C1 compounds into value-added chemicals
Supervisor: Dr. Joanna E. Olszówka (ÚFCHJH AV ČR)
C1 compounds such as carbon dioxide and methane are considered an abundant greenhouse gas and are the main concern when discussing climate change. Also, they are both very stable making their activation challenging, which is why studies on efficient catalytic systems for their transformation is recently bringing a lot of attention. Drawing structure-function relationships is of central importance for the development of catalysts. However, a fundamental understanding of the effect of the size and composition of the catalyst and of the support on performance remains challenging for powdered catalysts where a variety of species is present.
The primary goal of this PhD thesis is planned to benefit from the insights offered by both powder and model catalysts studied under reaction conditions to address fundamental questions on the important catalytic reactions focused on C1 transformation. The research will involve a comprehensive approach that includes synthesis, characterization, and testing of powder and model catalysts. Furthermore, the project will leverage a robust international network of collaborators, providing access to cutting-edge laboratories, advanced facilities, and computational methods offering opportunities for the career development of the chosen candidate.

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.

Analysis of distributional data in metabolomics
Supervisor: Prof. RNDr. Karel Hron, Ph.D.
In the analysis of spectral data obtained from metabolomic experiments, it is possible to consider either absolute intensity values or their distributional character. In a simplified (multivariate) setting, this can be described mathematically as compositional data, or alternatively as probability density functions when the functional nature of spectra is taken into account. Each object may be represented by a single such spectrum; however, this can be generalized up to matrices of spectra in the context of image data, where spectra are defined on a regular (matrix-based) grid and exhibit a certain degree of spatial dependence. The aim of this doctoral thesis is to analyze these data using appropriate methods from statistics and machine learning—within the context of distributional data employing the framework of Bayes spaces—by comparing different approaches in order to achieve effective classification of groups of objects, typically patients and controls.

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.

Identification problems for an extended Gao beam model
Supervisor: doc. RNDr. Jitka Machalová Ph.D., MBA
The dissertation will address identification problems for an extended Gao beam model involving state problems of bending and contact with deformable and perfectly rigid foundations. For the state problems, conditions ensuring existence and uniqueness of solutions will be investigated. This analysis will subsequently be followed by the formulation of parameter identification problems and the study of their solvability. Both the state and identification problems will be numerically solved using the finite element method with a spline-based basis.

Use of spline functions in neural networks
Supervisor: doc. RNDr. Jitka Machalová Ph.D., MBA
The dissertation will focus on the use of spline functions within neural network architectures, in particular through spline-based activation functions, spline bases, and spline regularization techniques. The aim is to investigate how incorporating splines into neural networks affects their approximation properties, training stability, generalization performance, and interpretability. The work will combine theoretical analysis of spline approximation with the design and evaluation of spline-based neural network models in the context of modern machine learning.

The impact of parameters of B-Spline data representation on machine learning
Supervisor: doc. RNDr. Jitka Machalová Ph.D., MBA
The dissertation will focus on the study of B-spline data representation and the impact of its parameters on machine learning tasks. The aim of the work is to analyze how the choice of B-spline representation parameters, in particular knot placement, spline order, and penalization, affects solution stability, regularization, and generalization performance of learning algorithms. The thesis will investigate the relationship between the structure of B-spline representation and the behavior of learning problems formulated within the empirical risk minimization framework. Emphasis will be placed on theoretical analysis of solution properties and their validation in regression and classification tasks. Artificial intelligence methods will be employed as standard learning tools to demonstrate the consequences of B-spline representation parameter choices.

Asymptotic Methods in Partial Differential Equations
Supervisor: RNDr. Rostislav Vodák Ph.D.
The aim of the thesis is to study and apply mathematical methods that enable the asymptotic analysis of solutions to partial differential equations, such as dimension reduction, behavior as time tends to infinity, and related topics.

Causal Models and Their Application in Medical Research
Supervisor: doc. Mgr. Ondřej Vencálek Ph.D.
Many fundamental questions in medical research are causal in nature—the aim is to understand whether and how a given phenomenon causes another, or, alternatively, what the probability is that an intervention on one variable will lead to a change in another variable. Traditional statistical methods typically focus on identifying and quantifying associations, without explicitly addressing the causal interpretation of these relationships (and, in practice, results from different analyses are often incorrectly interpreted in causal terms). In contrast, methods of causal inference, which have undergone substantial methodological development over recent decades, provide a formal framework for studying causal effects in the presence of so-called confounders and other sources of bias.
The doctoral thesis will focus on causal models in medical research, with particular emphasis on their application to survival analysis and the modeling of categorical outcomes. Attention will be paid both to the theoretical aspects of these models and to their practical use in the analysis of real medical data.

Analysis of equilibria
Supervisor: 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
Supervisor: 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
Supervisor: 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.

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.

Predictive modeling of landcover/landuse development in GIS
Supervisor: prof. RNDr. Vilém Pechanec, Ph.D.
The aim of the research is to develop algorithms and methodologies for predictive landscape modeling. Landscape predictions, or those of selected components, can be based on user-defined scenarios as well as on scenarios such as Business-as-Usual (BaU) or What-If scenarios. A significant part of the research should focus on advancing methods for creating logically consistent integrated datasets.

Patterns of spatial navigation and analysis of visual attention and orientation behaviour in different contexts
Supervisor: RNDr. Stanislav Popelka, Ph.D.
The aim of the doctoral dissertation is to uncover and systematically describe patterns of behavior in spatial navigation across different orientation contexts. The research will focus on route planning and spatial orientation processes, both under laboratory conditions during map-based route planning and in real-world environments during navigation with and without a map. The primary research method will be eye tracking, applied both in a stationary setting and using mobile eye-tracking glasses during field movement. The research will be conducted in various environments, including working with tourist maps, navigating urban spaces, and orienting oneself in complex indoor environments such as railway stations and shopping malls. The dissertation will also include the design, implementation, and testing of eye-tracking data analysis procedures, with particular emphasis on methodological challenges associated with mobile eye tracking (dynamic scenes, spatial referencing). In addition to eye tracking, other methods and technologies will be employed, especially galvanic skin response (GSR), the think-aloud method, and synchronized recording of participants’ GPS movement trajectories. The outcome of the dissertation will not only provide a better understanding of cognitive strategies in spatial navigation but also make a methodological contribution in the form of analytical procedures and tools for eye-tracking data analysis, which can be further applied in cartography, the design of navigation systems, and research on spatial behavior.